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Role of Molecular Phylogenetics in Studying
Disease Epidemiology and Evolution
Jyotsana Dixit
Praveen Karanth Lab
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Molecular Phylogenetics and
Infectious diseases
Evaluation of pathways of transmission among several hosts and polarity of
transmission events.
Can address whether the genomic record has evidence to support a
hypothesis for a particular transmission pathway.
Can reconstruct genomic changes at the level of each nucleotide and
unravel parental and descendent strains.
Influenza
virus
AIDS
virus
Malaria Parasite
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Role of Molecular Phylogenetics in understanding
Influenza Evolution
Influenza viruses are divided into three main types: influenza A, B, and C
 Influenza A virus is an enveloped,
single stranded, negative-sense
RNA virus of the family
Orthomyxoviridae, with a genome
consisting of eight gene segments.
 It has been classified into at least
16 HA and 9 NA subtypes according
to the distinct antigenic properties of
the viral HA and NA surface proteins
Webster et al., 1992; Fouchier et al., 2005
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Influenza A virus becomes pandemic for Humans: Through
Zoonotics
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Influenza A escapes immune response in host population to cause
Pandemic
Antigenic Drift
Virus infects
the host cell
Point mutations
produces new
antigenic variants
Antigenic Shift
Due to host
immune system
pressure new
antigenic variants
are selected
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Highly pathogenic Avian influenza A
Human influenza pandemic
involving avian influenza
virus if this virus
exchanges genetic material
with co-circulating
seasonal human influenza
viruses
Caused economic
burden through
excessive poultry
deaths
Recent emergence of the novel influenza
A(H1N1/2009) virus of swine origin
Tsan-Yuk Lam et al., 2010
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Genetic origins of Human pandemic Influenza
Molecular phylogenetic analysis of influenza virus in 1980s led to the conclusions about
possible origins of human pandemic influenza strains causing 1918, 1957 and 1968
pandemics.
Fig: Phylogenetic tree showing
H1 sequences, including the
1918 pandemic strains and the
1917 Brant goose (arrows)
(Fanning et al., 2002).
Reid and Toubenberger 2003; Fanning et al., 2002
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Origin of novel pandemic influenza A(H1N1/2009)
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GJD Smith et al. Nature 459, (2009)
Phylogenetic analysis a useful tool
Elucidate genetic origin, selection pressures, evolutionary rates,
reassortment histories, population dynamics, and migration patterns of
influenza viruses in different host populations.
Proved to be an essential tool in monitoring influenza virus infection in
birds, pigs and humans.
In future with the availability of sequence data from larger viral
populations will reveal the intricacies of influenza virus evolution at even
finer temporal and spatial resolutions.
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Human Immunodeficiency virus
 HIV is an enveloped, diploid, positive-sense, single
stranded RNA retrovirus (family Retroviridae) with a 9.75
kb genome.
 The virus has an extraordinarily high mutation rate
(around 1 error per 3x105 bases replicated), which gives
rise to a very diverse viral population, even within one host
(often referred to as quasispecies).
 This diversity and rapid mutation rate makes it attractive
to analyze HIV sequences using phylogenetic techniques,
and its sequence diversity has been the focus of various
aspects of both clinical and research studies and
applications
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Evolution of HIV
HIV belongs to lentivirus subgroup of retroviruses.
Sharp and Hahn 2011
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Origin of AIDS Virus
Sharp and
Hahn 2011
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Dating SIVs origin
 Wertherin and Worobey 2009, used the extent SIV sequences to derive the molecular
clocks and estimate the timing of ancestral SIVs .
 Found that it is only few 100 Years Ago.
 However, recent study by Worobey et al., 2010, taking SIV samples from a wider regions,
substantiated the earlier conclusion and found the infection to be present at least 30,000 years
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ago.
Evolutionary history of primate lentivirus is still Incomplete
So far SIV infections only found
in African monkeys and apes.
It seems likely that primate lentivirus
emerged in Africa sometime after the
split between lineages of African and
Asian old world monkeys i.e. ~6-10 MYA.
Since neither Asian nor new world
primates
have
been
sampled
exhaustively, the conclusion that SIVs are
restricted to African primates remain
tentative.
© Zinner et al., 2011
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Origin of HIV-1
Origin of HIV-2
Sharp & Hahn 2011
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Phylogenetics: an effective tool for tracking disease
transmission
Transmission of HIV: Identifying and
tracking the transmission of HIV
infection between individuals in a
population is one of the most
widely used applications of
phylogenetics.
One of the most famous, earlier
examples of this type of investigation is
the case of the HIV-infected Florida
dentist who, somehow, infected five of
his patients with HIV.
Yih Ou et al., 1992
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Phylogenetics and study of Human malaria parasite evolution
Malaria caused due to infection by
protozoan parasite of genus
Plasmodium.
Five Human malaria causing species:
Plasmodium
Plasmodium
Plasmodium
Plasmodium
Plasmodium
falciparum
vivax
ovale
malariae
knowlesi
P. falciparum and P. vivax has
widest distribution, P. falciparum is
highest in causing mortality and
morbidity.
Fig: P. falciparum attacking blood cells
 P. Ovale has most limited
distribution of all, endemic to New
Guinea and Philippines.
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Molecular Phylogenetics: Study of Human Malaria
Parasite Evolution
 Human Plasmodium is a polyphylectic
genus.
 The human malaria parasite species
are remotely related to each other.
 Suggesting that adaptation to humans
has occurred several times
independently during the history of the
genus.
 It is still unclear, however, when these
associations began
and from where they came.
Fig: Phylogenetic relationship among the 17 Plasmodium species
inferred from the gene encoding cytochrome b.
• Escalante et al., 1998
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Origin of P. falciparum: A highly debated topic
Early molecular phylogenetic studies Plasmodium genus
 P. falciparum clustered with
two avian parasites rather than
with those infecting mammals.
 Thus suggesting that P.
falciparum was the result of a
transfer from birds to humans.
Fig: phylogenetic tree of Plasmodium genus based
on SSU rRNA gene sequence data.
Waters et al., 1991 and 1993
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Subsequent analyses demonstrated that the closest sister taxon of P. falciparum
was Plasmodium reichenowi, a parasite isolated from a chimpanzee.
P. falciparum did not directly
originate from an avian
malarial parasite
escalante et al., 1998
The results of subsequent studies were contradictory
Closer to rodent or
primate Plasmodium
Closer to Avian
Plasmodium
Part of the confusion concerning the origin of P. falciparum arose because of:
• Biases in the representation of certain taxa,
• Small number of loci analysed and/or
• Improper rooting.
Perkins and Schall 2002; McCutchanet al., 1996
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Liu et al., 2010 Study: Revealed true evolutionary history of P. falciparum
 Utilized non invasive technique
 A large collection of fecal samples from:
• Three subspecies of chimpanzees
(P. t. troglodytes, P. troglodytes
ellioti), bonobos, and
• Two subspecies of gorillas
(subspecies G. gorilla gorilla and G.
gorilla graueri).
 Method of single template amplification to
sequence mitochondrial, apicoplastic, and
nuclear genes of Plasmodium isolates from
mixed infections.
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Phylogenetic evidences points to gorilla origin of Human P. falciparum
Single gorilla to
human cross-species
transmission
Liu et al., 2010
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Non-Laverania parasites form a separate clad
Liu et al., 2010
Plasmodium vivax Origin
Distribution correlated with the occurrence of Duffy negative phenotype
Fig: The world malaria map showing the distributional pattern of P. vivax
malaria across the continents (Guerra, et al., 2010). The black dots are
indicating the areas of high populations at risk of P. vivax infections.
Fig: Spatial distribution of Duffy negative phenotype
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P.vivax Origin
The Duffy antigen receptor for chemokines (DARC) is used by P. vivax trophozoits to invade RBCs
P. vivax
infection
No P. vivax
infection
T-33C point mutation leads to loss of expression of the gene in Erythrocytes thus Duffy
Negative phenotype.
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The consensus view has thus been that P. vivax emerged in Southeast
Asia following the cross-species transmission of a macaque parasite
Escalante et al., 2005
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Liu et al., 2014 : Large scale Molecular Phylogenetic study to reveal
the true history of P. vivax
Ape samples: highly endangered and live in remote forests regions thus
utilized fecal samples for detection and amplification of malaria parasite DNA.
5469 fecal samples from non-habituated Apes
998 Blood samples
from Macaques
Wild living
Chimpanzees (P.
troglodytus)
Western Gorillas
(G. gorilla)
Eastern
Gorillas
(G. beringei)
Liu et al., 2014
Bonobos (P. paniscus)
Human P. vivax arose from within a Plasmodium species that infects chimpanzees
and gorilla and indicate an origin in Africa rather than Asia (as previously assumed).
Ape P. vivax
Human P. vivax
Ape P. vivax
Liu et al., 2014
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Few Limitations of Molecular Phylogenetics
Available sequence data
Length of sequences and the choice of
genomic regions to be used in the
analysis
Continuous updation and reanalysis of
existing Phylogenetic relationships
Computing power required to handle
and analyze longer and longer
sequences involving more complex
Phylogenetic techniques
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Yet despite all these limitations Phylogenetics is currently a
rapidly expanding specialty, contributing useful insights to
the understanding of how diseases have evolved and how
they continue to evolve…. (Yuk Lam et al., 2010)
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