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The 20th International
BioInformatics Workshop
on Virus Evolution and
Molecular Epidemiology
Organized on behalf of the International Centre
for Genetic Engineering & Biotechnology
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
J. Craig Venter Institute
The University of the West Indies
Katholieke Universiteit
Rockville, USA
St. Augustine, Trinidad & Tobago
Leuven, Belgium
The International Centre for Genetic Engineering and Biotechnology (ICGEB) was established as a Centre of excellence for
research and training in molecular biology. It commenced operation in 1987 as a special project of UNIDO and became
an autonomous intergovernamental organisation in the United Nations System in 1994.
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sciences for the benefit of developing countries.
The Centre is supported by 64 Member States
ICGEB has operated under the United Nations System for 25 years as a centre of excellence, putting
scientists from Developing Countries in contact with the top experts in respective fields of research.
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The Centre organizes more that 20 international meetings and workshops each year and hosts
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gene therapy; advanced equipment for proteomic studies, and a laboratory dedicated to the
production of recombinant pharmaceuticals. ICGEB also offers a series of scientific services,
including technical assistance for research projects and transfer of know-how, through patent
innovation guidelines, to the industrial sector in the biotechnology field.
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Acknowledgments
This workshop was organized on behalf of the International Centre for Genetic Engineering and Biotechnology by The University of the West Indies, J. Craig Venter Institute and the University of Leuven. The organising committee acknowledges with gratitude the following for their generous financial support:
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VIRUS
EVOLUTION
E D I T O R S - I N - C H I E F
Prof. Oliver Pybus | Prof. Santiago F. Elena
Virus Evolution is a new Open Access journal providing
a forum for original research papers, reviews,
commentaries and a venue for in-depth discussion on
the topics relevant to virus evolution.
Visit ve.oxfordjournals.org for more information,
instructions to authors and to submit online today.
THE UNIVERSITY OF THE WEST INDIES
Office of the Campus Principal
Office of the Dean & Department of Preclinical Sciences
Faculty of Medical Sciences
Campus Research & Publication Fund
Faculty of Science & Technology
Funding for this conference was made possible in part by 1 R13 AI120533-01 from the NIH NIAID. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect
the official policies of the Department of Health and Human Services; nor does mention of trade names, commercial practices, or organizations imply endorsement by the U.S. Government.
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
3
We also acknowledge:
Members of the Local Organising Committee
Special thanks to:
Christopher Oura
Kevin Snaggs
Ria Swinnen
Karen Dhun
Adesh Ramsubhag
Naresh Seegobin
Sietse Huysmans
Renata Sankar-Jaimungal
Jerome Foster
Deborah Crichlow-Martin Randolph Cadiz
Vrijesh Tripathi
Noreen Pearson
Karen Ali
Sarah Moti
Orchid Allicock
Shadé Richardson
Tim Stayeas
Matthew LaPointe
Betty McComie
Christine Carrington, Karen Nelson, Anne-Mieke Vandamme
VEME 2015 Workshop Organisers
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The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
4/30/15 6:35 PM
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Contents
Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Workshop Organizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Module Organizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Phylogeny Inference Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Evolutionary Hypothesis Testing Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Large Dataset Analysis Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Half Day Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
UWI Campus Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Abstract Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Abstracts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Contact Details . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Participants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .92
Teachers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .103
Cover Photo: Middle East Respiratory Syndrome Coronavirus (MERS-CoV) virions /
National Institute of Allergy and Infectious Diseases (NIAID)
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
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Workshop Organizers
Dr. Christine Carrington
Christine Carrington is Professor of Molecular Genetics and Virology in the Department of Preclinical Sciences of the University of The West Indies (UWI), St. Augustine, where she has worked since 1996. She holds a BSc in Biotechnology from
King’s College, University of London and gained her PhD in Molecular Virology at
the Institute of Cancer Research, University of London in 1994.
Dr. Carrington served as Deputy Dean for Graduate Studies and Research at the
Faculty of Medical Sciences from 2007 to 2014. She is a 2004 Commonwealth Fellow and as part of the UWI’s 60th Anniversary celebrations was selected as one of
the 60 most outstanding researchers under 60. Other honours include recognition by the UWI for Outstanding Research Mentorship in the Sciences and by the National Institute of Higher
Education, Research, Science and Technology (NIHERST) as a “Caribbean Icon in Science Technology and
Innovation”.
Her current research involves using phylogenetics and other computational biology techniques to understand evolutionary and ecological factors involved in the emergence, spread and maintenance of viruses.
In particular, zoonotic and vector-borne RNA viruses, such as Dengue, Chikungunya and other arboviruses,
rabies and other viruses in bats. She is also interested in the use of next generation sequencing technologies
for viral discovery and is applying this approach to febrile illness surveillance.
Dr. Karen Nelson
Karen Nelson is the President of the J. Craig Venter Institute (JCVI) where she has
worked for the past 18 years. Prior to being appointed President, she held a number of other positions at the Institute, including Director of JCVI’s Rockville Campus, and Director of Human Microbiology and Metagenomics in the Department
of Human Genomic Medicine at the JCVI.
Dr. Nelson has extensive experience in microbial ecology, microbial genomics,
microbial physiology and metagenomics. Since joining the JCVI legacy institutes,
Dr. Nelson has led several genomic and metagenomic efforts, and led the first human metagenomics study published in 2006. Additional ongoing studies in her
group include metagenomic approaches to study the ecology of the gastrointestinal tract of humans and
animals, studies on the relationship between the microbiome and various human and animal disease conditions, reference genome sequencing and analysis primarily for the human body, and other -omics studies.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Dr. Nelson received her undergraduate degree from the University of the West Indies, and her Ph.D. from
Cornell University. She has authored or co-authored over 100 peer reviewed publications and edited three
books, and is Editor-in-Chief of the journals Microbial Ecology and Advances in Microbial Ecology. She also
serves on the Editorial Boards of BMC Genomics, GigaScience, and the Central European Journal of Biology.
She is also a standing member of the NRC Committee on Biodefense, a member of the National Academy of
Sciences Board of Life Sciences, a Fellow of the American Academy of Microbiology, and an Honorary Professor at the University of the West Indies.
Dr. Anne-Mieke Vandamme
Anne-Mieke Vandamme was trained as biochemist, and holds a PhD in sciences
since 1986. She joined the Rega Institute at the Katholieke Universiteit Leuven in
1990, where she started a unit on virus genetic testing for clinical practice. Together with Professor Van Ranst, she founded a new division, Clinical and Epidemiological Virology. She is Professor in Evolutionary Genetics and Bioinformatics
at the Katholieke Universiteit Leuven.
Anne-Mieke Vandamme and her team perform research on the molecular epidemiology of HIV, HTLV and HCV, on HIV and HCV drug resistance (genotyping, phenotyping) in clinical context, and on bioinformatics (data mining, phylogenetic
analysis) technology. In the fields of HIV molecular epidemiology and drug resistance, she has an extensive
and widely recognized expertise. She has been participating in several European projects (ENVA, SPREAD,
EHR, Virolab, CHAIN, VIROGENESIS). She supported the development of a few widely used (bioinformatics)
tools, the Rega HIV Drug Resistance algorithm, the Rega HIV typing and subtyping tool, and recently also RegaDB, a free and open source software for collecting and sharing HIV epidemiological, clinical and virological data. She authored more than 350 publications in international journals such as Lancet, Nature Medicine,
Lancet Infectious Diseases, PNAS, Journal of Virology, Trends in Microbiology, half of them with first and/or
last author from the lab. More than 550 abstracts were presented at International Meetings.
In addition to her research activities, Anne-Mieke Vandamme is founder and (co-)organizer of the yearly
International Bioinformatics Workshop on Virus Evolution and Molecular Epidemiology (20th in 2015), is
co-initiator and co-organizer of the European HIV Drug Resistance Workshop (13th in 2015), is coordinating
the European HIV Drug Resistance Guidelines initiatives, is Head of a Bioinformatics unit at the ‘Instituto de
Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal. She is also co-editor of one of
the major textbooks in molecular phylogeny, “The Phylogenetic Handbook: a practical approach to phylogenetic analysis and hypothesis testing” (Cambridge University Press, 2nd ed. 2009).
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
The Ministry of Health is the national authority vested with the oversight of the entire health system in Trinidad and Tobago. Oversight
of the health system does not extend only to treating the unwell but
also to ensuring that those who are healthy, remain so.
The Ministry has long treated infectious, vector borne diseases
such as yellow fever, malaria and dengue fever, greatly reducing
the number of cases since the nineties in Trinidad and Tobago. The
Chikungunya Virus, introduced into the T&T in 2014 presented new
and unique challenges, however an aggressive education campaign
sought to prevent the virus from affecting Trinidad and Tobago in a
way similar to our Caribbean neighbours.
The Ministry of Health has successfully implemented significant
improvements in the management and delivery of other infectious
disease health services through several programmes and initiatives
across Trinidad and Tobago. The Ministry also continues to support
the participation of our nationals in initiatives such as this International Bioinformatics Workshop to promote further research and
development that will only serve to improve the health of citizens of
Trinidad and Tobago, the Caribbean and the world.
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Module Organizers
Phylogenetic Inference: Dr. Marco Salemi
Dr. Marco Salemi is an internationally recognized expert in the field of molecular
evolution of viruses and phylogenetic analysis, producing seminal and elegant
work on the molecular evolution of the human immunodeficiency virus (HIV) at
both the global population level and within individual patients. He is perhaps best
known for his groundbreaking research on how HIV spreads through different tissues in the human body. More recently, his research has expanded to integrate
geographic information system and phylogenetic data to study the emergence
and spread of viral and microbial epidemics. He is also co-editor of one of the major textbooks in molecular phylogeny, “The phylogenetic Handbook: a practical
approach to phylogenetic analysis and hypothesis testing” (Cambridge University Press, 1st ed. 2003, 2nd ed.
2009). He has published 115 papers in peer-reviewed journals, including Nature, Science, Nature Medicine
and PNAS., and is an associate editor of Journal of Virology, Retrovirology and PLoS ONE.
Dr. Salemi is an Associate Professor at the Department of Pathology, Immunology and Laboratory Medicine
of the University of Florida (UF) College of Medicine, Gainesville, USA. He is a member of the UF Emerging
Pathogens Institute (EPI) where he leads a research group working on molecular evolution of pathogens.
In 1996 he was awarded the prestigious Marie-Curie Fellowship to join the Rega Institute of the Catholic
University of Leuven, Belgium. There he earned his PhD in 1999 under the supervision of Profs. Anne-Mieke
Vandamme and Jan Desmyter with a dissertation on the origin and evolution of human and primate T-cell
lymphotropic viruses. After a two-year postdoctoral fellowship at the Rega Institute, where he continued to
study the phylogeny of human retroviruses, he worked from 2002 to 2004 in the laboratory of Prof. Walter M.
Fitch, one of the founding fathers of molecular evolution, at the University of California, Irvine, USA.
Evolutionary Hypothesis Testing: Dr. Phillipe Lemey
Dr. Philippe Lemey obtained his PhD in 2005 from the Catholic University of Leuven where he now also holds a Principal Investigator position in the Department
of Microbiology and Immunology. He has received numerous awards for his scientific accomplishments, including fellowships from EMBO and the Royal Society.
He was a Marie-Curie fellow in the Evolutionary Biology Group at the Department
of Zoology, University of Oxford, and in 2010 he was awarded an ERC Starting
Grant. His research focuses on molecular evolution of viruses by integrating molecular biology and computational approaches. He is also co-editor of one of the
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
9
major textbooks in molecular phylogeny, “The Phylogenetic Handbook: a practical approach to phylogenetic analysis and hypothesis testing” (Cambridge University Press, 2nd ed. 2009).
Large Dataset Analysis Module: Dr. Mattia Prosperi
Dr. Mattia Prosperi is Associate Professor at the Department of Epidemiology, College of Medicine & College of Public Health and Health Professions, University of
Florida, Gainesville, Florida, USA. He holds a MEng in Computer Science and a
PhD in Computer Science and Automation. Dr. Prosperi ‘s research covers the
development and application of statistical and computational models in the
large interdisciplinary areas of computational biology, medicine and public
health. Among his projects, he developed methods and software for analysis
of mechanisms of evolution of drug resistance (human immunodeficiency
virus and hepatitis), personalized therapy optimization, phylodynamic tracing
of epidemics and relation with demographic factors (viruses and bacteria), new methods for phylogenetics, original algorithms to analyses large high-throughput sequencing data (e.g. viral population
assembly), and computational solutions for big data mining. In addition to his line of successful research,
supported by extramural funding (e.g. EU Horizon2020), he fosters MSc and PhD studentships in order to
create a specialized workforce that will enable the University to excel in the next-generation bioinformatics
and big data science.
Virus Analysis Tools: Dr. Tulio de Oliveira
Professor Tulio de Oliveira is a bioinformatician who has been working with HIV
research since 1997. He received his PhD at the Nelson R Mandela School of Medicine, University of KwaZulu-Natal, South Africa. He was a Marie Curie research
fellow at the University of Oxford, U.K. from 2004 to 2006, where he received in
depth training on virus genetic analysis and molecular evolution. He is recognized
as an expert on HIV genetic data and bioinformatics and has published many
high-impact articles including the one that presents the Rega Subtyping tools (de
Oliveira et al. Bioinformatics 2005), that proved the innocence of the six foreign
medical personnel condemned to death for infecting with HIV 438 children in a
hospital in Libya (de Oliveira et al. Nature 2006), open access and public HIV drug resistance databases in
Africa (de Oliveira et al. Nature 2010) and the first case of proven HIV surrogate transmission in South Africa
(Goedhals et al. Lancet 2012). He is currently a Professor of Genomics and Bioinformatics at University of KwaThe 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
10
Zulu-Natal and a senior researcher at the Wellcome Trust-Africa Centre for Health and Population Studies,
UKZN and the director of the Southern African Treatment Research Network (SATuRN).
Large Phylogenies: Dr. Heiko Schmidt
Dr. Heiko Schmidt has been working in the field of evolutionary Bioinformatics
since the mid-1990ies. He studied biology in Cologne and later gained his PhD in
Computer Science at Düsseldorf University in 2003. He worked at the German Cancer Research Center, the Max Planck Institute for Molecular Genetics and at the
University of Düsseldorf. Since 2005 he has been employed as a senior scientist at
the Center for Integrative Bioinformatics Vienna at the Max F. Perutz Laboratories
in Vienna where he also teaches Bioinformatics courses at different levels at the
University of Vienna and the Medical University of Vienna. His scientific focus lies
especially on the development and parallelization of phylogenetic software using
maximum likelihood. He was involved in a number of phylogenetic packages like TREE-PUZZLE, IQPNNI, and
IQ-Tree. He was part of a number of phylogenetic analyses of protein superfamilies and Hantaviruses. Furthermore he is working on the application of different levels of parallel computing for automatized larger scale
scientific analysis workflows. Recently he has been involved in the reconstruction of Archaean genomes from
metagenomic high-throughput sequencing projects.
Molecular Adaptation: Dr. Sergei Kosakovsky-Pond
Following formal undergraduate training in computer science (at Kiev State
University, Ukraine), Dr. Kosakovsky-Pond received a PhD from the interdisciplinary program in Applied Mathematics at the University of Arizona. Dr. Kosakovsky-Pond ‘s theoretical graduate research into statistical methodology for
evolutionary analyses of coding sequence alignments found an application in an
HIV research group at University of California, San Diego (UCSD), which he joined
as a postdoctoral fellow in 2003. Presently, Dr. Kosakovsky-Pond is an associate
professor in the Divisions of Infectious Diseases and Biomedical Informatics in the
UCSD Department of Medicine. In addition, Dr. Kosakovsky-Pond is the director
of the Bioinformatics and Information Technologies Core at the UCSD Center of
AIDS Research.
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
11
Transmission Chain Investigation: Anne-Mieke Vandamme
(see Workshop Organizers)
Visualisation – Large Trees with Metadata: Dr. Nuno Faria
Dr. Nuno Faria obtained his PhD in 2013 from the University of Leuven and now
holds a Research Lecturer position at the University of Oxford, from where he
received a reward and recognition in Excellence in 2014. In the past years he has
published +20 papers on HIV, Dengue and Chikungunya, covering statistical
tools to investigate virus epidemic history. Nuno has been teaching in Oxford, UK,
and Evandro Chagas, Brazil and in several international workshops. He was also
awarded one of the best science visualisations of 2014 for recent work on HIV-1
origins (Faria et al. Science 2014).
Recombination and Networks: Dr. Darren Martin
Dr. Darren Martin is a virologist at the University of Cape Town, South Africa. He
specialises in studying the contribution of genetic recombination to the evolution of viruses. Besides working on RDP4 (a computer program for recombination
analysis), he enjoys studying, and running evolution experiments on small single-stranded DNA viruses.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
12
Program
Phylogeny Inference Module
Sun 9 Aug
09:00-19:00
Registration, campus orientation and welcome event
Mon 10 Aug
7:30-8:30
Registration
8:30-9:00
Welcome and practical instructions
A.-M. Vandamme, C. Carrington
9:00-10:30
Fundamentals of molecular evolution: theory
A.-M. Vandamme
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Alignment algorithms: theory
12:30-13:30
Lunch
13:30-15:30
Sequence alignments and editing: practice
15:30-16:00
Coffee break and poster viewing
16:00 - 17:30
Free time
17:30-19:30
Official launch of workshop followed by key-
A.-M. Vandamme
L.C. Alcantara, D. Paraskevis
E. Holmes
note lecture 1: Pandemics Past and Present
19:30-21:30
Cocktail reception and launch of Oxford University Press journal “Virus Evolution”
Tue 11 Aug
8:30-10:30
Methods for phylogenetic tree reconstruc-
A.-M. Vandamme
tion: theory
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Constructing phylogenetic trees: practice
T. de Oliveira, LC. Alcantara
(NJ, ML)
12:30-13:30
Lunch and poster viewing
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
13
13:30-15:30
Free computer time
T. de Oliveira, LC. Alcantara,
D. Paraskevis
15:30-16:00
Coffee break
16:00-17:30
Evolutionary models: theory
M. Salemi
ML methods and hypothesis testing in mo-
M. Salemi
Wed 12 Aug
8:30-10:30
lecular phylogenetics: theory
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Molecular clocks: theory
12:30-13:30
Lunch
13:30-16:00
Testing evolutionary models: practice
16:00-18:30
Coffee break and poster judging
18:30-19:30
Keynote lecture 2: next generation technol-
M. Salemi
M. Salemi, B. Rife
K. Nelson
ogies and potential applications in human
health and disease
20:00
Teachers’ dinner
Thu 13 Aug
8:30-10:30
Introduction to phylodynamics
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Phylogenetic signal and noise
12:30-13:30
Lunch and poster viewing
13:30-15:30
Reconstructing ancestral states using parsi-
M. Salemi
H. Schmidt, D. Paraskevis
T. de Oliveira, D. Paraskevis
mony
15:30-16:00
Coffee break and poster viewing
16:00-17:30
Free computer time
M. Salemi, H. Schmidt,
D. Paraskevis, B. Rife
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
14
Evolutionary Hypothesis Testing Module
Sun 9 Aug
09:00-19:00
Registration, campus orientation and welcome event
Mon 10 Aug
7:30-8:30
Registration
8:30-9:00
Welcome and practical instructions
A.M. Vandamme, C. Carrington
9:00-10:30
Statistical inference in Phylogenetics & Phylody-
O. Pybus
namics
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Advanced Evolutionary Models and maximum like-
M. Salemi
lihood methods: Theory.
12:30-13:30
Lunch
13:30-15:30
Advanced Evolutionary Models and maximum like-
M. Salemi, H. Schmidt
lihood methods: Practice
15:30-16:00
Coffee break and poster viewing
16:00 - 17:30
Free time
17:30-19:30
Official launch of workshop followed by keynote
E. Holmes
lecture 1: Pandemics Past and Present
19:30-21:30
Cocktail reception and launch of Oxford University Press journal “Virus Evolution”
Tue 11 Aug
8:30-9:30
Advanced evolutionary models and ML methods:
H. Schmidt, M. Salemi
practice
9:30-10:30
Bayesian phylogenetic inference: theory
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Coalescent theory and phylodynamic inference:
M. Suchard
O. Pybus
theory
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
15
12:30-13:30
Lunch
13:30-15:30
Introduction to BEAST(/BEAGLE) and time-mea-
A. Rambaut
sured trees: theory
15:30-16:00
Coffee break
16:00-17:30
BEAST: practice (estimating rates)
A. Rambaut
and free computer time
Wed 12 Aug
8:30-10:30
Coalescent theory and phylodynamic inference:
A. Rambaut
BEAST practice
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Bayesian model testing: theory
12:30-13:30
Lunch
13:30-14:30
Bayesian model testing: practice
G. Baele, A. Rambaut
14:30-16:00
Free computer time
G. Baele, A. Rambaut
16:00-18:30
Coffee break and poster judging
18:30-19:30
Keynote lecture 2: next generation technologies and
G. Baele
K. Nelson
potential applications in human health and disease
20:00
Teachers' dinner
Thu 13 Aug
8:30-10:30
Phylogeography: theory
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Phylogeography: practice
12:30-13:30
Lunch and poster viewing
13:30-15:30
Free computer time
15:30-16:00
Coffee break and poster viewing
16:00-17:30
Free computer time
P. Lemey
P. Lemey, N. Faria
P. Lemey, N. Faria, G. Baele
P. Lemey, N. Faria, G. Baele
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
16
Large Dataset Analysis Module
Sun 9 Aug
09:00-19:00
Registration, Campus Orientation and Welcome Event
Mon 10 Aug
7:30-8:30
Registration
8:30-9:00
Welcome and practical instructions
A.-M. Vandamme, C. Carrington
9:00-10:30
NGS: Introduction to next generation sequencing
R. Scheuermann
10:30-11:00
Coffee break and poster viewing
11:00-12:30
NGS: Reference mapping & error correction algo-
M. Prosperi
rithms
12:30-13:30
Lunch
13:30-14:30
NGS: Pipelines for SNP analysis
T. Stockwell
14:30 -15:30
NGS software: practice
T. Stockwell, M. Prosperi
15:30-16:00
Coffee break and poster viewing
16:00 - 17:30
Free time
17:30-19:30
Official launch of workshop followed by keynote
E. Holmes
lecture 1: Pandemics Past and Present
19:30-21:30
Cocktail reception and launch of Oxford University Press journal “Virus Evolution”
Tue 11 Aug
8:30-9:30
NGS: De novo assembly (De Bruijn, overlap graph)
M. Gitzendanner
9:30-10:30
NGS: Genome-wide technologies, study design,
L. Prokunina-Olsson
biological validation, interpretation and clinical
implementation
10:30-11:00
Coffee break and poster viewing
11:00-12:30
SL: introduction to statistical learning
M. Prosperi
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
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12:30-13:30
Lunch and poster viewing
13:30-14:30
NGS: metagenomics
H. Schmidt
14:30-15:30
NGS software: practice
M. Prosperi, M. Gitzendanner,
J. Min
15:30-16:00
Coffee break and poster viewing
16:00-17:30
NGS software: practice
H. Schmidt, M. Gitzendanner
SL: Univariable tests (t-test, chi-square...) and gener-
S-Y. Rhee
Wed 12 Aug
8:30-9:30
al linear models (linear/logistic, stepwise, ridge/
LASSO)
9:30-10:30
SL software: practice
10:30-11:00
Coffee break and poster viewing
11:00-12:30
NGS: quasi-species assembly
M. Prosperi
Free computer time
M. Prosperi, S-Y. Rhee
12:30-13:30
Lunch and poster viewing
13:30-14:30
NGS software: practice
S-Y. Rhee, K. Theys, J. Min
M. Prosperi, M. Gitzendanner,
J. Min
14:30-16:00
Free computer time
16:00-18:30
Coffee break and poster judging
18:30-19:30
Keynote lecture 2: next generation technologies
M. Prosperi, S-Y. Rhee
K. Nelson
and potential applications in human health and
disease
20:00
Teachers’ dinner
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Thu 13 Aug
8:30-9:30
SL theory: causal inference and bayesian networks
K. Theys
9:30-10:30
NGS theory: transcriptomics, RNASeq
R. Scheuermann
10:30-11:00
Coffee break and poster viewing
11:00-12:30
NGS: mixed infection analysis (Influenza A in birds,
T. Stockwell
Rotavirus in swine)
12:30-13:30
Lunch and poster viewing
13:30-14:30
SL software: practice
K. Theys, J. Min
14:30-15:30
NGS: GWAS theory/practice
M. Gitzendanner, S-Y. Rhee,
J. Min
15:30-16:00
Coffee break and poster viewing
16:00-17:30
Free computer time
S-Y. Rhee, K. Theys
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
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Half Day Modules
Friday 14 August: Morning
Large Phylogenies — Responsible H. Schmidt
8:30-9:30
Partition of large phylogenetic trees
H. Schmidt
9:30-10:30
Fast methods for large phylogenies & mapping
H. Schmidt
10:30-11:00
Coffee break and poster viewing
11:00-12:30
Large phylogenies: practice
12:30-13:30
Lunch and poster viewing
H. Schmidt, D. Paraskevis
Transmission cluster investigation — Responsible A-M. Vandamme
8:30 - 9:30
Transmission cluster investigation: what for?
A-M. Vandamme
9:30 - 10:30
Clusters: practice
T. de Oliveira, A-M. Vandamme
10:30 - 11:00
Coffee break and poster viewing
11:00 - 12:30
BEAST 2: practice
12:30 - 13:30
Lunch and poster viewing
T. de Oliveira, A-M. Vandamme
Molecular adaption — Responsible S. Kosakovsky-Pond
8:30 - 10:30
Molecular adaptation: theory
10:30 - 11:00
Coffee break and poster viewing
11:00 - 12:30
Molecular adaptation: practice (HYPHY)
12:30 - 13:30
Lunch and poster viewing
S. Kosakovsky-Pond
S. Kosakovsky-Pond, D. Martin
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Friday 14 August: Afternoon
Visualization of large phylogenies with metadata — Responsible N. Faria
13:30 - 14:30
How to make fancy figures
A. Rambaut, N. Faria
14:30 - 15:30
Lineage through time plots
N. Faria
15:30 - 16:00
Coffee break
16:00 - 17:30
Phylogeotool
17:30 - 18: 30
Poster Prizes and workshop close
K. Theys, E. Vanden Eynden
Recombination and networks — Responsible D. Martin
13:30 - 14:30
Detecting recombination: theory
D. Martin
14:30 - 15:30
Detecting recombination: practical computer
D. Martin, D. Paraskevis
session
15:30 - 16:00
Coffee break
16:00 - 17:30
Advanced recombination detection and networks:
D. Paraskevis
practice
17:30 - 18: 30
Poster prizes and workshop close
Virus Analysis Tools — Responsible T. de Oliveira
13:30 - 15:30
Using pipelines for viral analysis
15:30 - 16:00
Coffee break
16:00 - 17:30
Rega DB: practical computer session
17:30 - 18: 30
Poster prizes and workshop close
T. de Oliveira, A-M. Vandamme
R. Camacho, A-M. Vandamme
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
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22
Sir Arthur Lewis Hall
UWI Campus Map
Bank
Opening Cocktail
Computer Rooms
TLC
Food
Canada Hall
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
23
Abstract Overview
No.
Presenting
Title
Author
1
León B.
Phylogenetic analysis of rabies virus (RABV) in Costa Rica.
2
D’arc M.
Enteric virome analysis of non-invasive samples from gorillas by
next-generation sequencing and correlation with SIV infection.
3
Fahmy I.F.
Identification of induced genes involved in TYLCV transmission putatively responsible for virus gating of begomoviruses through the organs of
their whitefly vector B. tabaci.
4
Bajak E.
Prevalence and genetic diversity of enteric viruses among different green
vervet monkey populations on the island of St. Kitts, West Indies.
5
Evangelista J.
Phylogeny of a new flavivirus isolated from Culex (Melanoconion) occossa
of urban place from Iquitos, Peru.
6
Kvisgaard L.K.
The genetic drift of porcine reproductive and respiratory syndrome virus
(PRRSV) in a closed population evaluated by next generation sequencing
(NGS) of complete genomes.
7
Kaikabo A.A.
Molecular characterization of T4-like myovirus lytic to avian pathogenic
Escherichia coli and extended spectrum β lactamase producing E. coli
isolates from chicken.
8
Hill S.C.
Unifying viral phylogeography and ecological data to study the origins
and spread of H5N8 avian influenza virus.
9
Afonso M.
Prevalence and molecular epidemiology of feline calicivirus in European
cats (Felis catus).
10
Brown A.
The presence of infectious bronchitis viruses of poultry in Trinidad and
Tobago and the implications for using traditional vaccination strains.
11
Nyachieo A.
Serological survey and molecular characterization of herpesvirus papio 2
in wild-caught olive baboons from selected regions in Kenya.
12
Brown-Joseph T.
Identification of the Culicoides species existing in Trinidad and determination of their impact as viral vectors for BTV and EHDV in livestock.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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13
Pinto A.
Phylogenetic analysis of HIV-1 seroconverters in Sydney, Australia: 20042013.
14
Vubil A.
Phylogenetic analysis of HIV-1 subtype C epidemic in Mozambique.
15
Dos Santos G.
The HIV-1 epidemic in the Caribbean: new data sets complicate the story.
16
Eynden E.V.
Development of a bioinformatics framework for detection of transmission of HIV-1 subtype G infection.
17
Grossman Z.
A population-structured HIV epidemic: roles of risk and ethnicity.
18
Kassaye S.
HIV transmission dynamics and primary drug resistance in Washington
DC.
19
Salmona M.
Impact of combination of chemotherapy and autologous hematopoietic
stem cell transplantation for lymphoma on HIV reservoir.
20
Balamane M.
Transmitted HIV drug resistance in Washington DC, 1994-2013.
21
Rodgers M.A.
Searching for rare HIV strains in rural Democratic Republic of Congo
(2001-2003).
22
Hofstra L.M.
Sexual networks across risk groups persistently contribute to local spread
of HIV.
23
Fridholm H.
Prevalence and genotypes of human papillomaviruses (HPV) in HIV-positive men who have sex with men (MSM).
24
Siripong N.
Molecular Epidemiology of human immunodeficiency virus (HIV) outbreaks among people who inject drugs in the Philippines.
25
Pimentel V.F.
High frequency of TDR in newly diagnosed human immunodeficiency
virus type 1 (HIV-1) patients from São Paulo/Brazil.
26
Martínez O.
Estimating the evolutionary history and origin of human immunodeficiency virus Type 1 (HIV-1) subtype B in Cuba.
27
Machado L.Y.
Identification of multiples unique recombinants forms of the human immunodeficiency virus type 1 (HIV-1) in newly diagnosed Cuban patients.
28
Temereanca A.
Human immunodeficiency virus Type 1 (HIV-1) subtype G among newly
diagnosed HIV-infected injecting drug users from Romania.
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
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29
Monaco D.C.
Phylogenetic reconstruction of the human immunodeficiency virus (HIV)
epidemic from a native community in Argentina unravels the impact of
viral adaptation on disease progression.
30
Coltart C.E.M.
The role of pathogen genomics in enhancing understanding of epidemic
transmission of infectious diseases using human immunodeficiency virus
type 1 (HIV-1) as an example.
31
Smith A.S.A.
Viral escape pathways and determinants of neutralization breadth in
early human immunodeficiency virus Type 1 (HIV-1) infection.
32
Gräf T.
The contribution of epidemiological predictors in unraveling the phylogeographic history of human immunodeficiency virus type 1 (HIV-1)
subtype C in Brazil.
33
Switzer W.M.
Prevalence and distribution of human immunodeficiency virus type 1
(HIV-1) non - B subtypes in the United States.
34
Hanke K.
Molecular surveillance of recent human immunodeficiency virus type 1
(HIV-1) infections in Germany allows the detection of transmission networks and putative new subtype clades.
35
Dennis A.M.
Assessing human immunodeficiency virus (HIV) transmission cluster
dynamics in North Carolina using a large statewide dataset.
36
Silva J.
Toward a resource and time consuption reduction on human immunodeficiency virus (HIV) drug resitance algorithms.
37
Delva G.G.
Human immunodeficiency virus type 1 (HIV-1) genetic diversity and drug
resistance in the Caribbean.
38
Jimenez-Silva C.
Evolutionary history of dengue virus serotype 2 (DENV-2) in Santander, a
dengue endemic region in Colombia.
39
Vicente-Santos A.
Ecology of the dengue virus (DENV) in domiciliary environments: is the
bat a reservoir, a host or accidentally involved in the transmission of
dengue?
40
Soto-Garita C.
Genetic diversity and viral fitness studies of dengue virus serotype 1
(DENV-1) isolated during the 2013 outbreak in Costa Rica.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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41
Ortiz-Baez A.S.
Intra-host genetic diversity of dengue virus type 4 (DENV-4) strains from
the municipality of Guarujá, Sao Paulo.
42
Adesina O.A.
Incidence of dengue virus (DENV) infections in febrile episodes in ILE-IFE,
Nigeria.
43
Drumond B.P.
Dynamics of dengue virus serotype 1 (DENV-1) circulation in a medium
size city in Brazil.
44
Santiago G.A.
Emergence and local transmission of two lineages of dengue virus type 1
(DENV-1) in North America: 2013-2014.
45
Casal P.E.
Evidence for homologous recombination in chikungunya virus (CHIKV).
46
Ramjag, A.
Protective B-cell epitopes in chikungunya virus infection.
47
Jain J.
Evolution of chikungunya (CHIKV) in India: whole genome sequencing
and clinical data correlation.
48
Carrera J-P.
Spatiotemporal dynamics of Venezuelan equine encephalitis virus (VEEV)
antigenic complex.
49
Rodríguez-
High incidence of bacterial co-infections in patients infected with pan-
Márquez A.M
demic H1N1/09 influenza virus in Mexico.
50
Kikwai G.
Antiviral resistance of influenza viruses isolated in Kenya, 2007 – 2011.
51
Watson S.J.
Phylodynamics of the Eurasian ‘avian-like’ H1N1 swine influenza virus in
Europe.
52
Wang H.
Full-length genome characterization and quasispecies distribution of
hepatitis A virus (HAV) isolates in China.
53
Parag K.
Comparative analysis of canonical phylodynamic data: hepatitis C virus
(HCV) in Egypt.
54
Pereira S.A.
An evolutionary approach of interspousal transmission of hepatitis C
virus (HCV) Infection.
55
Perveen S.
Rare genetic variation in hepatitis delta virus (HDV) that influence genotype determination.
56
Okoror L.E.
Lassa virus: codon usage and bias along with their host.
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57
Sånchez G.
Molecular detection and genotyping of sapovirus (SaV) and norovirus
(NoV) in children with acute gastroenteritis in a Hospital in Lima.
58
Phan M.V.T.
Diversity and dynamics of rotaviruses in human, pigs and rats in Vietnam
using agnostic whole-genome deep sequencing.
59
Nathaniel S.
First enterovirus D68 (EV-D68) cases detected in the Caribbean region.
60
Souza W.M.
Full genome sequences and molecular characterization of ten arboviruses from Brazil.
61
Rodriguez C.
Sequence analysis of the HBV PreC/C region by ultra-deep pyrosequencing as a predictor of nucleus colonies (Nucs) treatment outcome in
patients with HBeAg-positive chronic hepatitis B.
62
Chen Z.
Cervical microbiome diversity is associated with cervical precancer using
Next-Gen sequencing.
63
Shabman R.
Next generation sequencing highlights unique aspects of Ebola virus
(EBOV) biology and provides novel diagnostic platforms.
64
Ernest T.
Ebola viral disease (EVD) outbreak surveillance and response challenges
in prevention and control.
65
Lin A.E.
Time-dependent dynamics of intrahost variation during ebola virus
infection.
66
Wohl S.
Incorporation of within-host diversity to improve viral transmission
reconstruction.
67
Shrivastava S.
Diversity and evolution of human metapneumovirus (HMPV).
68
Sahadeo N.S.
Viruses associated with acute febrile illnesses in Trinidad and Tobago.
69
Dupont C.L.
Metagenomic profiles of the Amazon river.
70
Alleyne A.T.
Deep sequencing of the small RNAs of sweet potato leaf phytobiome
reveals potentially new virus disease causing complexes in Barbados.
71
Ramsahai E.
Combining gene interaction networks improves the identification of
driver genes.
72
Cedeno S.
Likelihood ratio dependent local false discovery rate (lFDR).
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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73
Naraine R.
Characterization of CRISPR-Cas operons and spacer elements in the acidophile, Ferroplasma acidarmanus fer1.
74
Rampersad S.N.
Genetic variation and population dynamics of members of the Fusarium
incarnatum-equiseti species complex (FIESC).
75
Seetahal J.F.R.
The role of mainland-island vampire bat movement and population
dynamics in rabies virus (RABV) activity in Trinidad.
76
Seraise B.
The frequency Of N348I mutation in patient failing combination antiretroviral treatment In Botswana.
77
Scheuermann R.H.
Integrated, enriched data and diverse bioinformatics analysis tools for
comparative genomics in the Influenza Research Database (IRD) and
Virus Pathogen Resource (ViPR).
78
Bletsa M.
Molecular epidemiology and evolutionary dynamics of echovirus 3 (E3)
serotype.
79
Khouri R.
Impact of TasP in Brazil: Setting a reference dataset for future comparison
analysis.
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Abstracts
Abstract 1
León B. *(1), Fallas-Rodríguez S. (2), Cordero-Solórzano J.M. (1), Aguilar-Argueda O. (1), Hutter S. (3), González-Barrientos R. (1).
1 Biosecurity Laboratory, Animal Health National Service Senasa, Lanaseve, Costa Rica.
2 Paternity Laboratory Caja Costarricense del Seguro Social CCSS, Costa Rica.
3 Institute of Veterinary Public Health, Veterinary University, Vienna, Austria.
Phylogenetic analysis of rabies virus (RABV) in Costa Rica.
Rabies also known as hydrophobia or lyssa is a fatal disease which affects both animals and humans and
is considered one of the most important zoonotic diseases worldwide. Rabies virus belongs to the family
Rhabdoviridae, order Mononegavirales, which groups large negative RNA viruses. Rhabdoviruses in general
are enveloped bullet shaped viruses with a diameter of 75 nm and a length of approximately 100-300 nm.
Rhabdoviruses are classified into 11 distinct genera, distinguishing the genera Vesiculovirus and Lyssavirus,
the latter is constituted by 14 species, including RABV as genotype 1.
Rabies (genotype 1) is found all over the world however it is the only genotype or species present in America
where is transmitted by mammals from the order Carnivora and Chiroptera. In America, there have been reports of bat rabies in different species of bats and in all countries. In Costa Rica there are not rabies outbreaks
associated to canine cases since 1987. However almost every year there are outbreaks in bovine produced
by hematophagous bats.
In order to establish the relation of rabies bat virus in Costa Rica outbreaks, a total of 30 bovine and 2 human
brain tissue samples belonged to 20 rabies outbreaks stored by SENASA from 2004 to 2015 were amplified
and sequenced. The nucleoprotein complete gene sequences were aligned with 35 rabies virus sequences
downloaded from GenkBank/DDBJ/EMBL database using Bioedit software. The phylogenetic analysis was
done using maximum likelihood method and GRT+G+I model included in Mega5. The topology of the tree
is discussed.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Abstract 2
D’arc M. *(1,2), Siqueira JD. (1), Ayouba A. (2), Furtado C. (1), Peeters M. (2), Soares M.A. (1).
1 Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil.
2 Institut de Recherche pour le Développement - IRD, Montpellier, France.
Enteric virome analysis of non-invasive samples from gorillas by next-generation sequencing and correlation with SIV infection.
The human immunodeficiency virus type 1 (HIV) is the etiological agent of AIDS and it is estimated that over
39 million people have died due to this disease worldwide. The ancestor of the HIV-1 groups M and N have
been described from two chimpanzee populations from Cameroon infected with simian immunodeficiency
viruses, SIVcpz. Recently, we identified the ancestor of HIV-1 groups O and P in two populations of western
lowland gorillas, also from Cameroon. The pathogenicity of SIV in great apes is unclear, but infection in chimpanzees has already been associated with the progression to an AIDS-like disease. The aim of our study is to
identify and compare enteric viromes of infected and uninfected gorillas, and to assess their impact on SIV
pathogenesis. To pursue this goal, we have used next generation sequencing (NGS) to analyze non-invasive
samples of two gorillas, one SIV-infected and the other uninfected. We conducted the NGS in the HiSeq 2500
Illumina platform. Preliminary results suggest that the virome diversity is reduced in the SIV-infected animal,
but with some viral taxa expanded. We are currently extending our study and will further correlate their
virome profiles to the presence or absence of SIV in the animals.
Abstract 3
Fahmy I.F. *(1), Faisal A. (1), Abou- Ismail R.M. (2), Ahmed A.M. (3).
1 Phytopathogen Plant Vector Interaction lab, Department of Microbiology, Agricultural Genetic Engineering Research Institute, Egypt.
2 Genomics department, Agricultural Genetic Engineering Research Institute, Egypt.
3 Microbiology Department, Gene silencing Lab, Agricultural Genetic Engineering Research Institute, Egypt.
Identification of induced genes involved in TYLCV transmission putatively responsible
for virus gating of begomoviruses through the organs of their whitefly vector Bemisia
tabaci.
Molecular studies of insect disease vectors such as B. tabaci are of increasing importance for understanding pathogen-vector relationship. Discovering the respected genes, which contribute in viral translocation
through insect organs will facilitate the development of novel strategies for interfering with vector transmission of plant viruses. Reaching the ultimate goal of silencing putative transmission responsible genes
in the future by the development of transgenics is the main objective of the study. A primary necessity for
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
31
this goal is information on gene expression and control in the target insect. Among the most important
plant viruses to be transmitted by B. tabaci are those in the genus Begomovirus (family, Geminiviridae). Unfortunately, little is known about the genome of this vector. This study is investigating molecular aspects of
the interaction between Whitefly B. tabaci and begomoviruses. As an initial step in this project differential
display reverse transcriptase-PCR and randomly amplified polymorphic DNA-PCR has been applied to characterize differentially expressed mRNA from viruliferous and non-viruliferous insects, and in one case, from a
B. tabaci feed on TYLCV infected plants. Among 120 EST have been sequenced, 27 ESTs identified that have
shown homology to known sequences from GeneBank. Of these, 15 ESTs code for up-regulated genes such
as NADP-dependent D-sorbitol-6- phosphate dehydrogenase (Aldoketoreductase family), cell wall associated hydrolase, cytochrome oxidase P450 of B. tabaci, mothers against decapentaplegic homolog 4-like gene,
alpha satellite repeat, maf Ham1 superfamily, periplasmic binding proteins, cation binding domain, odorant
binding protein. There are differentially expressed downregulated genes such as ubiquitin carboxyl-terminal hydrolase/protesase ubiquitin specific protease [Culex quinquefasciatus], ATP-binding cassette subfamily B, Apis mellifera, serine/arginine-rich splicing factor 2-like (and in most insects like Apis millifera aphids,
and Anopheles gambiae, saccharopine reductase, sugar (Glycoside-Pentoside-Hexuronide) transporter, aminophospholipid transporter, B. tabaci vitellogienin gene. Expression patterns were verified using qReal time
PCR and revealed the accuracy of ESTs in case of up and down-regulation.
Abstract 4
Bajak E. *(1), Gallagher C.A. (1), Agnes N. (1,2), Navarro R. (1), Ghosh S. (1).
1 Ross University School of Veterinary Medicine, Department of Biomedical Sciences, P.O. Box 334, Basseterre, St. Kitts and Nevis.
2 Ngee Ann Polytechnic, School of Life Sciences and Chemical Technology, 535 Clementi Road, Singapore.
Prevalence and genetic diversity of enteric viruses among different green vervet monkey
populations on the island of St. Kitts, West Indies.
During 2014-2015, a surveillance study was performed to study the prevalence of enteric viruses in green
vervet monkeys on the island of St. Kitts, West Indies. A total of one hundred and fifty fecal samples were collected from different monkey populations (wild and captive animals). These samples are being screened for
the presence of rotavirus and picobirnaviruses by RNA electrophoresis in polyacrylamide gels (RNA-PAGE)
followed by silver staining. The presence of rotaviruses and/or picobirnaviruses in the fecal samples will be
further confirmed by real-time polymerase chain reaction technique. Genome sequencing and sequence
analysis will be performed on select virus strains to study the genetic diversity of rotaviruses and/or picobirnaviruses in this part of the world.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Abstract 5
Evangelista J. *(1), Cruz C. (1), Guevara C. (1), Astete H. (2), Carey C. (3), Kochel T. (4), Morrison A.C. (2,5), Williams M.
(1), Halsey E. (1), Forshey B. (1).
1 Naval Medical Research Unit 6 (NAMRU – 6) Lima, Peru.
2 Naval Medical Research Unit 6 (NAMRU - 6) Iquitos, Peru.
3 Health Directorate, Loreto, Peru.
4 Naval Medical Research Center, Silver Spring, MD, USA.
5 University of California, Davis, CA, USA.
Phylogeny of a new flavivirus isolated from Culex (Melanoconion) occossa of urban place
from Iquitos, Peru.
In recent years, a number of flaviviruses that replicate only in arthropods have been discovered and characterized. Herein, we describe the isolation and characterization of a novel mosquito-only flavivirus. The
novel flavivirus was isolated from C. (Melanoconion) occossa mosquitoes from an urban area of Iquitos, Peru,
located in the Amazon basin in the northeastern region of the country. Evidence for a flavivirus was detected by indirect immunofluorescent assay in cell culture supernatant of infected C6/36 cells using polyclonal
flavivirus group antibodies and confirmed by RT-PCR. In pairwise comparison of the ENV region sequences, nucleotide (47.4%) and amino acid (39.8%) identity was observed with Nounané virus (NOUV). Pairwise
comparison of the NS5 region, nucleotide identity was observed with Spondweni virus (65.9%), Iguape virus
(IGUV; 65.7%) and Kedougou virus (65.6%); however, at the amino acid level, pairwise identity was observed
with IGUV (69.8%), Naranjal virus (69.6%) and Bussuquara virus (69.3%). Phylogenetic analysis using partial
ENV and NS5 amino acid sequences revealed forms a clade with NOUV. To investigate the host range of the
novel flavivirus, we inoculated a variety of mammalian cells (Vero 76, Vero E6, BHK, LLCMK, and MDCK) with
pools of third passage C6/36 isolates and monitored for cytopathic effect (CPE). No CPE was detected, and all
mammalian cells lines were negative for flavivirus antigen by IFA and flavivirus RNA by real-time polymerase
chain reaction following fourteen days of incubation. We propose that this genetically distinct flavivirus be
named nanay virus (NANV), after the zone of Iquitos, Peru, where it was first detected.
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Abstract 6
Kvisgaard L.K.*, Hjulsager C.K., Larsen L.E.
National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark.
The genetic drift of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) in
a closed population evaluated by next generation sequencing (NGS) of complete genomes.
PRRS viruses are divided into two major genotypes (type 1 and type 2). Type 1 PRRSV is further divided into
at least 3 subtypes, but until now only subtype 1 has been detected in Western Europe and North America.
Both genotypes are circulating in Denmark and since vaccinations are widely used it is essential to monitor
the diversity of circulating PRRSV to secure the vaccines are up-to-date. Prior to the present study, the diversity of circulating viruses in Denmark was virtually unknown. The main objective was to assess the diversity
of circulating PRRS viruses in Danish pigs and to investigate the genetic drift of the virus in a closed population with very limited introductions of new animals. The study included phylogenetic analysis of full genome
sequences of type 1 and type 2 PRRS viruses, including the very first Danish isolated type 1 virus and the very
first Danish type 2 virus which was isolated from a non-vaccinated pig herd. The results showed a very high
genetic diversity among the Danish viruses throughout the genome within the same genotype. A global
phylogenetic analysis showed that the Danish type 1 PRRSV formed two major clusters, one vaccine-like
clade exclusively containing viruses isolated after the Porcilis vaccine was introduced and another distinct
clade consisting mainly of viruses isolated in Denmark. Phylogenetic analysis in a global type 2 PRRSV framework classified all Danish type 2 viruses to a single cluster (sub-lineage 5.1) which comprised viruses closely
related to the type 2 prototype isolate VR2332.
Abstract 7
Kaikabo A.A.* (1,2), Abdulkarim S.M. (1), Faridah A. (1), Sieo C.C. (1).
1 University Putra Malaysia, UPM 43300 Serdang, Selangor, Malaysia.
2 National Veterinary Research Institute, Vom, Plateau State, Nigeria.
Molecular characterization of T4-like myovirus lytic to avian pathogenic Escherichia coli
and extended spectrum β lactamase producing E. coli isolates from chicken
Bacteriophage Φ KAZ14, is a T4-like myovirus which infects Avian pathogenic E. coli 01 (APEC 01) and extended spectrum β lactamase producing E. coli isolated from chicken. APEC 01 causes colibacillosis in poultry
leading to huge economic losses in the poultry industry worldwide and β lactamase producing E. coli is
resistant to commonly use third generation cephalosporins use in human medicine and thus, a threat to
public health. This virus ΦKAZ14 lytic to APEC 01 and β lactamase producing E. coli has been isolated; its
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partial genome has been sequenced and analyzed. The whole genome sequencing is in process. Based on
the analysis of the partial genome sequences of this virus, it belongs to the family Myoviridae. The detail
characteristics of this virus will be presented. However, it is envisaged that, this virus may be useful in the
biocontrol programs against colibacillosis and susceptible cephalosporins resistant E. coli in clinical settings.
Abstract 8
Hill S.C. *(1), Lee Y-L. (2), Song B-M. (2), Kang H-M. (2), Lee E-K. (2), Gilbert M. (3), Hanna A. (4), Brown I. (4), Pybus
O.G. (1).
1 Department of Zoology, University of Oxford, UK.
2 Animal and Plant Quarantine Agency, Anyangsi, Republic of Korea.
3 Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium.
3 Animal and Plant Health Agency, Weybridge, UK.
Unifying viral phylogeography and ecological data to study the origins and spread of
H5N8 avian influenza virus.
Highly pathogenic avian influenza (HPAI) viruses pose a global threat to human and animal health, and cause
considerable economic damage. The factors behind the emergence of these viruses are poorly understood,
in part because of sparse sampling immediately after the identification of H5N1 in 1996. Since 2009 there
has been a surge in novel reassortant HPAI H5 viruses, most notably H5N8 in 2013. The H5N8 virus epidemic
provides an opportunity to investigate the factors behind HPAI emergence in much more detail than before.
My dataset consists of 110 H5 HA segment sequences sampled during H5N8 outbreaks from late 2013 to
December 2014. Eighty-five of these samples were isolated from birds in twelve different provinces in the
Republic of Korea, the second country to report outbreaks of H5N8. Forty-six of these are new unpublished
isolates. The host species is known for almost all sequences. Ecological data (including domestic duck and
chicken density and wintering waterfowl numbers) are available for all provinces.
I hope to use phylogeographic and molecular clock methods to reconstruct the spread of H5N8. By integrating the spatial trajectory of the virus with existing ecological data, I will try to characterize the factors behind
the spread of H5N8 in the Republic of Korea. The results of this study will help illuminate key drivers of the
emergence of novel and historical HPAI in Asia, and their subsequent global spread.
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Abstract 9
Afonso M. *(1), Pinchbeck G. (1), Bonner S. (1), Dawson S. (2), Daly J. (3), Gaskell R. (1), Radford A. (1).
1 Institute for Infection and Global Health, University of Liverpool, UK.
2 School of Veterinary Science, University of Liverpool, UK.
3 School of Veterinary Medicine and Science, University of Nottingham, UK.
Prevalence and molecular epidemiology of feline calicivirus in European cats (Felis catus)
Feline calicivirus (FCV) is a highly diverse RNA virus causing acute respiratory disease in cats. Vaccination is
widely used to control disease but does not prevent infection, with ~10% of household cats shedding virus.
The objectives of this study are to estimate the prevalence of FCV and describe its molecular epidemiology
at a European level.
Sixty-three randomly selected veterinary practices in five European countries were asked to collect oropharyngeal (OP) swabs from their feline patients. Diagnosis of FCV was by isolation in cell culture. RT-PCR was
conducted on all isolates followed by consensus sequencing. Neighbour-joining phylogenetic trees were
constructed based on partial capsid and polymerase sequences.
Fifty (79.4%) of the recruited practices returned a total of 1521 OP swabs. A total of 150 samples tested positive for FCV (9.9%). Phylogenetic analyses showed high strain diversity evidenced by a radial phylogeny
containing 109 strains, with more than one strain isolated in each country. Field strains were restricted to
one country with no evidence of widespread international transmission as seen for other caliciviruses. Taken
together, FCV remains an ongoing threat to cats, with high prevalence and strain diversity emphasizing the
need for ongoing surveillance and vaccination.
Abstract 10
Brown A. *, Blake L., Oura C.
School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine,
Trinidad.
The presence of infectious bronchitis viruses of poultry in Trinidad and Tobago and the
implications for using traditional vaccination strains
Currently there is limited information about the naturally occurring infectious bronchitis virus (IBV) strains
that circulate in Trinidad and Tobago (T&T). Vaccination against the virus is widespread across the poultry
sector however not much work has been done to identify the strains that exist in T&T. Poultry farmers who
vaccinate their flock still experience clinical respiratory signs of disease on their farms and vaccines generally
elicit poor cross¬protection across serotypes. This research proposes to examine whether the occurrence of
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disease is due to novel strains, or other known strains of IBV, that differ from the traditionally used vaccination strains. Clinical poultry samples will be tested for the presence of IBV using the real-time polymerase
chain reaction testing method. Positive samples will be sequenced and analyzed alongside other strains of
IBV worldwide and the strains used for the vaccination program in Trinidad and Tobago. This research will
lead to improved knowledge about IBV that will be valuable to the poultry industry concerning vaccination
practices and disease control.
Abstract 11
Nyachieo A. * (1), Chepkwony S. (1,2), Kiulia N. (1), Gicheru M. (1,2).
1 Department of Reproductive Health and Biology, Institute of Primate Research, Nairobi, Kenya.
2 Department of Zoological Sciences, Kenyatta University, Nairobi, Kenya.
Serological survey and molecular characterization of herpesvirus papio 2 in wild-caught
olive baboons from selected regions in Kenya.
Herpes simplex virus (HSV) infection is caused by two HSV serotypes, HSV-1 and HSV-2. HSV has been associated with the risk of Human Immunodeficiency Virus acquisition and transmission, miscarriage, premature
labor, low fetal growth rate, meningitis, chronic skin infection and sometimes physical disability. Finding
drugs and vaccines to cure and thus completely eradicate HSV has been a great challenge since the current
drugs only lengthen recurrence period. Infection of baboons (Papio species) with herpesvirus papio 2 (HVP2) produces a disease that is clinically similar to HSV and hence can be used as models. However, the comparative prevalence of HVP 2 in male and female baboons, and the circulations strains of HVP 2 in baboons
from different regions in Kenya, is not known.
In this study, the seroprevalence of HVP 2 in baboons from the selected geographical regions was determined. The anti-HVP 2 antibodies in sera from 189 baboons captured from different geographical regions
were detected using ELISA. To identify the strains circulating in these baboons, DNA was extracted from trigeminal ganglia, oral and genital swabs from seropositive baboons. PCR was used to amplify the unique long
(UL23) region that code for thymidine kinase and positive amplicons were sequenced. This study showed
that 87% of the baboons in Kenya have been exposed to HVP 2 infection. Herpesvirus papio 2 strain A951
was identified as the circulating strain. This information is essential in developing a baboon model to study
the pathogenesis of HSV and in testing new vaccines and drugs.
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Abstract 12
Brown-Joseph T. *(1), Harrup L. (2), Baten C. (3), Frost L. (3), Hicks H. (3), Flannery J. (3), Ramkissoon V. (4), Ramdeen
R. (4), Carrington C.V.F. (4), Oura C. (1).
1 School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine,
Trinidad and Tobago.
2 Entomology Unit, The Pirbright Institute, Surrey, United Kingdom.
3 Non-vesicular Diagnostic Laboratory, The Pirbright Institute, Surrey, United Kingdom.
4 Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago.
Identification of the Culicoides species existing in Trinidad and determination of their
impact as viral vectors for Bluetongue Virus (BTV) and Epizootic Hemorrhagic Disease
Virus (EHDV) in livestock.
Culicoides midges are very small, hematophagous insects that live in moist, organic environments. There are
~1300 known species, some of which are vectors for important livestock viruses (e.g. BTV and EHDV) and human viruses (e.g. Oropouche virus). To determine which species currently exist in Trinidad, insect light-trapping was performed in different ecozones throughout Trinidad. Speciation was first done morphologically
using established biological keys, then unidentified specimens were classified using molecular methods
involving non-destructive DNA extractions, followed by PCR amplification, sequencing and phylogenetic
analysis of the mitochondrial Cytochrome oxidase I (mtCOI) gene.
To determine the serotypes and strains of BTV and EHDV circulating in livestock in Trinidad, 5 ml serum
and whole blood samples were taken monthly (for 6 months) from a cohort of imported naïve dairy cattle
starting from 3 days after entry into the country. Sera were tested for BTV and EHDV antibodies by ELISA to
establish when the animals first seroconverted. Viral RNA was extracted from first-positive whole blood samples and subjected to group-specific reverse transcription quantitative real-time PCR (RT-qPCR) for both BTV
and EHDV. Positive samples with the lowest Ct values were selected for virus isolation and serotype-specific
RT-qPCRs to identify which of the 24 BTV serotypes and 6 EHDV serotypes are currently circulating in Trinidad. To date 5 BTV isolates have been obtained representing 5 different serotypes. Viral protein (VP2) genes
from the different BTV and EHDV isolates will be amplified and sequenced for subsequent phylogenetic
analyses and viral evolution studies.
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Abstract 13
Pinto A. *(1), Di Giallonardo F. (2), Carrera A. (3), Shaik A. (1), Cunningham P. (4), Cooper D. (1), Kelleher A. (1).
1 The Kirby Institute, Sydney, New South Wales (NSW), Australia.
2 University of Sydney, Sydney, NSW, Australia.
3 SydPath, St Vincent’s Hospital, Sydney, NSW, Australia.
4 St. Vincent’s Centre for Applied Medical Research, Sydney, NSW, Australia.
Phylogenetic analysis of Human Immunodeficiency Virus type 1 (HIV-1) seroconverters in
Sydney, Australia: 2004-2013.
Background: In Australia, NSW is the state with the largest burden of HIV, and has seen the highest rates of
new infections in twenty years. Previous local seroconverter studies have differed from international rates of
transmitted drug resistance (TDR).
Aim: We analysed genotypes of seroconverters to evaluate the impact of transmission networks on TDR.
Methods: All genotypic antiretroviral resistance testing (GART) from 2004-2013 was included in a statewide
database, and a subgroup of seroconverters identified from one site using strict laboratory criteria. Duplicates were excluded and sequences analysed using Stanford dbProgram and WHO Surveillance Drug Resistance Mutations (SDRM 2010). Sequences were formatted, aligned and edited before phylogenetic inference
and cluster designation using maximum likelihood method, 70% bootstrapping and sequence distance
threshold of <1%.
Results: 7629 sequences were included in the database. There were 283 seroconverters from a single site,
91% were subtype B. Overall SDRM prevalence was 8.8% (25/283), with 1.4% PR, 5% NRTI and 2.8% NNRTI
mutations. Within the subtype B tree we identified 23 clusters (57 sequences) that matched our criteria.
10/25(40%) of TDR sequences were associated with clusters of other TDRs. There did not appear to be temporal cluster growth in this population over time.
Conclusions: Rates of TDR in NSW seroconverters are lower than that reported in other states of Australia
and overseas. Overall seroconverters do not appear to be associated with cluster formation, which has implications for targeted public health campaigns aimed at identifying early infections.
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Abstract 14
Vubil A. *(1), Mabunda N. (1), Bila D. (1), Fernandez J.C.C. (2), Jan I. (1).
1 Instituto Nacional de Saúde- Moçambique.
2 Instituto Oswaldo Cruz, Fiocruz, Brasil.
Phylogenetic analysis of Human Immunodeficiency Virus type 1 (HIV-1) subtype C Epidemic in Mozambique.
The HIV-1 subtype C is responsible for the majority of HIV-1 infection in Mozambique, but little information is
available about the genetic diversity and evolutionary history of this epidemic in the country. In order to reconstruct the origin of HIV-1 subtype C clades circulating in Mozambique, a total of 496 specimens collected
in DBS from children under 18 months old were obtained in the totally of the 11 Provinces of Mozambique
during 2013. The HIV-1 genetic subtypes was defined based on genotyping from the entire PR gene and
partial RT regions, using REGA HIV-1 Subtyping Tool version 3.0 algorithm.
From the total, 426 samples (86.5%) generated sequences for genetic characterization. The majority of HIV-1
strains was classified as subtype C (97.0%), subtype A1 (1.2 %), subtype G (0.5%) and subtype D (0.2 %). The
intersubtype recombinant form B/D was identified in 1.2% of infected children. Phylogenetic analyses revealed that the epidemic has origin from multiples independent introductions and distributed in different
lineages that wide dispersed in others southwestern African countries.
This is the first national HIV-1 molecular epidemiology survey performed in Mozambique and demonstrated
that HIV-1 subtype C is the most prevalent in the country and suggest the existence of autochthonous transmission networks of subtype C in Mozambique. Continuous surveillance of genetic diversity of HIV-1 in the
country is fundamental to provide a better understanding of subtype C epidemic spread and to inform the
design of optimal intervention strategies in Mozambique.
Abstract 15
Dos Santos G. *, Ouka M., Césaire R.
Service de virologie CHU de Martinique, Fort de France, Martinique
The Human Immunodeficiency Virus type 1 (HIV-1) epidemic in the Caribbean: new data
sets complicate the story.
The ^b epidemic in the Caribbean is mostly driven by the dissemination of the pandemic clade B and of older non-pandemic B lineages (BCAR). However, the low number of sequences from most Caribbean Islands
limits the information about the timing and the migration patterns of HIV-1B in the region. We used REGA
(version 3) to subtype HIV-1 (PR/RT) sequences from Martinique (MART, n=1275, 1995-2015), Guadeloupe
(GUA, n=1095, 1999-2014), St Martin/St Marteen (SMART, n=169, 2002-2007), Haiti (HAI, n=131, 2010), AKN
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(AKN, n=37). HIV-1 subtype B is dominating (MART, 71%; GUA, 68%; SMART, 72%; HAI, 60%. AKN, 62%) but
B/D recombinants (MART, 10%; GUA, 11%; SMART, 13%; HAI, 18%; AKN, 18.5%), B-like (MART, 5%; GUA, 7%;
SMART, 11%; Haïti 15%,) and B, potential recombinant (MART, 2%; GUA, 2.5%; HAIT, 1.8%) are also identified.
HIV-1 CRF 02_AG (MART: 5%; GUA 4%) as HIV-1 Subtype D (MART: 0.8%; GUA 1.5%) are also circulating. Neighbor-Joining analysis indicate presence of clusters with up to 30 individuals (B, MART), 11 (B/D, MART) and 21
(D, MART+GUA). Finally from the clinical reports we established that B/D recombinants are circulating at
least since 1986.
Next steps are to establish the prevalence of the BCAR clades in our dataset through ML analysis and to
investigate the spatiotemporal dynamics of dissemination of B subtypes and B/D recombinants in the Caribbean region.
Abstract 16
Eynden E.V. *(3), Theys K. (3), Winand R. (1,2), Vandamme A.M. (3,4,6), Abecasis A. (4,5).
1 KU Leuven, Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal
Processing and Data Analytics, Leuven, Belgium.
2 iMinds Medical IT, Leuven, Belgium.
3 KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical
and Epidemiological Virology, Leuven, Belgium.
4 Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.
5 Unidade de Saúde Pública Internacional e Bioestatística, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.
6 Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa,
Portugal.
Development of a bioinformatics framework for detection of transmission of Human Immunodeficiency Virus type 1 (HIV-1) subtype G infection
High evolutionary rates of HIV-1 enable rapid adaptation to antiviral treatment by selection of resistance
mutations. In addition, transmission of drug resistance (TDR) can challenge the effectiveness of first-line
treatment of newly diagnosed, drug-naïve patients. While most research on TDR has been done in the context of HIV-1 subtype B, we directed ourselves to subtype G infected patients from Portugal. We developed a
framework to investigate transmission dynamics, including both drug-treated and drug-naïve patients. After
subtyping the database using Rega subtyping tool version 2, and selecting subtype G infected patients, a
maximum-likelihood phylogenetic tree was built to identify HIV-1 transmission clusters and patterns of TDR
present in those clusters. Given that a consensus definition for a transmission cluster is lacking we investigat9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
41
ed the impact of different combinations of bootstrap (70% to 90%) and distance values (0.015 to 0.05) on the
identification of transmission clusters.
A population of 2529 subtype G infected patients was studied, with 1189 being drug-naïve and 1340 being
drug-treated. Using the most strict settings (bootstrap of 90% and genetic distance of 0.015) we did not
detect any TDR clusters. When the bootstrap support was lowered to 70% and genetic distance to 0.05, 7
clusters of TDR were identified, each including two drug naïve patients with resistance mutations on M41L
(1x), K101E/P (1x), K103N/S (4x) and F53L/Y (1x).
A low number of clusters with subtype G patients displaying TDR, indicates a different pattern in the subtype
G epidemic compared to subtype B, highlighting the importance of further investigations.
Abstract 17
Grossman Z. *(1,2), Avidor B. (3,4), Mor Z. (5), Chowers M. (6), Levy I. (7), Shao W. (8), Girshengorn S. (3,4), Turner D.
(3), Maldarelli F. (2).
1 School of Public Health, Tel-Aviv University, Tel-Aviv, Israel.
2 National Cancer Institute, Frederick, MD, USA.
3 Crusaid Kobler AIDS Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
4 Lab. of Viruses and Molecular Biology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.
5 Ramla Department of Health, Ministry of Health, Ramla, Israel.
6 Meir Medical Center, Kfar Saba, Israel.
7 Infectious Diseases Unit, Sheba Medical Center, Ramat-Gan Israel.
8 Advanced Biomedical Computing Center, SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
A population-structured human Immunodeficiency virus (HIV) epidemic: roles of risk
and ethnicity.
Background: A general aspect of the HIV epidemic in developed areas is that the infection spreads with
different dynamics across the ethnically and culturally diverse populations, reflecting differences in risk behavior. HIV in Israel started with a subtype-B epidemic among men who have sex with men (MSM), followed
in the 1980s and 1990s by introductions of subtype-C (largely acquired by heterosexual transmission) from
Ethiopia and subtype-A from the former Soviet Union (FSU, largely acquired by intravenous drug use). The
epidemic matured over the last 15 years without additional large influx of exogenous infections. Between
2005 and 2013 the number of infected MSM increased 2.89-fold, compared to 1.63-fold and 1.27-fold for
IVDU and Ethiopian-origin residents, respectively. Understanding the underlying dynamics is essential for
effective public health planning.
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Methods: We analyzed demographic and virologic data from 1,427 drug-naive HIV-infected individuals diagnosed with HIV-I during 1998–2012. HIV phylogenies were reconstructed with Maximum-likelihood and
Bayesian methods.
Results: Subtype-B viruses, but not A or C, demonstrated a striking number of large clusters with common
ancestors, including some suggesting presence of transmission networks. Transmitted drug resistance was
highest in subtype B (13%). In cross-ethnic transmission, demonstrated by the presence of Israeli-born with
non-B virus infections and FSU immigrants with non-A, MSM represented a frequent risk factor.
Conclusions: Reconstructed phylogenetic trees, demonstrating substantial grouping in subtype B but not
in non-MSM subtype-A and not in subtype C, reflect differences in transmission dynamics linked to risk-behavior. Cross-ethnic spread was due to multiple independent introductions, with a prevalent role of MSM
in transmissions. Such data provide a baseline to track epidemic trends and will be useful in informing and
quantifying efforts to reduce HIV transmission.
Abstract 18
Kassaye S. *(1), Grossman Z. (2), Johnston B. (3), Balamane M. (1), Teran R. (1), Young M. (1), Meyer III W. (4), Kumar P.
(1), Shafer R. (3), Maldarelli F. (5), Katzenstein D. (3).
1 Department of Medicine, Georgetown University, Washington DC.
2 Tel Aviv University, Tel Aviv, Israel.
3 Department of Medicine, Stanford University, Stanford, CA.
4 Quest Diagnostics, Baltimore, MD.
5 HIV Drug Resistance Program, National Cancer Institute, Frederick, MD.
Human immunodeficiency virus (HIV) transmission dynamics and primary drug resistance in Washington DC.
Background: In the era of improved biomedical interventions for prevention identification of HIV clusters,
using molecular epidemiology can inform public health efforts to interrupt ongoing HIV transmission.
Approach: This retrospective study uses sequence and HIV drug-resistance data from individuals enrolled
in clinical research studies at Georgetown University in Washington DC which has 2.5% HIV prevalence. 314
HIV pol gene sequences were collected from 1994-2013. Median age was 38 years, (71% female; 70% African
American). HIV exposure was heterosexual sex for 35%, MSM for 15%, IDU for 17%, blood transfusion for 3%
and unidentified or unknown for the remaining 30%. Transmitted drug resistance positions were removed
and analyses performed using BEAST (GTR+I substitution model, gamma distributed rates, relaxed molecular clock, and GMRF Bayesian skyline tree prior). 600,000,000 states were generated (MCMC method) to
achieve an ESS > 200 after 10% burn-in. Results were verified using the maximal likelihood method.
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
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Outcomes: A total of 9 transmission clusters with posterior probability >95% consisting of two to three individuals was identified using the GTR model implemented in BEAST. Additional analyses will include a
larger data set including prospective enrollment patients, and be used to identify timing of the entry of
the epidemic into the region, identify transmission “hot spots” using geospatial data, and to investigate the
relationship of the local epidemic with national and global transmissions. Additional skills acquired during
the workshop will enhance our ability to address these relevant questions using this unique and rich historic
and contemporary data set.
Abstract 19
Salmona M. *(1), Delagreverie H. (1), Gerard L. (2), Chaix ML. (1), Nere ML. (1), Galicier L. (2), Simon F. (1), Oksenhendler E. (2), Delaugerre C. (1).
1 Department of Virology, Saint-Louis Hospital, Paris - University Paris Diderot, France.
2 Department of Immuno-Hematology, Saint-Louis Hospital, Paris - University Paris Diderot, France.
Impact of combination of chemotherapy and autologous hematopoietic stem cell transplantation for lymphoma on human immunodeficiency virus (HIV) reservoir
Myeloablation and autologous stem cell transplantation (ASCT) lead to significant depletion of circulating
CD4+T cells and could impact the HIV-1 reservoir. The analysis of the viral population before and after ASCT
could help to address the origin of HIV blood reservoir after ASCT. We studied the longitudinal effect of
combination chemotherapy and ASCT for HIV-related lymphoma on cellular HIV-1 DNA quantification and
diversity in patients on antiretroviral therapy.
We analyzed thirteen antiretroviral successfully treated-HIV-infected patients who received myeloablative
chemotherapy and ASCT for relapsed or refractory lymphoma. HIV-DNA was quantified longitudinally using
real-time PCR assay on whole blood samples at different time points before, during, and after ASCT. No significant difference in median HIV-DNA for each patient before and after ASCT was observed.
Furthermore, HIV-1 envelope C2V3 genomes from longitudinal blood samples from two patients were sequenced with ultra-deep pyrosequencing (UDPS). Four time points were tested for each patient, two before
and two after ASCT. Viral variants were reconstructed from UDPS sequences using a heuristic algorithm
and viral dynamics were evaluated using nucleotide diversity. Sequences were evaluated for viral compartmentalization between viral population before and after ASCT. Analysis showed viral compartmentalization
and an emergence of new viral quasispecie after ASCT in the patient who has been virological controlled
by 7 years of antiretroviral treatment. This result suggested that virus found in blood after ASCT come from
long-lived ancient reservoirs or different compartment as the gut. Analysis of additional patients with other
compartment than blood and sorted cells in the graft is ongoing.
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Abstract 20
Balamane M. *(1), Johnston B. (3), Grossman Z. (2), Teran R. (1), Young M. (1), Meyer, III W. (4), Kumar P. (1), Shafer, R.
(3), Maldarelli, F. (5), Katzenstein, D. (3), Kassaye, S. (1).
1 Department of Medicine, Georgetown University, Washington DC.
2 Tel Aviv University, Tel Aviv, Israel.
3 Department of Medicine, Stanford University, Stanford, CA, USA.
4 Quest Diagnostics, Baltimore, MD, USA.
5 HIV Drug Resistance Program, National Cancer Institute, Frederick, MD, USA.
Transmitted Human Immunodeficiency Virus (HIV) Drug Resistance in Washington DC,
1994-2013.
Background: Primary HIV drug resistance increases with availability of antiretroviral therapy. Studies demonstrate ~16% transmitted drug resistance (TDR) in the U.S with regional heterogeneity. Little is known about
TDR in Washington DC despite high HIV prevalence of 2.5%.
Approach: HIV resistance data for 218 treatment-naïve individuals in Washington DC were included in this
analysis. TDR was estimated using the WHO-2009 surveillance list. Median age was 37, African-American
(57%) and female (65%). HIV risk groups included heterosexual (34%), MSM (20%) IDU (14%), blood transfusion
(4%) and unknown (28%). 118 sequences were from 1994-1995, 29 from 1996-2006 and 71 from 2007-2013.
TDR prevalence was 22% (95% CI: 16.7 - 28.1): 19.2% (CI: 14.2 - 25.1) nucleoside reverse transcriptase inhibitors (NRTI); 3.7% (CI: 1.6-7.1) non-NRTI (NNRTI); 2.8% (CI: 1 - 6) protease inhibitors (PI); 1.4% (CI: 0.28 - 4) dual
class NRTI/NNRTI and .9% (CI:0. 1 - 3.3) triple class PI/NRTI/NNRTI. 40 had TAMs: 41L (6.4%), 67N (8.7%), 70R
(9.6%), 210W (5.5%), 215Y/F (11.5%), 219Q (5%). 31 had > 1 TAM, and decreasing prevalence between 1994-95
and 2007-2013. M184V/I was present in 2.8% of sequences. The most common NNRTI mutations were 103N
(2.8%), and 181C (1.4%), and PI mutations were 54V (1.8%) and 90M (2.3%) primarily from 2007-2013.
Outcomes: Additional sequencing and prospective enrollment of participants is planned to build on the
contemporary cohort to permit a time-trend analysis. Phylogenetic methods will be applied to analyze viral
diversity and evolution and analyses performed to determine the long-term outcomes among those with
TDR.
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Abstract 21
Rodgers M.A. *(1), Vallari A. (1), McArthur C. (2), Sthreshley L. (3), Brennan C.A. (1).
1 Infectious Diseases Research, Abbott Diagnostic, Abbott Park, IL, USA
2 School of Dentistry, University of Missouri-Kansas City, Kansas City, MO, USA
3 Presbyterian Church (USA), Kinshasa, DRC.
Searching for Rare Human Immunodeficiency Virus (HIV) Strains in Rural Democratic Republic of Congo (2001-2003).
As a region within the epidemiological epicenter of the HIV pandemic, the Democratic Republic of Congo
(DRC) is a reservoir of circulating HIV strains exhibiting high levels of strain diversity and intersubtype recombination. In this study, we characterized HIV specimens collected in two rural areas of the DRC between
2001-2003 to identify and obtain sequences for rare subtypes and recombinants. A total of 262 HIV-infected
specimens from voluntary testing and pregnant women participating in a PMTCT program were characterized. Classification was determined by RT-PCR amplification and phylogenetic analysis of the env gp41
sequence. Analysis of 172 env sequences showed a high level of strain diversity. Subtype A predominated
(43.6%) but 8 different subtypes (33.1%), 5 CRFs (18.6%), and unclassified (4.7%) sequences were also found.
Of the rare subtypes, 18 specimens were selected for HIV-specific primer based next generation sequencing
to obtain full genome sequences. Near complete genome sequences with >86% genome coverage were
obtained for 13 HIV specimens. Phylogenetic and Simplot analysis identified pure subtypes D (n=1), F1 (n=1),
H (n=2), and CRF25 (n=1). The remaining 8 genomes were simple recombinants (n=1; URF_JK) or complex
recombinants of 3 or more subtypes, including A, C, F, G, H, J, K, and unclassified (n=7). The complexity of
these URFs makes recombination analysis challenging. These complete genomes are a valuable contribution
to surveillance of HIV strain diversity, which is important and essential to address the challenge posed by
ongoing evolution of HIV and to monitor the rapidly changing HIV pandemic.
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Abstract 22
Hofstra L.M. *(1,2), Mudrikova T. (3), Pingen M. (1), Richter C. (4), Langebeek N. (4), Schuurman R. (1), Hoepelman I.M.
(3), Wensing A.M.J. (1).
1 Dept. of Medical Microbiology, University Medical Center Utrecht, the Netherlands.
2 Dept. Of Infection and Immunity, Luxembourg Institute of Health, Luxembourg.
3 Dept. of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, the Netherlands.
4 Dept. of Internal Medicine and Infectious Diseases, Rijnstate Hospital, Arnhem, The Netherlands.
Sexual networks across risk groups persistently contribute to local spread of human immunodeficiency virus (HIV).
Background: Despite earlier diagnosis, start of treatment at higher CD4 counts and the sharp drop in influx
of immigrants from HIV endemic countries since 2003, HIV incidence is not decreasing in the Netherlands.
Therefore we aimed to get insight in local transmission dynamics.
Methods: Clinical and virological data was collected of 96% of newly diagnosed HIV patients of the UMCU
and Rijnstate from 2004 until 2013 (n=1220) with 973 pol sequences available. A maximum likelihood phylogenetic tree was constructed and clusters were identified using 95% support and 6 patients), showing
mixing of risk groups in 18 of them. Based on last negative test results of patients in the cluster, the minimal
duration of circulation was on average 53 months, ranging from 10-111 months. We identified 1 subtype C
cluster of 18 patients of Dutch origin (11 MSM, 2 female HSX, 3 male HSX, 2 unknown), 1 subtype A1 cluster
of 8 patients of Dutch origin (5 MSM, 1 male HSX, 2 female HSX) and 1 subtype CRF02_AG cluster of 6 MSM
patients of mixed origin. The non-B subtypes have been circulating for minimal 33 (CRF02_AG), 36 (A1) and
75 (C) months.
Conclusion: Strains from subtype B clusters were shown to be circulating for a prolonged period. Longstanding clusters of non-B subtypes were seen in patients of Dutch origin transcending different risk groups,
suggesting the increase in non-B HIV is due to local spread in the Dutch native population.
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Abstract 23
Olesen, M.L., Fridholm, H. *, Fomsgaard, A., Rosenstierne, M.W.
Virus Research and Development Group, Statens Serum Institut, Copenhagen, Denmark.
Prevalence and genotypes of human papillomaviruses in human Immunodeficiency Virus (HIV) - positive men who have sex with men (MSM).
Human papillomavirus (HPV) have been studied for many years as they are causative agent of cervical cancer. Despite being so well studied, a recent publication showed, by using next generation sequencing (NGS),
that the circulating HPV genotypes in vaginal samples are highly underestimated. Presently, over 170 different genotypes of HPV are described but new types are being discovered continuously.
HPVs are also present in penile, anal and oral malignancies (50%, 80% and 80%, respectively). However, the
genotypes and their oncogenic potential in these anatomical locations are not well characterized. We are
following a cohort of 100 HIV-positive MSM from which we are collecting urine, saliva and faecal samples
once a year for three years. All samples will be subjected NGS and analyzed for HPV infections.
HPVs oncogenic potential are directly related to an integration event where regulation of the viral genes
E6 and E7 becomes disrupted. The grouping of HPV into high- or low risk types is based on the sequence
variation of E6 and E7.
We aim to perform sequence and phylogenetic analysis of the circulating genotypes in this cohort. This is of
relevance when evaluating if the existing vaccines would provide the same protection to HIV-positive MSN
or if other HPV-types should be included in a vaccine. Furthermore, we will be able to perform sequence
analysis on the integrated HPV types with emphasis on E6 and E7 to see if they have similarity to known
oncogenic HPV types and thereby be able to assess their oncogenic potential.
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Abstract 24
Siripong N. *(1), Samonte G.M.J. (2), Abellanosa-Tac-An I.P. (3), Telan E.F.O. (4), Pence B.W. (1), Powers K.A. (1), Moody
J. (5), VanRie A. (6), Dennis A. (7).
1 Department of Epidemiology, University of North Carolina at Chapel Hill, NC, USA.
2 Department of Health, National Epidemiology Center, Manila, Philippines.
3 Cebu City Health Department, Cebu City, Philippines.
4 National Reference Laboratory, STD AIDS Cooperative Central Laboratory, San Lazaro Hospital, Manila,
Philippines.
5 Department of Sociology, Duke University
6 Unit of International Health, Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp.
7 Division of Infectious Disease, University of North Carolina at Chapel Hill, NC, USA.
Molecular epidemiology of human immunodeficiency virus (HIV) outbreaks among people who inject drugs in the Philippines.
Within a metropolitan area of the Philippines, surveillance surveys documented two separate HIV outbreaks
with rapid spread among people who inject drugs (PWID). The first occurred in Cebu City, where HIV prevalence in PWID rose from less than 1% in 2009 to 56% in 2010. The second took place in the neighboring
Mandaue City, where HIV prevalence in PWID increased from 3.5% in 2011 to 38% in 2013. While the delay
between the two epidemics may suggest two separate populations, we hypothesized that the transmission
of HIV started in Cebu City and spread to Mandaue by people who shared needles in both cities. Phylogenetic analysis offers an important tool to test this hypothesis by assessing genetic similarities and differences
within and between the two groups. We analyzed 111 HIV reverse transcriptase (RT) sequences collected
from people who inject drugs and men who have sex with men during surveillance in 2013. Another 278
sequences sampled in the Philippines or closely related sequences from a BLAST search were also included in the analysis. Sequences were aligned with HXB2 and a maximum-likelihood phylogenetic tree was
built using the GTR mode in FastTree. We found that 110 of the 111 sequences were subtype B grouped in a
monophyletic clade. This is consistent with our hypothesis that the HIV infections among people who inject
drugs in the two cities are clustered and that, despite the delay between the epidemics, the two epidemics
are closely linked.
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Abstract 25
Pimentel V.F. *(1), Abecasis A.B. (2), Portes L. (3), Pineda-Peña A.C. (2,4,5), Matsuda E.M. (6), Guimarães P.M.S. (3),
Hársi C.M. (1), De Paula J.L. (3), Vandamme A.M. (2,4), Brígido L.F.M (3).
1 University of São Paulo, São Paulo, Brazil.
2 Departamento de Saúde Pública Internacional e Bioestatística, Departamento de Microbiologia and Center
for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Lisboa, Portugal.
3 Institute Adolfo Lutz, São Paulo, Brazil.
4 KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, B-3000 Leuven, Belgium.
5 Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC)
and Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia.
6 Clinic of Infectious Diseases Reference, Santo André, Brazil.
High frequency of TDR in newly diagnosed human immunodeficiency virus type 1 (HIV-1)
patients from São Paulo/Brazil.
Background: The HIV-1 epidemic in São Paulo is dominated by subtypes B, F1 and C. The aim of this study
was to characterize genotypes and transmitted drug resistance (TDR) among newly diagnosed HIV-1 individuals from January 2014 to February 2015 in São Paulo.
Methodology: Population sequencing (PR+RT) was performed on plasma viral RNA for 179 patients. For
subtyping, we tested different automated tools - Rega v2.0, v.3.0, Blast Los Alamos, Scueal, Comet v1.0 and
jpHMM - and performed phylogenetic analysis using the Neighbor-Joining method under K2-P model with
MEGA and bootscanning using SimPlot. Sequences were submitted to the Stanford HIV Database CPR tool
(http://cpr.stanford.edu/cpr.cgi) to investigate TDR. Statistical analysis was performed using GraphpadPrism
software.
Results: Among the 179 sequences, the more prevalent subtypes were B (74%), C (12.3%), F (5.6%) and BF1
recombinants (5.6%). BC recombinants (1%) and subtypes D and G.
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Abstract 26
Martínez O. *(1), Machado L.Y. (2), Díaz H.M. (2), Blanco M. (2), Romay D. (2), Dubed M. (2), Silva E. (2), Pérez L.J. (3).
1 University of Informatics Sciences, La Lisa, La Habana, Cuba.
2 Research Laboratory of AIDS, San José de las Lajas, La Habana, Cuba.
3 National Center of Agricultural Health, San José de las Lajas, La Habana, Cuba.
Estimating the evolutionary history and origin of human immunodeficiency virus Type 1
(HIV-1) subtype B in Cuba.
In Cuba, the HIV-1 epidemic is characterized by a high genetic diversity with several circulating subtypes.
Previous studies have shown that subtype B is the predominant genetic form in Cuba. However, the evolutionary history of this viral variant in Cuba is still not clear. The aim of this study was to estimate the origin
and evolution of HIV-1 subtype B in the Cuban epidemic. Phylogenetic relationships among HIV-1 subtype
B pol Cuban sequences isolated in 1999, between 2009 and 2012 and sequences of different geographic
origins were estimated. A Bayesian statistical inference was used to estimate the time of HIV-1 subtype B
introduction, the nucleotide substitution rate and the demographic history. The phylogenetic relationships
revealed multiple introductions of subtype B (n>40) in Cuba. The most recent common ancestor of Cuban
HIV-1 subtype B was dated back to about 1977 (1974-1982). Estimated nucleotide substitution rate was 2.7
X 10-3 subs/site/year (2.37 x 10-3 to 3.09 x 10-3). The effective number of HIV-1 subtype B infections grew
exponentially between 1980 and 1995 but then decreased in infections since the year 2000. The decrease
in infections by HIV-1 subtype B appeared to have coincided with the emergence of CRF 20, 23, 24_BG and
CRF19_cpx in Cuba. The HIV-1 subtype B was introduced in Cuba to the last 1970´s. It was supported the idea
of subtype B introduction in Cuba from North America and Europe. The results presented herein, provide
new insights concerning the epidemic of HIV-1 subtype B in our region.
Abstract 27
Machado L.Y. * (1), Blanco M. (1), Díaz H.M. (1), Martínez O. (2), Romay D. (1), Ruiz N. (1), Dubed M. (1).
1 AIDS Research Laboratory, Mayabeque, Cuba.
2 Universidad de las Ciencias Informáticas, Havana, Cuba.
Identification of multiples unique recombinants forms of the human immunodeficiency
virus type 1 (HIV-1) in newly diagnosed Cuban patients.
The HIV-1 epidemic in Cuba is characterized for a high genetic diversity with circulation of several subtypes
and circulating recombinant forms (CRF). The aim of this study is identify the presence of unique recombinant forms (URF) of the HIV-1 in newly diagnosed Cuban patients. Three hundred and thirty two (332)
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
51
HIV- infected patients diagnosed between 2009 and 2014 were included. The viral RNA was isolated from
plasma and used as target to amplify the pol gen by reverse transcriptase - nested PCR. PCR products were
sequenced and the data generated used to determine the viral subtype by REGA HIV subtyping tool and
phylogenetic analysis. The sequences with evidences of recombination according to the bootscaning from
REGA HIV subtyping tool were analyzed by Simplot, RDP v 3.0, jpHMM and RIP.
8.4% of the sequence suggested the presence of multiple URF, as: CRF19_cpx/CRF18_cpx, CRF19_cpx/B,
CRF06_cpx/G, DF1, BC, CRF24_BG/C. The analysis of the classified sequences as CRF06_cpx/G not showed
recombination by RDP program and suggests classify it as a pure subtype. The presence of the subtype
G in the gag-pol region of the CRF06_cpx can be the possible explanation of this result. The analysis for
BLAST shows a high percentage of identity with strain classified as 02AG/G. The results of the present study
described the presence of multiple URF of the HIV-1 in the recently diagnosis seropositive population. The
analysis of the full-length genome of the respective virus dawns if it is the recombination between two or
more subtypes in a same infected individual or a new CRF of the HIV-1.
Abstract 28
Temereanca A. *(1,3), Oprea C. (1,2), Ianache I. (1,2), Ceausu E. (1,2), Mehta S. (4), Ruta S. (1,3).
1 Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.
2 Dr. Victor Babes Hospital for Infectious and Tropical Diseases, Bucharest, Romania.
3 Stefan S. Nicolau Virology Institute, Bucharest, Romania.
4 University of California, San Diego, USA.
Human immunodeficiency virus Type 1 (HIV-1) subtype G among newly diagnosed
HIV-infected injecting drug users from Romania.
Background. Injecting drug use (IDU) is a new HIV transmission route in Romania. Until 2010, the percentage of newly diagnosed HIV cases attributable to IDU was insignificant (less than 1.5%), however, a striking
increase was reported during the last 3 years (reaching 31% in 2012 and 2013). Our aim was to analyze the
pattern of HIV subtypes and the prevalence of transmitted drug resistance (TDR) in a group of treatment-naive injecting drug users, newly diagnosed with HIV infection between 2010-2013.
Methods. Drug resistance genotyping was performed using the ViroSeq HIV-1 Genotyping System (Abbott
Laboratories, USA). For subtypes determinations, all sequences were submitted to the REGA HIV-1 subtyping
tool; mutations associated with TDR were defined according to the WHO 2009 list.
Results. Among a cohort of 55 injecting drug users, 37 (67.27%) were HIV-1 infected. Although HIV subtype
F1 (that dominated the Romanian epidemic since 1990) remains prevalent (67.5%), other subtypes were frequently detected (21.6% subtype G, 5.4% subtype B, 5.3% B/G and B/F recombinants). Overall, the proportion of HIV infections involving non-F subtypes increased from 21.4% in 2010-2011 to 39.1% in 2012-2013.
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A preliminary phylogenetic analysis suggests the existence of several HIV transmission clusters in our IDU
group. No major TDR mutations were identified, but all isolates had multiple secondary mutations at polymorphic positions in protease and RT genes.
Conclusion. Injecting drug users might trigger new waves of HIV infections, with rapid spreading in the general population, changing both the prevalence of infection and the genetic profile of the epidemic.
Abstract 29
Monaco D.C. *(1,3), Dilernia D.A. (1,3), Quipildor M. (2), Di Paolo A. (2), Yue L. (1), Salomon H. (3), Hunter E. (1).
1 Emory Vaccine Center, Emory University, Atlanta, GA, USA.
2 San Vicente de Paul Hospital, Oran, Salta, Argentina.
3 INBIRS, University of Buenos Aires, Argentina.
Phylogenetic reconstruction of the human immunodeficiency virus (HIV) epidemic from
a native community in Argentina unravels the impact of viral adaptation on disease progression
Our objective was to study a recently initiated (~10 years) HIV epidemic on a native community that exhibits
a restricted human leukocyte antigen (HLA) diversity, with the initial hypothesis that HIV would rapidly select escape mutations to the limited number of HLA alleles and this increased adaptation would impact HIV
pathogenesis.
We performed high-resolution HLA Class-I typing and near-full length HIV genome sequencing from 65
chronically-infected HIV-positive individuals. Phylogenetic reconstruction was performed by neighbor-joining and only bootstraps >90 were accepted. Implementing statistical and phylogenetic based methods, we
identified HLA-linked viral polymorphisms associated with escape to the most frequent HLA alleles. Considering them as signatures of viral adaptation, we correlated their presence with VL and CD4 count.
We identified 24 HLA-linked viral escape mutations (p<0.05; q<0.1) distributed across the entire HIV proteome. On the phylogenetic reconstruction, we observed highly supported (bootstrap support=100) monophyletic clades that suggest independent introductions of HIV. Classifying the viral variants based on their
prevalence at the population-level, we found that viruses present in higher prevalence exhibit a higher number of escape mutations compared to those found at low prevalence (p=0.0114). In a subset of 41 antiretroviral-naïve patients, we found that the number of escape mutations was positively correlated with the CD4
count (p=0.044) and negatively correlated with the viral load (p=0.023) of the patients.
The ability to reconstruct the phylogenetic relationship between the variants allowed us to show a rapid adaptation of HIV to the HLA-I mediated immune response that could be leading to less pathogenic infections.
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Abstract 30
Coltart C.E.M. *(1), de Oliveira T. and genomics team at Africa Centre (2), Pillay D. (1,2), Johnson A. (1).
1 Department of Infection and Population Health, University College London, UK
2 Wellcome Trust-Africa Centre for Health and Population Studies, Mtubatuba, South Africa
The role of pathogen genomics in enhancing understanding of epidemic transmission of
infectious diseases using human immunodeficiency virus type 1 (HIV-1) as an example.
Understanding transmission dynamics of infectious agents is critical to developing effective public health
interventions. Novel tools such as molecular epidemiology and phylogenetic analysis, when used in combination with traditional epidemiological techniques, have demonstrated the potential to answer critical
questions that are not easily answered by epidemiological approaches alone. I propose to combine traditional epidemiology with molecular methods to understand the transmission dynamics of two contrasting
infections: HIV-1 and Ebola. These are two of the most serious epidemics in the last fifty years and I plan to
study them at the geographical epicentres.
Combining and adapting these tools might enhance real-time epidemic surveillance and inform evidence-based, innovative and targeted intervention strategies, leading to an improved global response.
Key objectives:
1. Develop methods for combining phylogenetic data with empirical epidemiological and clinical observations to elucidate the transmission dynamics of a) HIV-1 in KwaZulu-Natal (generalized epidemic) and b)
Ebola in Guinea (acute epidemic).
2. Define the utility of phylogenetic data in determining transmission events and who is infecting whom, in
order to inform targeted intervention strategies.
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Abstract 31
Smith A.S.A. *(1), Burton S.L. (1), Kilgore K.M. (1), Mulenga J. (2), Karita E. (3), Allen S. (4), Hunter E. (1, 4, 5), Derdeyn
C.A. (1, 4, 5).
1 Yerkes National Primate Research Center, Atlanta, GA, USA.
2 Zambia Emory HIV Research Project, Lusaka, Zambia.
3 Rwanda-Zambia HIV Research Project, Project San Francisco, Kigali, Rwanda, USA.
4 Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.
5 Emory Vaccine Center, Atlanta, GA, USA.
Viral escape pathways and determinants of neutralization breadth in early human immunodeficiency virus Type 1 (HIV-1) infection.
HIV-1 has proven difficult to protect against by vaccination, due in part to its ability to induce and tolerate
high levels of mutation. This hurdle could be overcome if a vaccine could induce antibodies that broadly
neutralize diverse HIV-1 strains. In natural HIV-1 infection, a majority of patients generate moderate breadth
after 2-4 years. Understanding how and why antibody breadth develops in some patients, but not others,
could inform HIV-1 vaccine design. We hypothesized that the initial targeting of certain epitopes on the envelope glycoprotein gp120, combined with the subsequent influence of viral escape pathways and evolution
of the B cell response, programs the development of antibody breadth.
We have identified and characterized the transmitted/founder and longitudinal escape Envelope variants
for 10 subtype A and C HIV-1 infected individuals who developed varying levels of antibody breadth. Preliminary sequence analysis of the transmitted/founder Envelopes did not associate breadth with an amino acid
signature, differences in gp120 variable loop length, or differences in the number of N-linked glycosylation
sites in gp120. We did find evidence for early nAb pressure in three major regions of gp120 that are targeted
by antibodies: the V1V2 hyper-variable domain, the CD4 binding site, and the N332-glycan patch, but with
considerable overlap between the higher and lower neutralizers.
Therefore, we postulate that analysis of the ensuing viral escape pathways, and the co-evolving B cell immunoglobulin variable domains, are key to understanding how early, strain-specific autologous antibodies
broaden their specificities over time.
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55
Abstract 32
Gräf T. *(1,2), Vrancken B. (3), Junqueira D.M. (2,4), de Medeiros R.M. (2,4), Lemey P. (3), Almeida S.E.M. (2,4), Pinto
A.R. (1).
1 Laboratório de Imunologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil.
2 Centro de Desenvolvimento Científico e Tecnológico, Fundação Estadual de Produção e Pesquisa em
Saúde, Porto Alegre, Brazil.
3 Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
4 Programa de Pós-graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade
Federal do Rio Grande do Sul, Porto Alegre, Brazil.
The contribution of epidemiological predictors in unraveling the phylogeographic history of human immunodeficiency virus type 1 (HIV-1) subtype C in Brazil.
The HIV-1 epidemic in south Brazil is mainly driven by subtype C (HIV-1C), in contrast to a dominance of the
subtype B in other Brazilian regions. Previous studies have traced the origin of the Brazilian HIV-1C epidemic
(HIV-1C_BR) to an introduction at the state of Paraná from an east African country. The fact that HIV-1C infections increase at a higher rate than HIV-1B in Brazil calls for a better understanding of the process of spatial
spread in Brazil. Previous phylogeographic studies have mainly focused on Brazilian capital cities. Here, we
analyzed around 500 pol and env HIV-1C Brazilian sequences obtained from samples collected throughout
13 cities and from public databases. A Bayesian phylogeographic Generalized Linear Model approach was
used to reconstruct the spatiotemporal history of HIV-1C in Brazil considering several potential explanatory
predictors of the viral diffusion process. Analyses were performed on several subsampled datasets in order
to mitigate for sample bias. Our results revealed that Porto Alegre city has a central role in the HIV-1C_BR
spread and the prevalence of HIV, as well as the population size of subtype C, are factors driving the epidemic expansion towards the north of Brazil. The current work highlights the importance of adding external
information to phylogeographical analyses and the impact of sample bias in the ancestral state reconstruction. The results presented here also add new insights in the ongoing discussion about the HIV-1C epidemic
in Brazil, raising an alternative hypothesis for its phylogeographic history.
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Abstract 33
Switzer W.M.*, Kabore H.J., Campbell E., Shankar A., Hernandez A., Hall H.I., Oster A.M.
Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Prevalence and distribution of human immunodeficiency virus type 1 (HIV-1) non-B subtypes in the United States.
HIV-1 evolves rapidly, increasing its genetic diversity and complexity, and is classified into four distinct lineages (groups M, N, O, P), with group M containing >80 subtypes and circulating recombinant forms (CRFs).
Subtype determination is important epidemiologically, and subtype can impact pathogenesis, treatment,
and vaccine development. Little is known about the prevalence of non-B subtypes in the U.S., where subtype
B predominates. We determined subtypes for 102,153 polymerase sequences reported to the U.S. National
HIV Surveillance System between 2001-2014 from 19 states using three automated tools (REGA V3, SCUEAL,
and COMET). Sequences not classified as subtype B (16,929, 16.6%) by all three tools were further analyzed
phylogenetically using a novel method that combined FastTree maximum likelihood inference with 2,864
curated reference sequences and cluster analysis with the program Phylopart. The majority of these discordant sequences (12,624, 74.6%) were subtype B, followed by C (1,309, 7.7%), CRF02_AG (917, 5.4%), A1 (418,
2.5%), CRF01_AE (337, 2.0%), unique recombinant forms (203, 1.1%), G (186, 1.1%), and 62 other subtypes/CRFs
(935, 5.5%). The greatest genetic diversity was seen in states with high levels of foreign-born immigrants.
Comparison of phylogenetic and automated results for the seven most prevalent subtypes showed overall that COMET had the highest mean sensitivity and specificity (89.1%, 98.6%), followed by REGA (83.6%,
96.8%), and SCUEAL (71.5%, 94.0%), respectively. We developed a phylogenetic-based subtyping method
for large datasets and show that phylogenetic analysis remains the gold standard for inferring subtypes. We
found that a broad non-B HIV-1 diversity exists across the US.
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Abstract 34
Hanke K. *(1), Hauser A. (1), Somogyi S. (1), Meixenberger K. (1), Hofman A. (2), Bartmeyer B. (2), Bannert N. (1), Kücherer C. (1).
1 Division 18 HIV and other retroviruses, Robert Koch Institute, Berlin.
2 Division 34 HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin.
Molecular surveillance of recent human immunodeficiency virus type 1 (HIV-1) infections
in Germany allows the detection of transmission networks and putative new subtype
clades.
The Robert Koch Institute (RKI) has established a system of molecular surveillance for incident HIV infections
in Germany. Dried serum spots from 60% of the newly diagnosed HIV-infections in Germany are sent to the
RKI by diagnostic laboratories and tested for recency of infection. HIV-1 pol sequences of samples classified
as recent are analyzed by molecular-epidemiological methods with the aim to identify potential new virus
variants and transmission networks. In phylogenetic tree analyses transmission clusters can be identified
and linked to epidemiological data. Moreover, the occurrence and trends in the spread of HIV subtypes and
transmitted drug resistance can be analyzed from the sequence data.
RNA was amplified by two overlapping M-group-generic RT-PCRs comprising PR aa 9-99 and RT aa 1-251.
Additionally, a Maximum likelihood (ML) tree analysis was performed to identify transmission clusters and
putative new variants. Subtyping was performed using the REGA subtyping tool. Unclassified subtypes and
URFs are further analyzed in a separate analysis using a subtype reference panel of 159 reference sequences
comprising 9 subtypes and 46 circulating recombinant forms.
In 880 newly infected cases (2012–2014) a putative clade of an unclassified URF was identified. Significant
monophyletic clades and putative transmission cluster were identified as defined by bootstrap values (≥70%)
and by mean pairwise divergence (≤1.5 %). Subsequently, available epidemiological data will be correlated
to the tree topology and statistically analyzed. The further aim of the project is to extend and to support the
ML analyses by Bayesian inference and to identify transmission chains.
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Abstract 35
Dennis A.M. *(1), Hué S. (2), Sebastian J. (3), Miller W.C. (1), Eron J.J. (1).
1 University of North Carolina, Chapel Hill, NC, USA.
2 London School of Hygiene and Tropical Medicine, London, UK.
3 Laboratory Corporation of America, Research Triangle Park, NC, USA.
Assessing human immunodeficiency virus (HIV) transmission cluster dynamics in North
Carolina using a large statewide dataset.
Background: Despite advances in HIV prevention, >1,000 new diagnoses are reported in NC annually. Integrating phylogenetic and surveillance data can identify HIV transmission hotspots to target prevention
and monitor epidemic trends. We evaluated temporal cluster expansion using a large sequence dataset to
characterize ongoing transmission across NC.
Methods: HIV-1 pol sequences were abstracted from genotypes performed by the largest commercial laboratory in NC. Following alignment, a maximum-likelihood tree was constructed using FastTree with the GTR
model. Putative transmission clusters were defined as clades with high branch support (≥0.90) and maximum pairwise genetic distance <3.5%. Clusters were confirmed and transmission dynamics evaluated using
BEAST with Bayesian skyline and relaxed clock priors.
Results: We analyzed 15,247 sequences (each from an individual patient), sampled 1997-2014. Most patients
were men (69.8%) with median age 40 years at sampling. 7,647 (50%) sequences were identified in 2,318
clusters (median size 3). Factors associated with clustering included: younger age (median 38 vs. 42 years),
more recent sample (median year 2009 vs. 2007), and sampling from Raleigh and Charlotte metropolitan
areas [P<0.001]. Among 8 largest clusters (n=22-36 members), clusters originated 1997-2004, spanned mean
12.7 years, and all grew from 2009-2014. Large clusters were predominantly young men (mean age 29 years);
however one cluster (n=23) was 57% female.
Conclusions: A large proportion of sequences clustered, indicating significant local transmission. Large
clusters have expanded for >10 years, and continue to grow, particularly among young men. Cluster expansion by cluster size, geographic spread, and drug resistance will be further evaluated.
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Abstract 36
Silva J., Garcia V.
Center of Informatics, Federal University of Pernambuco, Brazil.
Toward a resource and time consuption reduction on human immunodeficiency virus
(HIV) drug resitance algorithms.
Analyzing and comparing biomolecular information can present characteristics handled by computer science as big data. And it is very time and resource consuming. These kinds of data can be used in phylogenetic studies in general, as well as in the virology field to interpret viral drug resistance. The databases from
which these data come presents a certain degree of complexity, and traditional data management techniques are not really useful since they can sometimes present inconsistencies and can have unpredictable
combinations. This research aims to optimize the response time and computational resource consumption
of RegaDB HIV drug resistance interpretation algorithms using big data management and manipulation
techniques. To achieve it, will be necessary to know the performance of these algorithms and evaluate the
complexity in order to determine the consumption of time and computational resources for the worst, median, and better cases. Finally, use big data management and manipulation techniques to make interventions
in the algorithms. We expect as a result to offer empirical or mathematical proof of time or computational
resources consumption reduction in at least one of the algorithms that suffers intervention.
Abstract 37
Delva G.G. *(1), Gutierrez C. (1), Ravasi G. (2), Charles M. (3), Alemnji G.A. (3).
1 Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago.
2 Pan American Health Organization, Washington DC, USA.
3 Centers for Disease Control and Prevention, Atlanta, Georga, USA.
Human immunodeficiency virus type 1 (HIV-1) genetic diversity and drug resistance in
the Caribbean.
Background: There have been few phylogenetic analyses on HIV-1 drug resistant strains in the Caribbean
region. The primary objective of this study is to analyze the patterns of genetic diversity of HIV-1 in the Caribbean and describe the molecular epidemiology of HIV-1 drug resistance (HIV-DR) in the region.
Methods: The pol and env gene sequences obtained from HIV-1 genotyping for drug resistance will be collected within the country member states of the Caribbean Public health agency (CARPHA) and the Caribbean HIV-DR network and will be used to perform phylogenetic analyses. The Stanford University Database
(http://hivdb.stanford.edu/hiv) will be used to analyze the protease-RT sequences for mutations associated
with resistance to antiretroviral drugs.
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Implications/conclusions: This study will provide a global view of HIV-1 genetic diversity and drug resistance strains in the Caribbean region. Phylogenetic analysis of HIV-DR strains is absolutely necessary to monitor HIV-DR strain evolution, and will also contribute to strengthening the implementation of public health
strategies to prevent and address HIV-DR in the region.
Abstract 38
Jimenez-Silva C. *(1) and Ocazionez R.E. (1,2).
1 Centro de Investigaciones en Enfermedades Tropicales (CINTROP), Universidad Industrial de Santander,
Bucaramanga, Colombia.
2 Grupo de Investigación en Enfermedades Infecciosas y Metabólicas (GINEM), Universidad Industrial de
Santander, Bucaramanga, Colombia.
Evolutionary history of dengue virus serotype 2 (DENV-2) in Santander, a dengue endemic region in Colombia.
Santander, Colombia is a endemic and the principal hot zone in outbreaks for DENV. DENV-2 predominated
in Santander - the Bucaramanga metropolitan area since 1998. However, the evolutionary history of DENV-2
that has been circulating in the Bucaramanga metropolitan area are unknown. In this study, we present a
reconstruction of the evolutionary relationships of DENV-2 using the E gene sampled from 1998 to 2015. We
included sequences of others areas of Colombia and world sequences available in Genbank. We reconstructed the phylogenetic tree based on Bayesian analysis. The analyses revealed that Colombian strains were
grouped in four viral lineages showing different dispersal routes toward Colombia and in two genotypes
(American and American/Asian) that circulated in Colombia in different periods of time. The lineage 1 was
into American genotype and the lineages 2, 3 and 4 were of American/Asian genotypes. The Colombian
strains in the lineage 2 were related to Venezuela, Puerto Rico and Brazil strains from 90’s. The Colombian
lineage 3 and 4 were closely related with Venezuelan isolates from 1996 to 2008. Colombian strains isolated
in Norte de Santander in 2005, Guaviare in 2005 and Antioquia in 2004 were included in this two lineage,
for this reason, we supposed that this lineage was introduced from Venezuela through Norte de Santander/
Santander and it has been circulated in different areas of Colombia.
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Abstract 39
Vicente-Santos A. *(1,2), Moreira-Soto A. (1), Soto-Garita C. (1), Chaverri L.G. (3), Chaves A. (2), Morales J.A. (4), Alfaro
A. (4), Corrales-Aguilar E (1).
1 Centro de Investigación en Enfermedades Tropicales. Facultad de Microbiología. Universidad de Costa
Rica. San José. Costa Rica.
2 Laboratorio de Genética de la Conservación, Escuela de Biología, Universidad de Costa Rica, San José,
Costa Rica.
3 Escuela de Ciencias Exactas y Naturales, Universidad Estatal a Distancia, San José, Costa Rica.
4 Laboratorio de Patología, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica.
Ecology of the dengue virus (DENV) in domiciliary environments: is the bat a reservoir, a
host or accidentally involved in the transmission of dengue?
Dengue is the most important vector transmitted disease in Costa Rica, but research on the local factors that
affect the disease system is scarce. Recent studies show the presence of DENV in wildlife, including bats, but
the role they play in the transmission cycle is unknown. The significance of wildlife in (re)emerging infectious
diseases has been increasingly appreciated, and it is possible that some species of bats are susceptible to
DENV. This research aims to evaluate the presence of DENV in domiciliary bats that inhabit areas of high and
low incidence of dengue, in wet and dry season, in Costa Rica to identify ecological, environmental, anthropogenic and virological factors that could involve the bat in a possible viral transmission cycle. We sampled
houses in which humans and bats cohabit, took samples from bats and blood samples from humans, and
collected mosquitoes by EVS-CO2 traps. According to the sample type, we determined the presence (RT-PCR
and virus isolation) and frequency (serology) of DENV in bats (blood and pool of organs), mosquitoes and
humans to determine the possible virus circulation in them. We did a necropsy on a portion of the bats collected and histopathology on shock organs (heart, lung, liver, spleen, kidney, brain), to observe any possible
sign of sickness. Furthermore, we will establish the phylogenetic relationship of the strains of DENV obtained
from bats, with co-circulating strains of human and mosquito collected and the reported by the reference
center, by analyzing the sequences of the E region.
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Abstract 40
Soto-Garita C. *(1), Somogyi T. (1,2), Corrales-Aguilar E. (1).
1 CIET (Research Center for Tropical Diseases), Virology, Faculty of Microbiology, University of Costa Rica, San
José, Costa Rica.
2 Division of Molecular Diagnostics, Mexico Hospital, San José, Costa Rica.
Genetic diversity and viral fitness studies of dengue virus serotype 1 (DENV-1) isolated
during the 2013 outbreak in Costa Rica.
In order to get a better understanding and control of dengue outbreaks in hyperendemic settings is crucial
to have a description of the extent and structure of the genetic diversity in the circulating serotypes. In Costa
Rica, there have been few reports about the dengue genotypes circulating during outbreaks. For the serotype 1, only three isolates from the 1993 outbreak have been characterized. Despite this report, it has not
been done any further characterization of the circulating genotypes of DENV-1 during the latter outbreaks.
In order to analyze the genetic diversity of dengue circulating strains, we used sera from acute patients to
isolate dengue virus using C6/36 cells during the 2013 outbreak in Costa Rica. Fourteen isolations where successfully recovered and their serotyping showed the DENV-1 as the main circulating serotype. To study the
genetic diversity among the strains isolated, their envelope protein gene’s sequence will be analyzed with
phylogenetic tools. Furthermore, viral fitness will be determined with their in vitro replication in C6/36 cells
and dendritic cells, to evaluate the fitness variation among the isolates. These data will be used to highlight
factors that could explain the rate and the intensity of dengue transmission in Costa Rica.
Abstract 41
Ortiz-Baez A.S. *(1), Zanotto P.M. (1), Villabona-Arenas C.J. (2, 3).
1 Laboratory of Molecular Evolution and Bioinformatics, Institute of Biomedical Sciences, University of Sao
Paulo, Brazil.
2 TransVIHMI, Institut de Recherche pour le Développement (IRD), Université de Montpellier, France.
3 Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM), Institut de Biologie Computationnelle (IBC), Université de Montpellier, France.
Intra-host genetic diversity of dengue virus type 4 (DENV-4) strains from the municipality of Guarujá, Sao Paulo.
Characterizing intra-host genetic variability in DENV is paramount for understanding its evolution and population dynamics in the context of its current status as a major human pathogen. The extent to which viral
diversity accrues in infected hosts influences aspects such as pathogenesis, transmission, and host immunity. Although there are several studies about intra-host genetic diversity in dengue, limited amount of data
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has been reported for DENV-4 so far. In the Guarujá municipality in the State of Sao Paulo, the reemergence
and spread of this serotype was associated with its co-circulation and the displacement of serotypes 1, 2
and 3 during recent outbreaks. Based on this epidemiological framework, we seek to identify the intra-host
genetic variation of DENV-4 strains from samples collected during the 2013 outbreak by using deep sequencing technologies. We will estimate the level of variability and the evolutionary history of these viruses
in response to selective pressures imposed by an urban population previously exposed to the remaining
three dengue serotypes. This study will provide an important insight into surveillance of viral variants, and
will offer a new opportunity to study the evolution of DENV-4 in hyperendemic areas. This is the first effort
to investigate the intra-host diversity of DENV-4.
Abstract 42
Adesina O.A. (1), Johnson A. (2).
1 Department of Microbiology, Obafemi Awolowo University, P.M.B 13, Ile-Ife 220005, Osun State, Nigeria.
2 Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria.
Incidence of dengue virus (DENV) infections in febrile episodes in ILE-IFE, Nigeria.
Dengue viruses have been identified as the most important arboviral pathogen in the world. They are transmitted by mosquitoes of Aedes species. While dengue infection is accompanied by little or no subclinical
signs in many, about 1-2% may produce clinically severe Dengue Haemorrhagic Fever/Dengue Shock Syndrome. Early recognition, appropriate treatment and elimination of mosquito vectors will help control it.
The study is aimed at determining the incidence of dengue infections in Ile-Ife.
Three millilitres venous blood was collected from each of one hundred and seventy nine patients presenting
with fever in the last two weeks, and analyzed for the presence of anti-dengue IgM antibodies using Dengue
Virus IgM ELISA kit (DIA.PRO, Italy) according to the manufacturer’s instructions while the results and demographic data were analyzed using SPSS version 16.
It was observed that 46 (25.7%) of the 179 had detectable IgM antibodies to dengue virus with 9 of them
having no detectable malaria parasite. The incidence was 26.5% and 25% in male and female respectively.
Although the authors did not seek to know the relatedness of blood transfusion to the transmission of dengue, yet it was the only risk factor that showed a statistically significant result. Further studies will be necessary to confirm this.
The study established the presence of fresh dengue infections for the first time in Ile-Ife among different
groups of people. Clinicians are advised to prioritize laboratory diagnosis, especially of fever.
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Abstract 43
Drumond B.P. *(1), Biselli-Périco J.M. (2,3), Vedovello D. (2,3), Colombo T.E. (2,3), Pinheiro T.M. (2), Ullman L.S. (4),
Araujo Jr J.P. (4), Nogueira M.L. (2).
1 Virology Lab - Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil.
2 Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil.
3 Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto, São Paulo, Brazil.
4 Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, São Paulo, Brazil.
Dynamics of dengue virus serotype 1 (DENV-1) circulation in a medium size city in Brazil.
Phylogenetic, phylogeographic and evolutionary analyses were performed based on the envelope sequences of 30 DENV-1 strains obtained in São José do Rio Preto (SJRP), Southeast, Brazil. Five lineages of DENV-1
(BR1st-BR5th), genotype V were introduced in the country from Caribbean region (BR1st- BR3rd) and Venezuela (Br4th-BR5th). Intense migration pathways took place and North, Northeast and Southeast regions acted
as regions of entrance and spread of DENV-1 throughout the country. The ancestors of SJRP/DENV-1 dated
at 2006 and 2008 and both were from Southeast region. The introduction of BR5th in SJRP was followed by
small increase (3 times) in DENV-1 population size. BR3rd and BR5th co-circulated in SJRP from 2010 (high
season) to 2012 (high season). No positive selection was associated with the introduction of lineages in Brazil
or SJRP, but 6 amino acid substitutions were observed in the envelope protein. A significant genetic diversity
not only within Brazilian DENV-1 lineages (2.30±0.50 to 6.17±1.03) but also within SJRP/DENV-1 (5.76±0.86)
was observed. In this work, we observed the co-circulation of BR3rd and BR5th two lineages without spatiotemporal association, since lineages co-circulated in the periods and regions, as Northeast region and Southeast region. Further studies are necessary to determine and compare the biological properties of different
lineages circulating in SRJP and in Brazil in order to understand the lineage circulation, the fitness of these
lineages and to predict if future vaccine candidates will be able to induce a neutralizing immune response
against this variety of DENV-1 circulating in the country.
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Abstract 44
Santiago G.A.* (1), Thomas D. (1), Smith B. (2), Heberlein-Larson L. (3), Rivas A. (4), Blackmore C. (3), Gaul L. (2), Tomashek K. (1), Muñoz-Jordan J.L. (1).
1 Centers for Disease Control and Prevention, Division of Vector Borne Diseases, Dengue Branch, San Juan,
Puerto Rico.
2 Department of State Health Services, Austin, Texas, USA.
3 Florida Department of Health, Tallahassee, Florida, USA.
4 Universidad Autónoma de Monterrey, School of Medicine, Mexico.
Emergence and local transmission of two lineages of dengue virus type 1 (DENV-1) in
North America: 2013-2014.
Dengue, one of the most important arthropod-borne tropical diseases globally, is a significant public health
concern affecting an estimated 100 million people in 2010. The proliferation of urban areas, frequent international travel and climatic changes, have been proposed to contribute to the increased dissemination of
DENV. We have previously reported local transmission of a monophyletic lineage of DENV-1 in Key West,
Florida in 2011-2012. In 2013-2014, DENV-1 was identified in febrile patients with no travel history residing
in two Texas counties, Cameron and Hidalgo, adjacent to the border with Mexico. During the same period,
DENV-1 was also identified in febrile patients with no recent travel history residing in two Florida counties, Martin and St. Lucie. In this study we have conducted an in-depth envelope gene sequence analysis to
characterize the emergence of DENV-1 in North America. All sequences grouped within the American-African genotype of DENV-1. Bayesian phylogenetic analyses show a strong association of Texas and Northern
Mexico DENV-1 with viruses from Central America, with the Texas isolates forming a monophyletic group.
In contrast, the Florida isolates formed two independent subgroups: the previously reported Key West virus
of Central American origin and the Martin-St. Lucie virus of Caribbean origin. SPREAD software was used to
visualize transmission and emergence of DENV-1 through time in North America. Phylogeny of these lineages supports local transmission of DENV-1, and that conditions are suitable to sustain transmission with the
potential to cause outbreaks.
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Abstract 45
Casal P.E. (1*), Chouhy D. (1,2), Bolatti E.M. (2), Perez G.R. (1), Stella E.J. (2), Giri A.A. (1,2).
1 Virology Area, School of Biochemistry and Pharmaceutical Sciences, National University of Rosario, Rosario,
Argentina.
2 Human Virology Group, IBR-CONICET/National University of Rosario, Rosario, Argentina.
Evidence for homologous recombination in chikungunya virus (CHIKV).
CHIKV, a mosquito-transmitted alphavirus, causes acute fever and joint pain in humans. Recently, endemic
CHIKV infection outbreaks have jeopardized public health in wider geographical regions. Here, we analyze
the phylogenetic associations of CHIKV and explore the potential recombination events on 152 genomic isolates deposited in GenBank database. The CHIKV genotypes [West African, Asian, East/Central/South African
(ECSA)], and a clear division of ECSA clade into three sub-groups (I-II-III), were defined by Bayesian analysis;
similar results were obtained using E1 gene sequences. A nucleotide identity-based approach is provided to
facilitate CHIKV classification within ECSA clade. Using seven methods to detect recombination, we found a
statistically significant event (p-values range: 1.14×10-7-4.45×10-24) located within the nsP3 coding region.
This finding was further confirmed by phylogenetic networks (PHI Test, p=0.004) and phylogenetic tree incongruence analysis. The recombinant strain, KJ679578/India/2011 (ECSA III), derives from viruses of ECSA III
and ECSA I. Our study demonstrates that recombination is an additional mechanism of genetic diversity in
CHIKV that might assist in the cross-species transmission process.
Abstract 46
Ramjag A. *(1), Simmons G. (2), Carrington C.V.F. (1).
1 Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago.
2 Blood Systems Research Institute, 270 Masonic Ave, San Francisco, CA, USA.
Protective B-cell epitopes in chikungunya virus (CHIKV) infection
CHIKV (Family Togaviridae, genus Alphavirus) is the aetiological agent of chikungunya fever (CHIKF) and an
important newly emerging virus in the Americas. Although not usually life threatening, CHIKF is very debilitating and is often associated with chronic arthritis, resulting in major economic losses. No licensed therapeutic treatments or vaccines exist. However neutralizing antibodies that can protect animals have been described and there is evidence to suggest that therapeutic antibody therapy may also be helpful in relieving
symptoms and interrupting transmission. CHIKV exists as a single serotype (which confers lifelong immunity) with three genotypes (West African, East /Central/ South African (ECSA), Asian). In this study we will generate and characterize new antibodies that block CHIKV, and describe the full B-cell repertoire in response to
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CHIKV infection – both in acutely infected patients and recovered individuals from the Trinidad population.
To maximize their therapeutic and economic efficiency in a field setting, anti-CHIKV mAbs would have to
be broadly cross-reactive against existing CHIKV variants, and should target epitopes that are refractive to
immune escape We will therefore determine the nature and extent of sequence variation in targeted genes,
both within and among the individuals enrolled in the study (during consecutive outbreak years) and also
compare to global CHIKV sequences derived from the wider Americas with emphasis on detecting variation
and signatures of selection at B-cell epitopes. Whole genome sequences derived to date confirm the presence of the Asian genotype in Trinidad and low sequence diversity both within and between individuals.
Abstract 47
Jain J. *(1), Shrinet J. (1), Shastri J.S. (2), Gaind R. (3), Bhatnagar R.K. (1), Sunil S. (1).
1 Insect Resistance Group, International Center for Genetic Engineering and Biotechnology, New Delhi, India.
2 Department of Microbiology, T.N Medical College and B.Y.L Nair Ck. Hospital, Mumbai, India.
3 Department of Microbiology, Vardhman Mahavir Medical college and Safdarjung Hospital, New Delhi, India
Evolution of chikungunya (CHIKV) in India: whole genome sequencing and clinical data
correlation.
CHIKV is a vector-borne disease transmitted by Aedes mosquito and has a very high morbidity rate and its
chronic state can persist for more than 2 years in some cases. Chikungunya is prevalent in most parts of India
and has now become a global issue. We aimed to study the evolution of CHIKV in India, and for the same
purpose more than 100 clinical field isolates were collected from across India over the span of four years
(2010 - 2013). All the clinical samples along with CHIKV virus passaged 6 times in Vero cells in vitro were subjected to clinical, molecular and next generation whole genome analysis. Activity of the virus was studied via
viral load experiments, plaque assays, quantitative PCR and Sanger sequencing before processing it further
for whole genome sequencing. The main purpose of this study was to perform in depth analysis of CHIKV
genome which could help to understand the underlying single nucleotide changes and mutation events
that might have occurred within the CHIKV genome leading to its evolution. The genomic data, molecular
analysis along with the SNP’s and mutation information was further correlated with the clinical information
for the determination of virus evolution and its molecular epidemiology.
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Abstract 48
Carrera J-P. *(1), Forrester N. (2), Auguste A.J. (2), Kautz T. (2), López-Verges S. (1), Weaver S. (2).
1 Department of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama.
2 Department of Pathology and Institute for Human Infection and Immunity, The University of Texas Medical
Branch, Galveston, Texas, USA.
Spatiotemporal dynamics of Venezuelan equine encephalitis virus (VEEV) antigenic complex.
VEEV (Alphavirus, Togaviridae) antigenic complex is composed for 16 virus species of single strand RNA virus.
Enzootic strains that circulate in sylvatic, rodent-mosquito enzootic cycles, regularly spillover to infect people and also emerges periodically to cause equine epizootics, characterized by an equid-mosquito amplification cycle that spills over to humans, causing major epidemics. Large humans and equines epidemics since
1920s have been related to the epizootic strains IAB and IC, however around 10 % of the clinical diagnosis
dengue febrile cases in Latin America have been estimated as VEEV ID or IE enzootic infections. Only the
enzootic VEEV ID and IE circulate in Panama, and the last VEEV Panamanian strains described were isolated
in 2010 during a VEEV-EEEV outbreak in the sylvatic region close to Colombia. Differences in the geographic
distribution of VEEV complex and epidemiologic profiles prompted evaluation of their evolutionary histories. In order to elucidate the pattern of transmission and dispersal of VEEV species through the Americas, we
expanded the sequence length and the number of available VEEV strains, introducing more recent isolates,
and analyzed them using basic phylogenetic tools. The models and training that will be gained during this
course will allow us to reproduce the phylodynamic and phylogeographic history of this complex through
the years.
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Abstract 49
Rodríguez-Padilla C. (1), Saavedra-Alonso S. (1), Ramirez-Palacios L.R. (2), Rodríguez-Márquez A.M. *(1), Willis-Rodriguez C. (1), Rodriguez-Pérez M.A. (3), Guo X. (3), Silva-Ramírez B. (4), Bermudez-de Leon M.A (4), Rodriguez-Luna
I.C. (3), Reséndez-Pérez C. (1), Tamez-Guerra R.S. (1).
1 Facultad de Ciencias Biológicas. Universidad Autónoma de Nuevo León. San Nicolás de los Garza, Nuevo
León, México.
2 Laboratorio Estatal de Salud Pública de Oaxaca. Carretera a Sola de Vega, Km 18.5. Reyes Mantecón, Oaxaca, 71257.
3 Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Blvd. del Maestro esquina Elías Piña S/N,
Colonia Narciso Mendoza, 88710, Reynosa, Tamaulipas, México.
4 Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, IMSS, 64720 Monterrey, NL, México.
High incidence of bacterial co-infections in patients infected with pandemic H1N1/09 influenza virus in Mexico.
Background: There have been at least four waves of pandemic H1N1/09 virus in Mexico since 2009. One
factor linked to the severity of the disease is viral/bacterial co-infections. Therefore, monitoring co-infection
pathogens along with influenza virus could help improve medical care for influenza patients.
Methodology/Principal Findings: We collected 104 throat swab samples from Mexican patients showing
influenza-like signs or symptoms and analyzed them using real-time PCR and the TessArray RPM-Flu assay
to determine respiratory pathogens. Multiple bacterial infection together with pandemic H1N1/09 virus
predominated in patients. Main pathogens are Streptococcus spp., Pseudomonas spp., and Haemophilus influenzae from which S. pneumonia seems to have preference of co-infection with pandemic H1N1/09 virus. We
detected three cases of viral co-infection with Coronavirus, Flu B and Coxsackievirus. The seasonal AH3N2
virus, parainfluenza virus and rhinovirus were not present in co-infections associated to pandemic H1N1/09
virus. Patients infected with 2009 pandemic influenza reported severe symptoms such as myalgia, fever, rhinorrhea, malaise, headaches, and coughing. The number of patients hospitalized and ambulatory patients
with multiple infections was more than two times greater than the number with single infection by pandemic H1N1/09 virus. This indicates that infection by multiple pathogens relates to the severity of disease.
Conclusions/Significance: Our findings of Influenza / co-infection indicate a high prevalence of bacterial
co-infection with pandemic H1N1/09 virus, which leads to a greater number of patients with severe symptoms.
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Abstract 50
Kikwai G. *(1), Waiboci L. (2), Shigoli T. (1), Muthoka P. (3).
1 Kenya Medical Research Institute, Nairobi, Kenya.
2 University of Nairobi, Kenya.
3 Kenya Ministry of Public Health and Sanitation, Nairobi, Kenya.
Antiviral resistance of influenza viruses isolated in Kenya, 2007 – 2011.
The continued threat of emergence of novel influenza viruses with pandemic potential in humans, underscores the need for information on effective antivirals for management of influenza infections. Specimens
collected from patients with respiratory illness were tested by real time reverse transcription polymerase
chain reaction for influenza A and B. Influenza A positive samples were subtyped. Influenza viruses, isolated by cell culture were assessed for susceptibility to neuraminidase inhibitors in neuraminidase inhibition
assays. Virus isolates showing elevated IC50s in the NI assay were genetically analyzed by conventional sequencing and/or pyrosequencing to detect molecular changes in the neuraminidase protein associated with
reduced susceptibility to neuraminidase inhibitors and to detect markers of resistance to adamantanes. All
influenza A and B isolates tested were susceptible to zanamivir, while 668 (91.2%) were susceptible to oseltamivir. All influenza B, A (H3N2) and A (H1N1)pdm09 isolates tested were susceptible to oseltamivir. Of the
350 influenza A isolates tested for resistance to adamantanes, 224 had the most commonly detected marker,
S31N. A single A (H1N1)pdm09 isolate contained a combination of two markers of resistance to adamantanes,
A30T and S31N and one influenza A/H1N1 with L26F marker. More than half of the viruses characterized
were resistant to adamantanes. However, more than 90% of the viruses circulating during the period were
susceptible to oseltamivir and zanamivir. Thus there would be benefit in their use for influenza infections
management in Kenya. Further surveillance and characterization is important for detection of drifts and
shifts to inform on formulation of policies by the key stakeholders.
Abstract 51
Watson, S.J.* (1), Faria, N. (2), Edwards, S. (1), Reid, S. (3), ESNIP3 Consortium., Brown, I. (3), Pybus, O.G. (2), Kellam, P. (1).
1 Wellcome Trust Sanger Institute, Hinxton, UK.
2 Department of Zoology, University of Oxford, Oxford, UK.
3 Animal and Plant Health Agency, Addlestone, Surrey, UK.
Phylodynamics of the Eurasian ‘avian-like’ H1N1 swine influenza virus in Europe.
The A (H1N1)pdm09 influenza A virus that emerged in humans in 2009 had a complex history that involved
lineages of swine influenza viruses (SIV) circulating in different regions of the world. Two of the eight viral
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segments were derived from the Eurasian ‘avian-like’ (EA) H1N1 lineage. Viruses from this lineage have circulated enzootically in European swine since 1979, and despite the emergence of other, more recent SIV
lineages, it remains the most prevalent genotype isolated from swine across mainland Europe. Despite this
prevalence, there are scarce genomic data from European SIV, and little is known about the molecular epidemiology of this lineage in Europe. Through the European Surveillance Network for Influenza in Pigs (ESNIP)
project, we have sequenced 243 SIV isolates from 14 countries across Europe between 2009 and 2013 using
high-throughput sequencing platforms. Of these, 180 contain internal genes derived from the EA lineage,
and 79 have complete EA genotypes. These data allow for analysis of the phylogeography and molecular
evolution of EA viruses in Europe; for example, calculating the intra-lineage reassortment rate, inferring the
evolutionary rate of the lineage since the introduction of the A(H1N1)pdm09 virus into European swine, inferring the spatial dynamics of the virus across Europe, and determining predictors associated with these
patterns.
Abstract 52
Wang H. *, Wang X., Cao J., Gao Y., Zhou W., Bi S.
National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Full-length genome characterization and quasispecies distribution of hepatitis A virus
(HAV) isolates in China.
HAV infection is the most common cause of acute viral hepatitis and has significant implications to public
health worldwide. To characterize HAV strains circulating in China, five samples collected in different provinces from 2006–2009 were entirely sequenced. Phylogenetic analysis based on distinct segments showed
that all five sequences belonged to subgenotype IA, but with slight differences in some fragments. No amino acid mutations were found at the known neutralizing epitope sites, and one unique substitution was
identified near the immunodominant site. While no intertypic recombination was detected, intratypic recombination signals were found in the study. Molecular evolution analyses showed the estimated mean
substitution rate of genotype I worldwide was 3.27 × 10 -4 substitutions/site/year, and the time to the most
recent common ancestor (tMRCA) was about 267 years ago. The quasispecies distribution across the complete genome was also evaluated, and the nucleotide mutation frequency was found to range from 7.26 ×
10 -4 to 2.30 × 10 -3 substitutions per nucleotide. The amino acid mutation frequency ranged from 1.38 × 10-4
to 4.27 × 10 -3 substitutions per amino acid, and the high mutation frequency regions were mainly at the
nonstructural protein coding sequences. This study contributed information on the genotype distribution,
selection pressure, neutralizing epitope site mutations, recombination events and quasispecies distribution
of HAV strains in China. The evolutionary status of genotype I worldwide was also analyzed, which will provide a reference for future HAV molecular epidemiology studies.
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Abstract 53
Parag K. *, Pybus O.
Department of Zoology, University of Oxford, Oxford, UK.
Comparative analysis of canonical phylodynamic data: hepatitis C virus (HCV) in Egypt.
HCV is a global health threat with anomalously high prevalence in Egypt. Previous epidemiological studies
have implicated inadequate needle sterilisation, during a large-scale 20th century parenteral antischistosomal treatment (PAT) campaign, as the primary cause of the Egyptian HCV epidemic. The well characterised
epidemic history of Egyptian HCV and its interesting iatrogenic cause makes it appropriate for appraising
various phylodynamical models. Consequently, a 1993 genomic dataset (Ray et al. 2000) from the dominant
HCV-4a subtype has been used to evaluate many phylodynamic techniques for estimating population history, including skyline, skyride and skygrid methods, as well as birth-death model based approaches.
However, recent work (Cuadros et al. 2014) has suggested that PAT influence may be overstated. Additionally,
many new HCV-4a gene sequences have been obtained since 1993, including whole genomes, and these
have not been integrated with the 1993 data. Moreover, the different phylodynamic approaches sometimes
disagree on virus dynamics prior to PAT initiation. I propose to combine and align all available HCV-4a sequences to generate an updated benchmark dataset for testing phylodynamical techniques.
I aim to apply methods, taught in this workshop, on evolutionary hypothesis testing, to resolve uncertainty
surrounding the epidemic history of Egyptian HCV and hopefully clarify the importance of the PAT campaign. Furthermore, by contrasting and comparing results of existing models on a canonical data set, I hope
to gain insight into their relative merits as statistical estimators. This would support my long-term aim of
developing richer and more informative Bayesian phylodynamic models.
Abstract 54
Pereira S.A. *(1), Espirito Santo M.P. (1), Lauer G.M. (2), Lampe E. (1), Lewis-Ximenez L.L. (1).
1 Viral Hepatitis Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
2 Gastrointestinal Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
An evolutionary approach of interspousal transmission of Hepatitis C virus (HCV) Infection.
Even though there is evidence of sexual transmission of HCV the actual risks in different types of sexual behavior have been difficult to assess and it is still unclear as to which factors actually contribute to this route
of transmission. In this study we report transmission associated with lack of lubrication during sex from
fifteen HCV-infected individuals to their heterosexual partners. Forty female patients with symptomatic
acute HCV infection were identified at the Viral Hepatitis Laboratory, Fiocruz, Rio de Janeiro, Brazil. To confirm HCV transmission between spouses, nested Reverse transcription polymerase chain reaction products
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were submitted to direct nucleotide sequencing of the NS5B region. The obtained sequences were aligned
with corresponding nucleotide sequences of 23 HCV reference sequences retrieved from GenBank and 13
local unrelated HCV sequences and phylogenetic tree was constructed with Mega 4 software using Neighbor-Joining method. The evolutionary distances were computed using the Maximum Composite Likelihood
method and their reliability was assessed by bootstrap resampling 1000 replicates. Among the 40 subjects
that reported sexual risk behavior, 29 had sexual partners that volunteered samples to investigate possible
HCV genomic similarities. The phylogenetic analysis of the nucleotide sequence of HCV genome was limited
to the remaining 15 subjects and their sexual partners, which revealed nucleotide identity > 95% among 14
of the 15 couples, which strongly suggests these partners to be the source of infection, after ruling out possible contamination through personal item sharing. These findings provide strong molecular evidence that
the women had acquired HCV infection most likely by interspousal sexual transmission.
Abstract 55
Perveen S. (1)*, Azhar A. (1), Khan O.Y. (2).
1 The Karachi Institute of Biotechnology & Genetic Engineering (KIBGE), University of Karachi, Karachi-Pakistan.
2 Department of Genetics, University of Karachi, Karachi-Pakistan.
Rare genetic variation in hepatitis delta virus (HDV) that influence genotype determination.
Background: HDV only infects the hepatic cells already infected with Hepatitis B virus (HBV). The delta virus
infection leads to a clinical outcome, which is more severe than HBV infection alone with severity of infection varying with the delta virus genotype. During sampling of delta virus in Karachi, Pakistan, a variant of
genotype I delta virus was encountered that was initially misdiagnosed as genotype II, based on Polymerase
Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis using SmaI restriction enzyme. Correct genotype determination of the newly found strains was carried out using phylogenetic analysis and an attempt was made to analyze its origin and propagation in our population.
Methods: Blood samples were collected from Hepatitis B surface Antigen (HBsAg) +ve and Hepatitis Delta
Antigen (HDAg) +ve patients and viral RNA was extracted, reverse transcribed and used to amplify HDV R0
region by Reverse Transcriptase (RT)-nested PCR. The PCR products were screened with Restriction Fragment Length Polymorphism (RFLP) using SmaI restriction enzymes. Nucleotide sequences were used for
phylogenetic analysis for clade determination. In silico analysis for evidence of recombination was also carried out in order to determine the origin of the delta virus isolates of interest.
Results: PCR-RFLP analysis using SmaI enzyme showed that three of our delta virus isolates belonged to
genotype II. A deeper nucleotide analysis exposed a single base pair selectively neutral mutation at the single SmaI restriction site within the B cell epitope, which caused these three strains to be falsely categorized
as genotype II. Sequences analyzed in silico for recombination showed putative exchange of genetic material within and across genotype I and II.
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Conclusions: Phylogenetic analysis of our sequences have shown a clear misdiagnosis of genotype in our
HDV isolates and proved the short-comings of SmaI Polymerase Chain Reaction-Restriction Fragment Length
Polymorphism (PCR-RFLP) based delta virus genotype. Recombination analyses have suggested a possible
reason for the high frequency of occurrence of this mutation in our sampling.
Abstract 56
Okoror L.E. *(1), and Eludire A.A. (2).
1 Department of Biological Sciences, Joseph Ayo Babalola University, Ikeji-Arakeji, Nigeria.
2 Department of Computer Sciences, Joseph Ayo Babalola University, Ikeji-Arakeji, Osun State, Nigeria.
Lassa virus: codon usage and bias along with their host.
Lassa virus continues to be endemic with frequent outbreak in areas of endemicity which is of a public
health concern due to its fast evolutionary rate. There has been a report of new strains in different epidemic
outbreak. We used seven different codon usage bias tools and indexes targeting synonymous codon usage which included GC content, ENC, SCUO, Codon Volatility, RSCU, Odd ration and Graphical Codon Usage
Analysis tool. This study observed evolutionary pattern in Lassa virus from human, rodents and bats. It also
observed the evolutionary pattern and influence of different geographical location in its evolutionary pattern and periodic outbreak. There was variation in the GC content in the glycoprotein gene, nucleoprotein
gene, Z-protein gene, S-protein gene and polymerase gene. RSCU value was positively correlated with the
Odd Ratio of dinucleotide in the codons. RSCU values of humans, rodents and bats were slightly different,
though this result was not completely true for odd ratio. The GC content, ENC, SCUO and Codon Volatilty
were similar across all the hosts. However, there was slight variation of genes from different geographical
locations, thereby supporting reports that Lassa virus varies by strains from different locations. Though there
was slight variation from years of isolation, the difference in host explains why the virus causes fever in humans as against being normal in other hosts.
Abstract 57
Sånchez G. *(1), Sarabia V. (1), Jahuira H. (1), Oyola G. (1), Neira K. (1), Mayta H. (1), Gilman R. (2), Baillard S. (2).
1 Laboratorio de Investigación en Enfermedades Infecciosas, LID-UPCH, Peru.
2 Bloomberg School of Public Health, Johns Hopkins University, Maryland, USA.
Molecular detection and genotyping of sapovirus (SaV) and norovirus (NoV) in children
with acute gastroenteritis in a hospital in Lima.
Gastroenteritis remains one of the main problems for under five children. Most of gastroenteritis studies
caused by viruses are limited to Rotavirus and NoV. In this study we look for SaV and NoV in 695 children (416
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cases and 279 controls) sampled from November 2013 to October 2014. Preliminary results are presented of
the ongoing project. Stool samples were collected from children and stored frozen at -70oC until processed.
Aliquots of 0.1g (formed) or 0.1 ml (watery) stools will be diluted 1:10 and RNA extracted using QIAamp viral
RNA kt. RNA was used for detection of NoV GI and GII in a duplex one step PCR by using Cog 1F, Cog 1R, Cog
2F and Cog 2R primers and Ring 1A, Ring 1B and Ring 2TP as probes, genotyping was performed using the
sequence from the product of GI SKF/SKR and G2 SKF/SKR primers for capsid N/S domain. cDNA synthesis
was performed with SuperScript III reverse transcriptase, SaV detection was performed using SaV124F, SaV1F,
SaV5F, and SaV1245R as primers and SaV124TP and SaV5TP as probes, genotyping was performed using
the sequence from the product of SaV F22 SaV R2 primers for a partial capsid region. Preliminary data for
detection result in 38% of NoV prevalence, with NoV GII as the main genotype found in the specimens, the
prevalence of SaV was 9.6% and the genotyping for 22 according the partial cápside region was GI=7, GII=9,
GIV=4 and GV= 2, from these data, 6 samples result with co infection for SaV and NoV. Controls, non-diarrheic, samples were negative for NoV and SaV. According to this preliminary results, NoV remains as an important etiologic agent and SaV seems to be responsible of a substantial number of cases in Lima, SaV detection
should be include in future research of viral gastroenteritis epidemiology.
Abstract 58
Phan M.V.T. *(1), Munnink B.B.B.O. (2), Anh P.H. (3), Cuong N.V. (3), Dung T.T.N. (3), Phat V.V. (3), Rabaa M. (3), van der
Hoek L. (2), Baker S. (3), Kellam P. (1,4), Cotten M. (1).
1 Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
2 Laboratory of Experimental Virology, Center for Infection and Immunity Amsterdam, Academic Medical
Center, Amsterdam, The Netherlands.
3 Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
4 Department of Infection, University College London, London, United Kingdom.
Diversity and dynamics of rotaviruses in human, pigs and rats in Vietnam using agnostic
whole-genome deep sequencing
Rotavirus is the major diarrhoeal pathogen in human and other mammals. Given the propensity of rotavirus
for genetic reassortment and interspecies movement, it is important to sequence the entire 11-segment
genome to understand diversity, evolution and zoonotic chatter. Current rotavirus sequencing approaches are challenged by the segmented genome, particularly the primer design step. Using an agnostic deep
sequencing method for enteric viruses that requires no prior knowledge of the virus contents for primer
design, rotavirus genome sequences were obtained from human, porcine and rat stools, in addition to full
genomes from peripheral enteric viruses in the samples. Particularly, 36 genomes of rotavirus group A were
documented in 50 human stool samples (45 rotavirus A-positive by real-time polymerase chain reaction)
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with more than one genotype detected in 6 samples. Rotavirus was found in 36/150 random porcine stool
samples (13 group A, 10 group B, 8 group C and 5 newly identified group H). Rotavirus B was found in 4/10
rats with one sample of mixed infections. Maximum-likelihood phylogenetic analyses of the new Vietnamese rotavirus A sequences showed that the viruses were closely related to existing Vietnamese and global
strains, yet were different from the vaccine strains. Importantly, several amino acid differences from vaccine
strains were observed in neutralizing epitopes of VP4 and VP7. The method also provided genomes for other
enteric viruses in the samples, such as norovirus, sapovirus, astrovirus and various picornaviruses. This detailed viral sequence data will provide an important basis for examining the rate and properties of virus host
switching.
Abstract 59
Nathaniel S. *(1), Salazar P. (1), Gutierrez C. (1), Chadee D.D. (2), Nix W.A. (3).
1 Caribbean Public Health Agency, 16-18 Jamaica Boulevard, Port of Spain, Trinidad and Tobago.
2 The University of the West Indies, St. Augustine, Trinidad and Tobago.
3 The Center for Disease Control and Prevention, Atlanta, GA, USA.
First enterovirus D68 (EV-D68) cases detected in the Caribbean region.
Enteroviruses are a common cause of illness in infants and children, with over one hundred types in existence that cause a range of respiratory, gastrointestinal and neurological diseases. In 2014, the global reemergence of human enterovirus 68 (EV-D68) commonly associated with severe respiratory illness was identified with outbreaks occurring in the USA and Canada. With the recent awareness regarding EV-D68 and as
part of the continuous surveillance program on respiratory illness, respiratory samples sent to the Caribbean
Public Health Agency (CARPHA) that initially tested negative for influenza and non-influenza viruses were
tested for EV-D68 using molecular diagnostics. In October and December 2014 enteroviruses were detected
in respiratory samples from patients coming from Bermuda and Dominica respectively. The patients were
all children under 5 years old and symptoms were mainly respiratory. No patient exhibited neurological
symptoms. Genetic analysis of partial VP1 sequences confirmed that the detected enteroviruses belonged
to the D68 subtype, making these the first EV-D68 cases detected in the Caribbean region. By phylogenetic
analysis the strains from Bermuda showed to be closely related to the recent outbreak in the USA, confirming the circulation of that strain in regions out of the US. The strains from Dominica showed however, some
level of diversity when compared with the strains from US. The isolation of EV-D68 in the Caribbean region
may represent a major public health challenge not just for the region but the rest of the Americas due to the
potential spread of the virus through the continent, the wide range of symptoms at presentation, the need
of molecular diagnosis to confirm the isolation and the expected morbidity mostly in young children.
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Abstract 60
Souza W.M. *, Romeiro M.F., Tolardo A.L., Vieira L.C., Figueiredo L.T.M.
Virology Research Center, School of Medicine of Ribeirao Preto of University of São Paulo, Ribeirao Preto, São
Paulo, Brazil.
Full genome sequences and molecular characterization of ten arboviruses from Brazil.
The arboviruses (arthropod-borne viruses) are an important emerging problem in public health in worldwide. Currently are described five families of viruses as human pathogens in the Americas are Togaviridae,
Flaviviridae, Bunyaviridae, Reoviridae and Rhabdoviridae. However, currently there is a gap in genomic information for arboviruses non-dengue virus in South America. In this study, we performed sequencing and
molecular characterization of ten viruses discovered in the 1950s to 1990s in Brazil. The four viral families
includes in our study are Orthobunyaviruses (Catu, Itaqui, Enseada, Tacaiuma, Capim and Apeu, Phlebovirus
(Bujaru)), Vesiculovirus (Piry), Alphavirus (Mucambo), and Flavivirus (Cacipacore). These viruses were characterized in cell cultures and electron microscopy. Then, the viruses were sequenced in 9 lanes in HiSeq 2500
sequencer with paired-end 2x150 pair bases in length in “Rapid run mode”. The reads were delivered in
FASTQ format with minimum quality of 80%> = Q30. The sequences from each sample type have been processed individually. The reads has been de novo assembled using four assembly algorithms Velvet, ABySS,
MetaIDBA and MetaCortex. These data will represent the first complete coding region sequences for each
one species of viruses. Our results will provide the molecular basis for the developments of diagnostics,
further genetic analyses, and future epidemiologic studies to these arboviruses in South America, especially
the Brazil.
Abstract 61
Rodriguez C. *(1), Audureau E. (2), Chevaliez S. (1), Darthuy F. (1), Pawlotsky J.M. (1).
1 Microbiology Dept, University Hospital Henri Mondor, INSERM U955 Team 18, Paris-Est Creteil University,
France.
2 Clinical Investigation Laboratory, LIC- EA 4393, Paris-Est Creteil University, France.
Sequence analysis of the Hepatitis B virus (HBV) PreC/C region by ultra-deep pyrosequencing as a predictor of nucleus colonies (Nucs) treatment outcome in patients with
HBeAg-positive chronic hepatitis B.
One of the main goals of HBV antiviral therapy in patients with HBeAg-positive chronic hepatitis B is the
HBe seroconversion with sustained inhibition of viral replication. Whether and when such patients receiving
nucleos(t)ide analogues can stop treatment without exposing the patient to a relapse is unknown. Thus,
predictive markers are needed, both at baseline to evaluate the risk of treatment failure and during therapy
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to predict treatment success and evaluate the likelihood of a viral rebound at its withdrawal. We studied a
cohort of 156 treatment-naïve patients with chronic HBeAg-positive chronic hepatitis B treated with adefovir dipivoxil and followed for a maximum of 180 weeks. HBV PreC/C domain which overlapping with X
gene was sequenced in sequential samples by means of ultra-deep pyrosequencing (UDPS) using Genome
Sequencer FLX (Roche Molecular systems/454) and analyzed by Pyropack® (in-house software). Then, each
found mutation were logit modelized overtime, clustered (methods k-means, STEM-FLAME) and visualized
on heat-map. From 337 serial samples from the 156 patients, we found 4 groups of patients harboring patterns of mutations located in critical domain of HBV (promotors, replication regulation domains…) associated to phenotypic characteristics as viral load decrease, or seroconversion. In conclusion, we used ultra-deep
pyrosequencing to assess whether signature sequences in the PreC/C region could help tailor antiviral treatment of HBeAg-positive chronic hepatitis B. Results are promising to better understand evolution of HBV
under nucleotide inhibitors treatment and to better manage treatment of patients.
Abstract 62
Chen Z. *(1,2), Chan P.K.S. (1), Burk R.D. (2,3).
1 Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
2 Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
3 Departments of Microbiology & Immunology, Epidemiology & Population Health, and Obstetrics, Gynecology & Woman’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
Cervical microbiome diversity is associated with cervical precancer using Next-Gen sequencing.
Background: A variety of microbial communities exist throughout human ecosystems, such as, the gut, skin,
oral cavity and vagina, with fundamental roles in human development, physiology, immunity and nutrition. The cervicovaginal microbiome plays an important role in female reproductive health, affecting rates
of preterm-birth and neonate mortality; prevalence, susceptibility to and transmissibility of sexually transmitted infections (sexually transmitted infections, including HIV); and other important clinical conditions.
Despite the importance, however, little is known about how cervicovaginal microbiome communities differ
in function and, more importantly, how their constituent members interact with each other and the host to
form a dynamic ecosystem that responds to various host and environmental factors.
Methods: We used a nested case-control design to investigate the cervical microbiome in 94 HPV16-positive cervical samples from the Persistence and Progression (PaP) Cohort, a collaborative study with the NCI
and KPNC. There were 44 controls and 50 cases with Cervical Intraepithelial Neoplasia Grade 3 (CIN3). To
characterize the microbiome, we PCR amplified an approximately 145 bp fragment spanning the V6 region
of the bacterial 16S rRNA gene. Each sample was amplified using a unique barcoded primer set. Barcoded
PCR products were pooled at approximately equal molar DNA concentrations and sequenced on an Illumina
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HiSeq 2000 platform at Einstein. The NGS reads (~100 millions) were processed using two 3rd-part taxonomy
algorithms, usearch and pplacer, and additional in-house developed bioinformatics tools. Classification tables were generated from input data at the species-level, based on the vaginal 16S rRNA sequence database.
The characterized reads were organized using a heat map and squash clustering. Pairwise Kantorovich-Rubinstein (KR) distances were calculated for principal component analysis and Simpson diversity indices to
evaluate the difference of cervical microbiome communities between case and control groups.
Results: The cervical microbiome of the 44 controls revealed two predominant genera, Lactobacillus and
Gardnerella, consistent with previous reports of female reproductive tract microbiota. 35 (80%) control samples were dominated by one or more species of Lactobacillus that constituted 86% of all Illumina reads. All
5 types of vaginal communities previously defined that are predominated by Lactobacillus crispatus (type I,
27%), L. gasseri (type II, 5%), L. iners (type III, 43%), and L. jensenii (type V, 5%). The type IV community group
(20%) lacked detectable Lactobacillus spp., but contained other bacterial groups with high proportions of anaerobic bacteria, including Gardnerella, Prevotella, Sutterella, Atopobium, Sneathia, Eggerthella, Pseudomonas,
Acinetobacter and Streptococcus. The CIN3 group had similar cervical microbiome communities, but showed
significantly higher measures of diversity compared to the control group (Mann-Whitney-Wilcoxin p <0.05).
Abstract 63
Shabman R.*, Dilley K., Halpin R.A., Lin X., Das S.R., Stockwell T.B., Nelson K.E.
Infectious Disease group, J. Craig Venter Institute, Rockville, MD, USA
Next generation sequencing highlights unique aspects of Ebola virus (EBOV) biology
and provides novel diagnostic platforms.
Filoviruses (Ebola and Marburg viruses) are a significant threat to human health illustrated by the recent Ebola outbreak in West Africa. The mortality rate from filovirus infection can approach 90%, and there are currently no approved filovirus vaccines or therapeutics. We seek to better understand filovirus biology to aid
in our ability to design effective antiviral treatments. Through next generation sequencing (NGS), our collaborative work has uncovered unique features of filovirus transcription, replication, protein translation and
innate immune evasion. We have deep sequenced RNAs produced by Zaire EBOV and the Angola strain of
Marburgvirus (MARV-Ang) to identify novel viral and cellular mechanisms that diversify the coding and noncoding sequences of filovirus RNAs (PMID: 25370495). Moreover, we have applied sequence-independent
NGS methods to further define how the Ebola virus protein VP35 antagonizes the human innate immune
response, specifically by detecting immunostimulatory RNAs bound by VP35. Improving diagnostic assays
that rapidly detect EBOV infection are critical to quickly identify and respond to EBOV infection. Toward this
goal, our work has validated an Ion AmpliSeq™ Ebola Panel Assay in collaboration with Thermo Fisher Scientific. We will discuss data from each of these studies to illustrate how NGS can improve our understanding
and diagnosis of this lethal pathogen.
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Abstract 64
Tambo E. *(1,5), Olalubi O.A. (2), Wurie I. (3), Jonhson J.K. (4), Ngogang J.Y. (5).
1 Sydney Brenner Institute for Molecular Bioscience, Wits 21st Century Institute, Faculty of Health Sciences,
University of the Witwatersrand, Johannesburg, South Africa.
2 School of Allied & Environmental Health, Kwara State University, Malete, Federal Republic of Nigeria.
3 Health and Education Quality Systems Strengthening (HQESS), Freetown, Sierra Leone.
4 Public Health Development Initiative (PHDI), Monrovia, Liberia.
5 Faculté des Sciences Biomédicales et Pharmaceutiques, Université des Montagnes, Bagangté, République
du Cameroun.
Ebola viral disease (EVD) outbreak surveillance and response challenges in prevention
and control
The scale, duration, and complexity of the EVD outbreak in West Africa have underscored the need for
prompt and effective implementation of evidence-based containment measures. Prompt identification,
case investigation and contact tracing in West Africa Ebola outbreak posed serious challenges, is one of the
interventions have been challenged to lack of appropriate tools in laboratory and epidemiological investigation, surveillance identification and follow-up, and poor contextual evidence in guidance for establishing and conducting contact tracing during filovirus disease outbreaks as well as national and sub-national
emergency management in all affected communities. For this reason, it is critical that all potential contacts
of suspect, probable and confirmed Ebola cases are systemically identified and put under observation for 21
days (the maximum incubation period of Ebola virus) from the last day of contact.
In the absence of integrated disease surveillance data and contact tracing in most Africa countries, understanding of the EVD phylodynamic and phylogenetics may provide insights into the rate of epidemic growth
and the reproduction and the undetected infections or reveal epidemiological history. Also there is urgent
need in assessing the natural selection and selective pressures acting upon viral emergence and potential
resistance or evolutionary adaptations and most importantly, characterization of EVD spreading patterns using epidemiological population genetic model simulations that are crucial in useful supplement to epidemic
surveillance and timely intervention efforts.
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Abstract 65
Lin A.E. *(1,2), Whitmer S. (3), Honko A.N. (4), Gire S.K. (1,2), Matranga C.B. (1,2), Wohl S. (1, 2), Andersen K.G. (1,2),
Park D. (1,2), Hensley L.E. (4), Stroeher U. (3), Sabeti P.C. (1,2).
1 FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University,
Cambridge, MA, USA.
2 Broad Institute, Cambridge MA, USA.
3 Viral Special Pathogens Branch, Centers for Disease Control, Atlanta, GA, USA.
4 Integrated Research Facility, National Institutes of Health, Frederick MD, USA.
Time-dependent dynamics of intrahost variation during ebola virus infection.
Lack of proofreading during RNA virus replication generates diverse viral quasispecies within a single host.
Strong bottlenecks (e.g., viral entry, virion production, immune evasion) shape the emergence and frequency of viral variants and new phenotypes. Therefore, deep sequencing of the viral quasispecies over a time
course of infection provides invaluable information regarding biological processes and outcome in a single
host. We sequenced viral RNA from multiple serum samples from West African patients infected with Ebola
virus strain Makona, as well as from non-human primates infected with Ebola virus strain Kikwit, and identified intrahost single nucleotide polymorphisms (iSNPs) at >0.5% frequency. Using phylogenetic tools, we
aim to gauge the amount of viral diversity in the quasispecies and determine if diversity increases (diversifying selection) or decreases (purifying selection) over time. Moreover, emergence or disappearance of iSNPs
can help us identify biological bottlenecks shaping the viral quasispecies. Taken together, these studies will
shed light on the forces molding Ebola virus evolution in individual hosts during the course of infection, and
will help identify biological processes to disrupt during design of vaccines and therapeutics.
Abstract 66
Wohl S. *(1,2), Park D. (2), Andersen K.G. (1,2), Matranga C.B. (2), Sabeti P.C. (1,2).
1 FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University,
Cambridge, MA, USA.
2 Broad Institute, Cambridge, MA, USA.
Incorporation of within-host diversity to improve viral transmission reconstruction
During a disease outbreak, reconstructing transmission chains is an important tool for curtailing disease
and evaluating control measures. Recently, several groups have developed statistical frameworks for inferring outbreak transmission trees from both epidemiologic and genomic data, which produces better results
than epidemiological tracing alone, especially during large outbreaks, where epidemiological data may be
difficult to obtain. Transmission models could be further improved by incorporating viral intrahost variation,
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but have yet to do so, largely because extensive intrahost data has not typically been available during an
outbreak. We have deep sequencing data available for over 200 Ebola virus genomes from the current epidemic in West Africa, and have identified sites of intrahost variation in these samples. Patient samples that
share intrahost variants are more likely to be linked in a transmission chain, so this information can be used
to more accurately understand the spread of the virus. I aim develop a new transmission model that can be
used to identify individuals or events that result in extensive spread of the virus, which may further inform
disease control efforts.
Abstract 67
Shrivastava S. (3), Lorenz HA. (3), Halpin R. (3), Stockwell TB. (3), Mackay IM. (4), Nissen MD (4), Sloots TP. (4), Tollefson
SJ. (1), Melendi G. (5), Polack F.(5), Staat MA. (6), Bose M. (7), Henrickson K. (7), Edwards KM. (1), Williams JV. (1,2).
1 Departments of Pediatrics1 and Pathology, Microbiology and Immunology
2 Vanderbilt University Medical Center, Nashville, TN, USA.
3 J. Craig Venter Institute, Rockville, MD, USA.
4 Queensland Children’s Medical Research Institute (QCMRI), University of Queensland, Australia.
5 Fundacion INFANT, Buenos Aires, Argentina.
6 Cincinnati Children’s Hospital, Cinciianti, OH, USA.
7 Milwaukee Children’s Hospital, Milwaukee, WI, USA.
Diversity and evolution of human metapneumovirus (HMPV).
HMPV, a paramyxovirus associated with acute respiratory infection (ARI) is the leading cause of serious lower
respiratory tract infection in young children worldwide and is associated with severe disease in immunocompromised hosts or persons with underlying conditions. HMPV is divided into four different subgroups:
A1, A2, B1 and B2 and based on the phylogeny, the closest virus to HMPV is the Avian metapneumovirus
type C (AMPV-C). Partial sequencing of the glycoprotein and the fusion protein genes from several groups
suggest that the lineages of HMPV are preserved over time. We have sequenced and analyzed 59 complete
genomes and their individual coding regions from several global locations to determine the diversity of
HMPV at the genomic level, and viral evolution over time. Lineages A and B were found to co-circulate globally, and host gender or age had no bearing on the type of subgroup infecting the host. Analysis of selection
pressure for individual coding region suggested very few positively selected sites, although a higher dN/
dS ratio for the B lineage in six of the nine coding regions were observed. Further analysis to identify clade
deterministic amino acid residues yielded very distinct residue changes in HMPVA versus HMPVB for all nine
coding regions. Using BEAST, the mean rates of evolution were calculated for each coding region and the
time to most recent common ancestor (tmrca) was calculated to be around 1804 using the whole genome.
The intended phylodynamic studies have not yet been undertaken.
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Abstract 68
Sahadeo NS. *(1), Allicock OM. (1), Auguste AJ. (2), Widen SG. (3), Weaver SC. (2), Carrington, CVF. (1).
1. Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Republic of Trinidad and Tobago.
2. Institute for Human Infections and Immunity and Department of Pathology, University of Texas Medical
Branch, Galveston, TX 77555, USA.
3. Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX
77555, USA.
Viruses associated with acute febrile illnesses in Trinidad and Tobago (T&T).
Dengue viruses (DENVs) and now chikungunya virus (CHIKV) are important public health problems in T&T.
Both present as acute fevers, clinically indistinguishable from each other, from a range of other febrile illnesses. Accurate, up-to-date information on the nature, prevalence and distribution of viruses circulating in a given population is critical for efficient and effective targeting of public health interventions. In this regard, we
have been screening individuals presenting with acute undifferentiated febrile illnesses (AUFIs), presenting
at a major hospital in T&T, in order to determine the rate of DENV and CHIKV as well as identify other viruses associated with AUFIs. Of 158 individuals screened using DENV and CHIKV specific reverse transcription
quantitative polymerase chain reactions (RT-qPCRs), CHIKV was detected in 19% (n=30) and DENV in 5.1%
(n=8; 6 DENV-1, 1 DENV-3, 1 DENV-4) of cases. Using an Illumina platform, 8 CHIKV sequences were derived
from the aforementioned samples. Phylogenetic analysis of their complete coding regions confirmed that
they belonged to the Asian genotype (Sahadeo et al., manuscript in preparation). Untreated serum samples
from 6 patients who were RT-qPCR negative for DENV and CHIKV were also subjected to Illumina sequencing. Sequence reads included several similar to human gut and skin flora, and in one individual, Human
Immunodeficiency Virus 1 (HIV1). In order to enrich for viral sequences, the subsequent samples (n=22) from
DENV and CHIKV qRT-PCR negative patients were treated by a 3-step (centrifugation, filtration and nuclease
treatment) procedure prior to deep sequencing, which is currently underway.
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Abstract 69
Dupont C.L. *(1), Oliviera G. (2), Hoffman J. (1), Cuadros S. (2), Richter R.A. (1), Yooseph S. (1), Friedman R. (1), Lee C.
(3), Harkins T. (3).
1 J. Craig Venter Institute, La Jolla, CA, USA.
2 FIOCRUZ Minas CEBio, Belo Horizonte, Brazil.
3 Life Technologies, Inc. Oyster Point, CA, USA.
Metagenomic profiles of the Amazon river.
In February 2014, size fractionated metagenomic samples were collected at 20 locations of the Amazon River
watershed. These include samples just upstream of Manaus all the way to the mouth at Belem. Samples
were collected just upstream of confluences as well as after significant mixing between the main branch and
the tributaries. Detailed analyses of the water chemistry has revealed dramatic differences in the samples,
particularly in terms of carbon, iron, and calcium content, which corresponds with the drainage basin and
land usage. Sequencing is underway. The analyses of the 60 metagenomes (20 samples, three size fractions)
with regards to changes in water chemistry and land usage will be presented.
Abstract 70
Alleyne A.T. *, Cummins C.
The University of the West Indies Cave Hill Campus, Bridgetown, Barbados.
Deep sequencing of the small RNAs of sweet potato leaf phytobiome reveals potentially
new virus disease causing complexes in Barbados.
In 2000-2003, a decline in yields by more than 50% was observed in some sweet potato fields in Barbados
and symptoms of yellowing, swollen leaf veins and deep grooves on the tubers suggested the possibility
of Sweet potato virus disease (SPVD). SVPD is a complex synergy of several virus species belonging to the
two main genera: Potyviridae and Closterivirdiae and other minor viruses. This study sought to characterize
the viruses in the SVPD complex affecting sweet potato varieties in Barbados by using PCR amplification
of viral RNA and genomic siRNA sequencing of affected sweet potato leaves. Initial PCR of viral RNA using
specific primers only detected the Potyvirus SPFMV. Deep sequencing however revealed the presence of
several DNA viruses. Geminivridae (genus Begomovirus) and Caulimoviridae (genus Badnavirus) accounted
for more than 75% of the viruses found in the sweet potato leaf phytobiome in Barbados. The results possibly suggest new virus associations in the leaf phytobiome, largely composed of symptomless DNA viruses
previously unreported in the Caribbean, in sweet potato.
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Abstract 71
Ramsahai E. *(1), Tripathi V. (1), Walkins K. (2), John M. (2).
1 Department of Mathematics and Statistics, The University of the West Indies, St Augustine, Trinidad and
Tobago
2 Faculty of Medical Sciences, The University of the West Indies, Mt Hope, Trinidad and Tobago
Combining gene interaction networks improves the identification of driver genes.
Bioinformatics has implemented different strategies to distinguish driver genes from passenger genes. One
of the more recent strategies is a pathway-oriented approach. Methods that employ this strategy are highly
dependent on the quality and size of the pathway interaction network, and require a powerful statistical
environment for their analysis. Existing genomic libraries are available in the R-Bioconductor package. One
of these packages, DriverNet is a pathway-based method that uses a gene interaction network in the form
of an adjacency matrix. In our analysis we set out to combine data from 3 different networks (VarWalker,
DawnRank, and DNA tumour viruses) for analysis. We found this increased the sensitivity and specificity of
the identification of driver genes significantly. Human interaction data from the families of DNA tumour viruses: Human Papillomavirus (HPV), Epstein-Barr Virus (EBV), Adenovirus (Ad5), and Polyomavirus (PyV) were
incorporated into the combined network. An enriched data set was produced that included 11,648 genes
and 211,894 edges.
Abstract 72
Cedeno S. * and Dialsingh I.
Department of Mathematics and Statistics, The University of the West Indies. St. Augustine, Trinidad and
Tobago.
Likelihood ratio dependent local False Discovery Rate (lFDR).
Multiple hypothesis testing has become a major research topic once again because of the emergence of
differential expression in high dimensional genomics data. Traditional methods like Bonferroni’s correction
which controls the family wide error rate (FWER) is inappropriate when it comes to high dimensional data. As
a result, research into false discovery rates (FDR) is becoming increasingly popular.
The local false discovery rate (lFDR) developed by Bradley Efron has a Bayesian flavor. However, the main
drawback of Efron’s lFDR is that it can only be computed if the proportion of null hypotheses is high (usually
above 0.80). We develop an lFDR method which relies on the likelihood ratio. We show via simulations of
microarray data, that our method is superior in terms of power and in terms of true rejections. Our method
can be extended to discrete tests as well.
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Abstract 73
Naraine R. *, Joseph A., Khvostova O., McEwen A., Yeates S., Kotelnikova S.
Department of Microbiology, St. George’s University, Grenada
Characterization of CRISPR-Cas operons and spacer elements in the acidophile, Ferroplasma acidarmanus fer1.
The CRISPRs (clustered regularly interspaced short palindromic repeats) Cas operon has been shown to consist of genes involved in adaptive immunity, gene repair, gene regulation and genome remodelling. Herein
we report on the annotation of two CRISPR-Cas operons located in the acidophilic Euryarchaeum, Ferroplasma acidarmanus fer 1. The presence of CRISPR spacer elements within the analysed genome may represent
a chronological order of the acquisitions of protospacer sequences from prior infections by Mobile Genetic
Elements (MGE).
Potential direct repeats, spacer sequences and associated Cas genes within fer1 genome were detected
using the CRISPRdb database from the CRISPRs web server. Further searches within IMG, Biocyc, Uniprot
and NCBI databases were done to detect other potential orthologs in fer1. The information was then used
to manually annotate proteins and spacer sequences using the Geni-Act toolbox, and characterize the structure of two Cas operons.
Manual annotation identified two CRISPR operons of Type I. Type I CRISPR is known to target DNA MGE.
Remarkably, no significant sequence similarity was observed between the detected spacer sequences and
known MGE within the NCBI database (nr), which agrees with the fact that archaeophages targeting Ferroplasma are currently unknown. Due to the lack of sequence homology, further in situ analysis maybe
required to target and identify the MGEs within the host’s environment. This research represents the first
documented analysis on the CRISPR-Cas operon structure and spacer elements in F. acidarmanus. Future
research in this area has the potential to reveal the MGE-host dynamics in extreme environments.
Abstract 74
Rampersad SN.
Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine. Trinidad and Tobago - West Indies.
Genetic variation and population dynamics of members of the Fusarium incarnatum-equiseti species complex (FIESC).
Correct identification of Fusarium species in food products allow for more accurate prediction of mycotoxigenic risk. Members of the Fusarium incarnatum-equiseti species complex (FIESC) are known to be trichothecene producers. Trichothecenes are potent inhibitors of protein synthesis in eukaryotic cells as they in9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
87
terrupt peptidyl transferase activity during the elongation phase of translation. These fungi cause different
acute and severe diseases in humans and animals depending on the type of trichothecene ingested. The
Trinidad strains belonged to at least 8 different phylogenetic species of the FIESC: F. equiseti strains belonged
to 3 phylogenetic species and the F. incarnatum strains belonged to 5 phylogenetic species. The partial
sequences of the translation elongation factor gene (EF-1a) and of the internally transcribed spacers of the
rDNA region (ITS1-5.8S-ITS2) were used in a multi-locus sequence comparison. Additionally, the genetic diversity of 95 strains of the FIESC belonging to 5 different global populations was investigated. Sequence
exploration indicated that the aligned DNA sequences of the EF-1a gene were more informative than the ITS
sequences based on DNA polymorphism indicators. Phylogenetic relationships, gene flow and the potential
for migration of the pathogen across continents are to be determined.
Abstract 75
Seetahal J.F.R. *(1), Allicock O.M. (1), Oura C. (2), Carrington C.V.F. (1).
1 Department of Preclinical Sciences, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Trinidad and Tobago
2 School of Veterinary Medicine, Faculty of Medical Sciences, The University of the West Indies, St. Augustine,
Trinidad and Tobago
The role of mainland-island vampire bat movement and population dynamics in rabies
virus (RABV) activity in Trinidad.
Our previous phylogenetic studies implicate the vampire bat species Desmodus rotundus as the source of
RABV outbreaks in the Caribbean island of Trinidad and provide evidence for RABV importation from the
nearby South American mainland on at least three occasions between 1972 and 2010, each with subsequent
in-situ lineage expansion. RABV activity in Trinidad is greatest in the southwestern peninsula closest to the
mainland. The main method of control is chemical culling of vampire populations, which can indiscriminately
affect co-roosting non-vampire species. The aim of the current study is to investigate the role of D. rotundus
population dynamics and mainland-island movement in determining patterns of RABV activity in Trinidad.
Between Feb 2012 to Aug 2013, 103 D. rotundus were collected at various locations in Trinidad (primarily
during routine eradication exercises by the Anti-Rabies Unit of the Ministry of Food Production). They were
humanely euthanized and swabs (oral and rectal), blood and tissue samples were harvested using all appropriate laboratory safety precautions. Samples were then frozen (-80 °C) until further use. D. rotundus from
selected areas in South America (Venezuela, Suriname, Guyana) will be captured and similarly processed.
Genomic DNA will be extracted from tissue samples and comparative bat population genetic analysis will be
performed using the mitochondrial cytochrome b gene and selected microsatellite markers. Bat tissues will
be screened for RABV using rabies-specific reverse transcriptase-polmerase chain reaction (RT-PCR). RABV
seroprevalence will also be determined. The BEAST software package will be used on data sets of derived
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
88
and previously published viral sequences to infer evolutionary relationships, population dynamics and patterns of gene flow. D. rotundus population sizes will also be estimated using partial roost counts and capture/
recapture data. The relationship between bat population dynamics in Trinidad and movements estimated
from the bat population genetic analyses, and patterns of RABV gene flow and outbreaks will then be investigated
Abstract 76
Seraise B. *(1,2), Andrea-Marobela K. (1), Moyo S. (2), Musonda R. (2), Makhema J. (2), Essex M. (2,3), Gaseitsiwe S. (2).
1 University of Botswana, Department of Biological Sciences, Gaborone, Botswana.
2 Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.
3 Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, USA.
The frequency Of N348I mutation in patient failing combination antiretroviral treatment
In Botswana.
Background: The N348I mutation in the connection subdomain of HIV-1 Reverse Transcriptase (RT) has been
reported to reduce susceptibility to Nevirapine (NVP), Efavirenz (EFV) and Zidovudine (AZT), and is frequently selected in HIV-1 patients experiencing virologic failure. We here sort to investigate the frequency of the
N348I mutation in HIV-1 subtype C infected patients in Botswana failing different antiretroviral therapy regimens as there is no data on the prevalence of this mutation in patients failing cART in Botswana.
Methods: HIV-1 drug resistance genotyping was done on samples from two previous clinical trials conducted at Botswana Harvard Partnership investigating the efficacy of different ART regimens. Plasma samples
from 43 patients who experienced virologic failure from the two studies were available for genotyping.
Results and Discussions: Thirty-four of the 43 (79.1%) virologic failure samples were successfully genotyped.
Amongst the 34, 9(26.5%) were found to harbour the N348I mutation. The N348I mutation emerged in 10%
of patients failing AZT containing cART and 33.3% of participants failing regimens containing NVP or EFV.
Conclusions: We found a frequency of 26.5% for N348I mutation among HIV-1C patients experiencing virologic failure in Botswana. The association of the N348I mutation with virologic failure in this population
warrants further investigation but in this cohort it seemed to be more closely linked with non-nucleoside
reverse transcriptase Inhibitor failure than with AZT failure. The kinetics of the mutation in relation to other
RT mutations also needs to be investigated to better understand its impact.
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
89
Abstract 77
Scheuermann RH.* (1), Zhang Y. (1), Greer DS. (1), Aevermann B. (1), Lee A. (1), Stewart L. (1), Zhou L. (2), Gu Z. (2),
Kumar S. (2), Zaremba S. (2), Sun G. (3), Larson CN. (3), Jen W. (2), Klem EB. (2).
1 J. Craig Venter Institute, 4120 Capricorn Ln, La Jolla, CA 92037, USA
2 Northrop Grumman Health Solutions, Rockville MD, USA
3 Vecna Technologies, Greenbelt MD, USA.
Integrated, Enriched Data and Diverse Bioinformatics Analysis Tools for Comparative Genomics in the Influenza Research Database (IRD) and Virus Pathogen Resource (ViPR
The Influenza Research Database (IRD, www.fludb.org) and Virus Pathogen Resource (ViPR, www.viprbrc.
org) are freely available, online resources supported by the U.S. National Institute of Allergy and Infectious
Diseases to search, analyze, visualize, save and share infectious disease research data for a broad range of
human virus pathogens, including influenza virus, and other viruses in the Arenaviridae, Bunyaviridae, Caliciviridae, Coronaviridae, Flaviviridae, Filoviridae, Hepeviridae, Herpesviridae, Paramyxoviridae, Picornaviridae, Poxviridae, Reoviridae, Rhabdoviridae, and Togaviridae families. IRD and ViPR provide access to sequence records,
enriched gene and protein annotations, Gene Ontology classifications, protein ortholog groups, experimentally determined and computationally predicted immune epitopes, Sequence Feature Variant Types, 3D protein structures, clinical metadata, host factor data, influenza serology and animal surveillance data, influenza
virus phenotypic data, and other data types through an intuitive web-based search interface. IRD/ViPR data
or user custom data can be analyzed and visualized through web-based tools including: BLAST, multiple sequence alignment, phylogenetic tree construction leveraging supercomputing resources, metadata-driven
comparative analysis, sequence variation determination, PCR primer design, Sequence Feature Variant Type
analysis, 3D protein structure visualization, gene enrichment analysis, genome annotation, genotype recombination detection, sequence format conversion, and genome viewing in GBrowse. A personal Workbench
space is also provided to the user for saving and sharing sequences, searches and analysis results for future
use. The data management and analysis tools have been designed to facilitate the research and development of diagnostics, prophylactics, and therapeutics against these human virus pathogens.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Abstract 78
Kyriakopoulou Z. (1), Bletsa M. *(2), Tsakogiannis D. (2), Dimitriou T.G. (2), Amoutzias G.D. (2), Gartzonika C. (3),
Levidiotou-Stefanou S. (3), Markoulatos P. (2).
1 Department of Biochemistry & Biotechnology, University of Thessaly, 26, Ploutonos & Aeolou str., Larissa
41 221, Greece.
2 Department of Biochemistry & Biotechnology, University of Thessaly, 26, Ploutonos & Aeolou str., Larissa
41 221, Greece.
3 University of Ioannina, Medical School, Department of Microbiology, Ioannina, Greece.
Molecular epidemiology and evolutionary dynamics of echovirus 3 (E3) serotype.
E3 serotype has been related with several neurologic diseases, although it constitutes one of the rarely isolated serotypes, with no report of epidemics in Europe. The aim of the present study was to provide insights
into the molecular epidemiology and evolution of this enterovirus serotype, while an E3 strain was isolated
from sewage in Greece, four years after the initial isolation of the only reported E3 strain in the same geographical region. Phylogenetic analysis of the complete VP1 genomic region of that E3 strain and of those
available in GenBank suggested three main genogroups that were further subdivided into seven subgenogroups. Further evolutionary analysis suggested that VP1 genomic region of E3 was dominated by purifying
selection, as the vast majority of genetic diversity presumably occurred through synonymous nucleotide
substitutions and the substitution rate for complete and partial VP1 sequences was calculated to be 8.13×10 -3
and 7.72×10 -3 substitutions/site/year respectively. The partial VP1 sequence analysis revealed the composite
epidemiology of this serotype, as the strains of the three genogroups presented different epidemiological
characteristics.
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
91
Abstract 79
Silva M.P. (1, 2), Arruda L.B. (3), Paixão L. (2), Oliveira M. (1), Haguihara T. (1), Oliveira A. (1), Queroiz A.T.L. (2), Casseb
J. (3), Duarte A.J. (3), Siqueira I.C. (4), Grassi F. (4), Camacho R. (5), Vandamme A.M. (5, 6), Khouri R. *(2)
1 CEDAP – Specialized Center of Diagnosis, Assistance and Research - Salvador-Bahia, Brazil.
2 LIMI-LIP, CPqGM, Oswaldo Cruz Foundation (FIOCRUZ), Salvador-Bahia, Brazil.
3 Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, SP, Brazil.
4 LASP, CPqGM, Oswaldo Cruz Foundation (FIOCRUZ), Salvador-Bahia, Brazil.
5 KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
6 Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical,
Universidade Nova de Lisboa, Lisbon, Portugal.
Impact of TasP in Brazil: Setting a reference dataset for future comparison analysis
Recently, the World Health Organization (WHO) HIV/AIDS guidelines proposed CD4 5000 patients with a
stored serum/plasma sample at HIV-1 diagnosis between 2003-2014, and included 2% of them in a study
aiming at evaluating HIV-1 genetic diversity, transmission of resistance mutation, coreceptor use, and clinical
outcome. For this purpose, we performed pol and V3 loop genotyping, collected epidemiological information and reviewed the clinical history. We plan to investigate subtype distribution, TDR prevalence and
potential associated transmission chains, in silico fitness using protease fitness landscape predictions, predicted coreceptor use using Geno2Pheno, and associate these variables with epidemiological and clinical
information. Thus, the data generated from this analysis will be used to establish a reference dataset to study
the impact of TasP in Brazil prospectively.
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Contact Details
Participants
Adesina, Olufisayo Adeyemi
Bajak, Edyta
Department of Microbiology,
Ross University School of Veterinary Medicine
Biological Sciences Building,
P.O. Box 334
Obafemi Awolowo University,
Basseterre
Ile-Ife, Osun State, Nigeria
St. Kitts and Nevis
[email protected]
[email protected]
Afonso, Maria Manuel
Balamane, Maya
University of Liverpool
Georgetown University
Leahurst Campus Chester High Road
Division of Infectious Diseases
UK CH64 7TE
2115 Wisconsin Ave, NW Suite 130
[email protected]
Washington DC, 20007
[email protected]
Ahmad, Adamu Kaikabo
Faculty of Food Science
Bletsa, Magdalini
University Putra Malaysia
KU Leuven, University of Leuven, Department of
43300 UPM Serdang
Microbiology and Immunology, Rega Institute
Serdang, Selangor
for Medical Research, Laboratory for Clinical and
Malaysia
Epidemiological Virology, Minderbroedersstraat 10,
[email protected]
3000 Leuven, Belgium
[email protected]
Alleyne, Angela T.
Department of Biological and Chemical Sciences
Brown-Joseph, Tamiko
Faculty of Science and Technology
Biochemistry Unit,
The University of the West Indies
Department of Pre-Clinical Sciences,
Bridgetown, Barbados
Faculty of Medical Sciences,
[email protected]
The University of the West Indies,
St. Augustine, Trinidad and Tobago
[email protected]
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
93
Brown, Arianne
Coltart, Cordelia
Basic Veterinary Sciences,
Department of Infection and Population Health,
School of Veterinary Medicine,
University College London,
University of the West Indies,
Mortimer Market Centre, London, WC1E
Eric Williams Medical Sciences Complex,
[email protected]
Mount Hope, Trinidad and Tobago
[email protected]
D'arc, Mirela
Instituto Nacional de Câncer
Carrera, Jean-Paul
Rua André Cavalcanti, 37 - 4o andar Bairro de Fátima
Deparment of Virology,
20231-050 Rio de Janeiro, RJ, Brazil
Gorgas Memorial Institute of Health Studies,
[email protected]
Columbus University
Panama
de Souza, William Marciel
[email protected]
Centro de Pesquisa em Virologia
Faculdade de Medicina de Ribeirão Preto,
Casal, Pablo
Universidade de São Paulo. Av. Bandeirantes,
Virology Area,
3900 - Monte Alegre - CEP 14049-900 - Ribeirão
School of Biochemical and Pharmaceutical Sciences,
Preto, São Paulo, Brasil.
Suipacha 531 S2002LRK
[email protected]
Rosario, Argentina
[email protected]
Delva, Glavdia Greatchens
Caribbean Public Health Agency (CARPHA)
Cedeno, Sherwin
16-18, Jamaica Blvd, Federation Park,
Department of Mathematics and Statistics.
Port of Spain, Trinidad & Tobago
The University of the West Indies
[email protected]
St. Augustine. Trinidad, West Indies
[email protected]
Dennis, Ann
130 Mason Farm Road,
Chen, Zigui
CB 7030 Chapel Hill,
Department of Microbiology,
NC 27599-7030
Faculty of Medicine,
[email protected]
The Chinese University of Hong Kong
1/F Lui Che Woo Clinical Sciences Building Prince of
Dos Santos, Georges
Wales Hospital,
Service de virologie,
Shatin, N.T., Hong Kong
CHU de Martinique,
[email protected]
Fort de France, Martinique
[email protected]
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
94
Drumond, Betania Paiva
Florencio Da Silva, Jackson Raniel
Universidade Federal de Juiz de Fora
Center of Informatics,
Instituto de Ciências Biológicas -
Federal University of Pernambuco,
Departamento de Parasitologia, Microbiologia e
Pernambuco, Brazil
Imunologia, sala 2407
[email protected]
Microbiologia - Laboratório de Virologia
Rua José Lourenço Kelmer, s/n -
Fridholm, Helena
Campus Universitário
Statens Serum Institut
Bairro São Pedro - CEP: 36036-900 - Juiz de Fora - MG
Artillerivej 5 DK 2300 Copenhagen S Denmark
[email protected]
[email protected]
Dupont, Christopher Lee
Gräf, Tiago
J. Craig Venter Institute
Laboratório de Imunologia Aplicada Departamento
Rockville, MD, USA
de Microbiologia,
[email protected]
Imunologia e Parasitologia
Universidade Federal de Santa Catarina
Ernest, Tambo
Florianópolis/SC - Brasil
Sydney Brenner Institute for Molecular Bioscience,
Postcode: 88040-900
Johannesburg South Africa &
[email protected]
Departement des sciences Biomedicales and
Pharmaceutiques, Universite des Montagnes,
Grossman, Zehava
Bangangte, Yaoundé, Cameroon
Sackler school of Medicine
[email protected]
Tel Aviv University
Ramat-Aviv Tel Aviv
Evangelista, Julio
[email protected]
Av. Venezuela S/N Callao 02. Lima - Peru
Naval Medical Research Unit - 6. Namru - 6
Hanke, Kirsten
[email protected]
Robert Koch Institute
FG18- HIV and other retroviruses
Fahmy, Inas Farouk
Nordufer 20
Agricultural Genetic Engineering Research Institute
13353 Berlin
Agricultural Research Center Ministry of Agriculture
[email protected]
and Land Reclamation
9 Gamaa St. P.O.Box 12619
Egypt
[email protected]
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
95
Hill, Sarah Catherine
Khouri, Ricardo
Department of Zoology
Laboratorio de Imunologia e Microbiologia
University of Oxford
FIOCRUZ/Centro de Pesquisas Gonçalo Moniz
Tinbergen Building
Rua Waldemar Falcão, 121, Candeal
South Parks Road
Salvador, Brasil
Oxford, OX1 3PS. UK
[email protected]
[email protected]
Kikwai, Gilbert Kipkorir
Hofstra, Laura Marije
Kenya Medical Research Institute,
Department of Infection and Immunity
Box 12672 GPO Nairobi
Luxembourg Institute of Health
Kenya
1A-B rue Thomas Edison,
[email protected]
L-1445 Strassen Luxembourg
[email protected]
Kvisgaard, Lise Kirstine
Technical University of Denmark
Jain, Jaspreet
National Veterinary Insitute
Insect Resistance Group
Bülowsvej 27 1870 Frederiksberg C Denmark
ICGEB, New Delhi ICGEB Campus
[email protected]
Aruna Asaf Ali Marg
New Delhi-110 067 India
Leon, Bernal
[email protected]
Servicio Nacional de Salud Animal,
SENASA Costa Rica Barreal de Heredia Costa Rica de
Jimenez-Silva, Cinthy Lorena
Jardines del Recuerdo 1KM al oeste y 400 metros al
Universidad Industrial de Santander
Norte en el Campus Universitario Benjamin Nuñez
Kilometro 2 via el Refugio,
[email protected]
Guatiguará, Piedecuesta
Santander, Colombia
Lin, Aaron
[email protected]
Harvard University
Northwest Labs Rm 456
Kassaye, Seble
52 Oxford St
Division of Infectious Diseases
Cambridge, MA 02138
Georgetown University
[email protected]
2115 Wisconsin Avenue,
N.W. Suite 130 Washington DC, 20007 U.S.A.
[email protected]
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
96
Machado Zaldivar, Liuber Yans
Okoror, Lawrence
Carretera Tapaste y Autopista Nacional,
Department of Biological Sciences,
San José de las lajas,
Joseph Ayo Babalola University,
Mayabeque, Cuba. CP:32700
Ikeji-Arakeji, PMB 5006, Ilesha
[email protected]
[email protected]
Martínez Pérez, Orlando
Ortiz Baez, Ayda Susana
Universidad de Ciencias Informáticas (UCI)
Laboratory of Molecular Evolution and
Carretera a San Antonio Km 2 1/2 ,
Bioinformatics
La Lisa, La Habana, Cuba.
Department of Microbiology
[email protected]
Institute of Biomedical Sciences
University of São Paulo 1
Monaco, Daniela Celeste
374 Sao Paulo - SP - Brazil - 05508-000
954 Gatewood Road,
[email protected]
Atlanta, GA, USA
Parag, Kris Varun
[email protected]
Department of Zoology
Naraine, Ravindra
University of Oxford
True Blue Grand Anse
South Parks Road
St. George Grenada
OX1 3PS, UK.
[email protected]
[email protected]
Nathaniel, SueMin
Pereira, Sergio
Caribbean Public Health Agency 16-18 Jamaica Blvd,
Av. Brazil, 4365 - Manguinhos,
Federation Park
Cep21040-900. Hepatitis Laboratory,
Port-of-Spain, Trinidad, West Indies
Oswaldo Cruz Institute,
[email protected]
FIOCRUZ, Rio de Janeiro, Brazil
[email protected]
Nyachieo, Atunga
Institute of Primate Research
Perveen, Shadab
P.O Box 24481-00502 End of Karen Road,
Karachi Institute of Biotechnology and Genetic
Oloolua Forest, Karen,
Engineering,
Nairobi, Kenya
University of Karachi,
[email protected]
Karachi-Pakistan
[email protected]
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
97
Phan, Vu Tra My
Ramsahai, Emilie
Virus Genomics group,
The University of the West Indies St. Augustine
The Wellcome Trust Genome Campus,
Campus
Hinxton, Cambridge CB10 1SA, UK
St. Augustine Trinidad & Tobago
[email protected]
[email protected]
Pimentel, Victor
Shabman, Reed
1374 - Ed. Biomédicas II Cidade Universitária
9704 Medical Center Drive
CEP 05508-900
Rockville, MD 20853
São Paulo - SP - Brasil
[email protected]
[email protected]
Rodriguez, Christophe
Pinto, Angie
Department of microbiology
The Kirby Institute Level 5 Wallace
Henri Mondor Universitary-Hospital
Wurth Buildling
94010 CRETEIL FRANCE
Randwick 2052 NSW Australia
[email protected]
[email protected]
Rodgers, Mary
Ramjag, Anushka
Abbott Laboratories
Building 36, Biochemistry Unit Department of Pre-
AP20, Dept 09NG
Clinical Sciences
100 Abbott Park Road
Faculty of Medicine,
Abbott Park, IL 60064, USA
Eric Williams Medical Sciences Complex
[email protected]
University of the West Indies St Augustine Campus
Trinidad and Tobago
Rodríguez, Arely Marina
[email protected]
Pedro de Alba S/N
Ciudad Universitaria, 66450,
Rampersad, Sephra
San Nicolás de los Garza,
University of the West Indies,
Nuevo León, México
Faculty of Science and Technology,
[email protected]
Dept. of Life Sciences,
St. Augustine, Trinidad and Tobago - West Indies
Sahadeo, Nikita
[email protected]
University of the West Indies
St. Augustine Campus
St. Augustine, Trinidad & Tobago
[email protected]
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
98
Salmona, Maud
Siripong, Nalyn
Laboratoire de Microbiologie
Department of Epidemiology
1 avenue claude Vellefaux
Gillings School of Global Public Health
75010 Paris
France
University of North Carolina at Chapel Hill
[email protected]
135 Dauer Dr. Chapel Hill, NC 27599
[email protected]
Sanchez, Gerardo
LLID 114, Facultad de Ciencias y Filosofia
Smith, Stacey Abigail
Universidad Peruana Cayetano Heredia Av. Honorio
Emory Vaccine Center
Delgado 430 Urb. Ingeniería S.M.P Lima 31, Peru
Rm 1023 954 Gatewood Road
[email protected]
Atlanta, GA 30329
[email protected]
Santiago, Gilberto
Molecular Diagnostics and Research Laboratory
Soto, Claudio
Dengue Branch, Division of Vector-Borne Diseases
Faculty of Microbiology,
Centers for Disease Control and Prevention
University of Costa Rica,
1324 Cañada Street
Ciudad Universitaria Rodrigo Facio,
San Juan, PR 00920
San Jose, Costa Rica
[email protected]
[email protected]
Scheuremann, Richard
Svirskis, Simons
4120 Capricorn Lane
Riga Stradins University
La Jolla, CA 92037
Ratsupites 5, LV-1067
[email protected]
Riga
Latvia
Seetahal, Janine
[email protected]
Veterinary Diagnostic Laboratory
Building 49 Eric Williams Medical Sciences Complex
Switzer, William
Champs Fleurs
Laboratory Branch Division of HIV/AIDS Prevention
Trinidad and Tobago
Centers for Disease Control and Prevention
1600 Clifton Road, Mailstop G-45
Shrivastava, Susmita
Atlanta, GA 30329
J. Craig Venter Institute
[email protected]
9704 Medical Center Dr Rockville,
MD 20850 USA
[email protected]
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99
Temereanca, Aura
Watson, Simon James
Carol Davila University of Medicine and Pharmacy,
Wellcome Trust Sanger Institute,
37, Dionisie Lupu Street, 020021,
Wellcome Trust Genome Campus,
Bucharest, Romania
Hinxton, Cambridgeshire CB10 1SA
[email protected]
United Kingdom
[email protected]
Vanden Eynden, Ewout Wilfried Jozef
KU Leuven, University of Leuven, Department of
Wohl, Shirlee
Microbiology and Immunology, Rega Institute for
Broad Institute
Medical Research, Minderbroedersstraat 10, 3000
Cambridge, MA 02142
Leuven, Belgium
[email protected]
[email protected]
Vicente Santos, Amanda
Centro de Investigación de Enfermedades
Tropicales,
Facultad de Microbiología,
Universidad de Costa Rica,
San José, Costa Rica
[email protected]
Vubil, Adolfo
Instituto Nacional de Saude-Ministry of Health,
Mozambique
[email protected]
Wang, Hao
155 Changbai Road,
Central Laboratory, National Institute for Viral
Disease Control and Prevention (IVDC),
Chinese Center for Disease Control and Prevention
(CDC),
Changping District,
Beijing, China
[email protected]
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Teachers
Alcantara, Luiz Carlos
de Oliveira, Tulio
Bioinformatics Unit Coordinator and Scientific
Africa Centre for Health and Population Studies,
Researcher
University of KwaZulu-Natal,
Advanced Public Health Laboratory
South Africa
Gonçalo Moniz Research Center
[email protected]
Oswaldo Cruz Foundation
Waldemar Falcão Street 121
Faria, Nuno
Candeal, Salvador, Bahia
Department of Zoology,
Brazil
University of Oxford,
[email protected]
South Parks Road, Oxford, UK
[email protected]
Baele, Guy
KU Leuven, University of Leuven, Department of
Gitzendanner, Matthew
Microbiology and Immunology, Rega Institute
Department of Biology,
for Medical Research, Laboratory for Clinical and
University of Florida,
Epidemiological Virology, Minderbroedersstraat 10,
Gainesville, FL, USA
3000 Leuven, Belgium
[email protected]
[email protected]
Holmes, Edward C.
Camacho, Ricardo
NHMRC Australia Fellow & Professor of Biology
KU Leuven, University of Leuven, Department of
& Medicine, Marie Bashir Institute for Infectious
Microbiology and Immunology, Rega Institute
Diseases & Biosecurity, School of Biological Sciences
for Medical Research, Laboratory for Clinical and
& Sydney Medical School,
Epidemiological Virology, Minderbroedersstraat 10,
The University of Sydney, Australia.
3000 Leuven, Belgium
[email protected]
[email protected]
9 – 14, August 2015 — St. Augustine, Trinidad and Tobago
101
Kosakovsky-Pond, Sergei
Paraskevis Dimitrios
CFAR BIT: Bioinformatics & Information Technologies
Department of Hygiene Epidemiology & Medical
Department of Medicine
Statistics, Medical School, National & Kapodistrian
University of California, San Diego
University of Athens
220 Dickinson St, Suite A
Greece
San Diego, CA 92103
[email protected]
USA
[email protected]
Prokunina-Olsson, Ludmila
Division of Cancer Epidemiology & Genetics,
Lemey, Philippe
Laboratory of Translational Genomics, NIH,
KU Leuven, University of Leuven, Department of
Atlanta, GA
Microbiology and Immunology, Rega Institute
USA
for Medical Research, Laboratory for Clinical and
[email protected]
Epidemiological Virology, Minderbroedersstraat 10,
3000 Leuven, Belgium
Prosperi, Mattia
[email protected]
University of Florida
College of Medicine,
Martin, Darren
Department of Pathology, Immunology and
Institute of Infectious Disease and Molecular
Laboratory Medicine
Medicine (IDM)
Emerging Pathogens Institute
Faculty of Health Sciences
P.O. Box 103633
University of Cape Town
[email protected]
Private Bag X3
Rondebosch 7701
Pybus, Oliver
Cape Town
Department of Zoology,
South Africa
University of Oxford,
[email protected]
South Parks Road, Oxford, UK
[email protected]
Min, Jae
Emerging Pathogens Institute,
Rambaut, Andrew
University of Florida,
Institute for Evolutionary Biology
Gainesville, FL, USA
Centre for Infection, Immunity & Evolution
[email protected]
Ashworth Laboratories
University of Edinburgh
Edinburgh, EH3 9JT
UK
[email protected]
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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Rhee, Soo-Yon
Stockwell, Tim
Division of Infectious Disease,
J. Craig Venter Institute
Stanford University, CA, USA
Rockville, MD, USA
[email protected]
[email protected]
Rife, Brittany
Suchard, Marc
Department of Biochemistry and Molecular Biology
David Geffen School of Medicine at UCLA
College of Medicine
Departments of Biomathematics, Biostatistics and
University of Florida, Box 100245
Human Genetics
Gainesville, FL 32610
6558 Gonda Building,
USA
695 Charles E. Young Drive, South
[email protected]
Los Angeles, CA 90095-1766
USA
[email protected]
Salemi, Marco
Department of Pathology, Immunology and
Laboratory Medicine
Theys, Kristof
College of Medicine
KU Leuven, University of Leuven, Department of
University of Florida, Box 100245
Microbiology and Immunology, Rega Institute
Gainesville, FL 32610
for Medical Research, Laboratory for Clinical and
USA
Epidemiological Virology, Minderbroedersstraat 10,
[email protected]
3000 Leuven, Belgium
[email protected]
Scheuermann, Richard
Director of Informatics
Vandamme, Anne-Meike
J. Craig Venter Institute
KU Leuven, University of Leuven, Department of
4120 Capricorn Ln.
Microbiology and Immunology, Rega Institute
La Jolla, CA 92037
for Medical Research, Laboratory for Clinical and
USA
Epidemiological Virology, Minderbroedersstraat 10,
[email protected]
3000 Leuven, Belgium
[email protected]
Schmidt, Heiko
Center for Integrative Bioinformatics Vienna (CIBIV)
Max F. Perutz Laboratories (MFPL)
Dr. Bohr Gasse 9
A-1030 Vienna
Austria
[email protected]
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Notes
The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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The 20th International BioInformatics Workshop on Virus Evolution and Molecular Epidemiology
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