* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Mathematical modeling The dynamics of infection
Onchocerciasis wikipedia , lookup
West Nile fever wikipedia , lookup
Anaerobic infection wikipedia , lookup
Cross-species transmission wikipedia , lookup
Hookworm infection wikipedia , lookup
Neglected tropical diseases wikipedia , lookup
Herpes simplex wikipedia , lookup
African trypanosomiasis wikipedia , lookup
Henipavirus wikipedia , lookup
Middle East respiratory syndrome wikipedia , lookup
Eradication of infectious diseases wikipedia , lookup
Leptospirosis wikipedia , lookup
Trichinosis wikipedia , lookup
Sarcocystis wikipedia , lookup
Dirofilaria immitis wikipedia , lookup
Marburg virus disease wikipedia , lookup
Hepatitis C wikipedia , lookup
Schistosomiasis wikipedia , lookup
Human cytomegalovirus wikipedia , lookup
Sexually transmitted infection wikipedia , lookup
Coccidioidomycosis wikipedia , lookup
Hepatitis B wikipedia , lookup
Neonatal infection wikipedia , lookup
Mathematical modeling the dynamics of infection 1/47 Mathematical modeling The dynamics of infection Niel Hens www.simid.be FTNLS 24 April 2015 Mathematical modeling the dynamics of infection Overview 1 Prologue Introduction Discrete time models The basic reproduction number 2 Who acquires infection from whom? How it all started . . . The social contact approach Research based on social contact data 3 Epilogue Further research Discussion 2/47 Mathematical modeling the dynamics of infection Prologue Introduction Mathematical Modelling of Infectious Diseases Purposes: prediction: requires the inclusion of known complexities and population-level heterogeneity understanding: investigating the factors that drive dynamics Building a model presents a trade-off: accuracy: reproduce what is observed and predict future dynamics transparency: ability to understand how model components influence the dynamics and interact flexibility: ease of adapting the model to new situations 3/47 Mathematical modeling the dynamics of infection Prologue Introduction Mathematical Modelling of Infectious Diseases Limitations: models present a simplification of reality chance events of infectious disease transmission hinder perfect prediction A good model: suited to its purpose: simple as possible, but no simpler balance accuracy, transparency, flexibility parametrisable from available data 4/47 Mathematical modeling the dynamics of infection Prologue Introduction Mathematical Modelling of Infectious Diseases Daniel Bernoulli was the first to present a mathematical model for smallpox in 1760 Since then many people have developed models to describe infectious disease dynamics, see e.g. Bailey (1975); Anderson and May (1991); Grenfell and Dobson (1995); Daley and Gani (1999); Hethcote (2000) Historical perspectives by Klaus Dietz. 5/47 Mathematical modeling the dynamics of infection 6/47 Prologue Introduction Contacts between individuals Predicting the number of infections at time t + 1 based on the circumstance at time t The force of infection λ the per capita rate at which a susceptible individual contracts infection it is assumed proportional to the number of infectious persons at time t and depending on how the contact structure is assumed to change with population size N it is given by: λt = βIt λt = βIt /Nt Mathematical modeling the dynamics of infection Prologue Introduction Contacts between individuals The number of new infections at time t + 1 is given by λt St and thus: It+1 = βSt It It+1 = βSt It /Nt This is referred to as the mass action principle density-dependent transmission: It+1 = βSt It : - as the population size increases, so does the contact rate - mostly applicable to plant and animal diseases (homogeneity) frequency-dependent transmission: It+1 = βSt It /Nt : - the contact rate is assumed constant regardless of a change in population size - mostly applicable to human and vectorborne diseases (heterogeneity) 7/47 Mathematical modeling the dynamics of infection Prologue Introduction Contacts between individuals Heterogeneity airborne infections: age - example: children at school have more contacts with children of the same age sexually transmitted infections: age and sexual behavior temporal heterogeneity seasonality, week vs weekend, holiday vs non-holiday, . . . ... 8/47 Mathematical modeling the dynamics of infection Prologue Introduction Modeling Frameworks compartmental models the population is subdivided into broad subgroups (compartments) individuals are tracked collectively roughly either deterministic or stochastic (probabilistic) deterministic models describe what happens ‘on average’ in a population stochastic models allow the number of individuals who move between compartments to vary through chance transmission dynamic or static models microsimulation or agent-based models network models metapopulation models 9/47 Mathematical modeling the dynamics of infection 10/47 Prologue Discrete time models Discrete time deterministic models SIR compartmental model Equations: St+1 It+1 Rt+1 = St − λt St = It + λt St − νIt = Rt + νIt with Nt+1 = St+1 + It+1 + Rt+1 = St + It + Rt = Nt . λt = βIt and ν are risks risks are related to rates as follows: risk = 1 − e−rate Mathematical modeling the dynamics of infection Prologue Discrete time models Discrete time stochastic models The number of newly infected cases arises from a stochastic process with mean βIt St The number of newly recovered individuals arises from a stochastic process with mean νt It 0 50000 100000 150000 200000 250000 Our best option: the binomial distribution 1 9 18 29 40 51 62 73 84 95 107 121 135 149 163 11/47 Mathematical modeling the dynamics of infection 12/47 Prologue Discrete time models Discrete time models When do you expect the number of new infections to decrease? Focus on the second equation: It+1 = It + βIt St − νIt clearly It+1 = It if βSt = ν The epidemic will die out if St < ν/β continue if St > ν/β At the start of an epidemic in a susceptible population: S0 = N The epidemic will die out if N β/ν < 1 take of if N β/ν > 1 Mathematical modeling the dynamics of infection 13/47 Prologue The basic reproduction number The basic reproduction number Consider the total number of new infections in the population between time t and t + 1: βIt St At the start of an epidemic, say t = 0: I0 = 1 and S0 = N and thus the total number of new infections between t = 0 and t = 1 equals βN By the end of the infectious period of duration D = 1/ν time units, the infectious person would have infected βN D individuals N βD is called the basic reproduction number R0 Therefore R0 is the number of secondary cases caused by a single infective introduced into a wholly susceptible population of size N during the infective’s infectious period. Mathematical modeling the dynamics of infection Prologue The basic reproduction number The basic reproduction number R0 constitutes a threshold: if R0 > 1 then the epidemic can grow if R0 ≤ 1 then the epidemic will die out Using R0 , one defines the number of effective contacts by each person per unit time by ce = R0 /D. Therefore β = ce /N is the “per capita number of effective contacts made by a given individual per unit time”, or equivalently “the per capita rate at which two specific individuals come into effective contact per unit time” For a given pathogen, it is difficult to define an effective contact 14/47 Mathematical modeling the dynamics of infection 15/47 Prologue The basic reproduction number The herd immunity threshold The epidemic will die out if St < ν/beta: Equivalently st R0 < 1, where st = St /N Re = st R0 is called the effective reproduction number Monitoring an epidemic is best done using Re Vaccination: lowering st → control: Re < 1 Critical vaccination coverage pc = 1 − 1/R0 . Examples: Measles: R0 = 20 → pc = 0.95, Varicella R0 = 8 → pc = 0.875 But issues of primary and secondary vaccine failure complicate matters Mathematical modeling the dynamics of infection 16/47 Who acquires infection from whom? How it all started . . . Who Acquires Infection From Whom? Many infections are transmitted by contact or air Influenza, Varicella, Measles, Parvovirus B19, . . . The transmission rate β depends on person-to-person contact c the probability of transmission given a contact q but this is not the same for everyone β ≡ β(a, a0 ) = q(a, a0 ) × c(a, a0 ) Two decades ago math. convenient WAIFW-structures (Anderson and May, 1991) Mathematical modeling the dynamics of infection 17/47 Who acquires infection from whom? How it all started . . . Who Acquires Infection From Whom? Heterogeneity: Age The age-heterogeneous mass action principle: ND λ(a) = L Z L A 0 0 β(a, a )λ(a ) exp − Z a0 A ! λ(s)ds da0 with life expectancy L, population size N and mean infectious period D and age A the age of maternal antibody loss The Next Generation Operator The operator that defines the next generation of infected individuals g(a, a0 ) = ND β(a, a0 ) L Mathematical modeling the dynamics of infection Who acquires infection from whom? How it all started . . . Who Acquires Infection From Whom? Basic reproduction number R0 The dominant eigenvalue of the ‘next generation operator’ Initial Spread Simulate the initial epidemic phase by iterating the next generation operator Identical to the right eigenvector of that operator 18/47 Mathematical modeling the dynamics of infection Who acquires infection from whom? How it all started . . . The Traditional ‘WAIFW’ approach Discretization into several age-categories Anderson and May (1991): mixing patterns impose mixing pattern on βij constrain # distinct elements based on prior knowledge of social mixing behaviour 19/47 Mathematical modeling the dynamics of infection 19/47 Who acquires infection from whom? How it all started . . . The Traditional ‘WAIFW’ approach Discretization into several age-categories Anderson and May (1991): mixing patterns age age age age class class class class 1→ 2→ 3→ 4→ age class 1 ↓ β1 β4 β4 β4 age class 2 ↓ β4 β2 β4 β4 age class 3 ↓ β4 β4 β3 β4 age class 4 ↓ β4 β4 β4 β4 Mathematical modeling the dynamics of infection 19/47 Who acquires infection from whom? How it all started . . . The Traditional ‘WAIFW’ approach Discretization into several age-categories Anderson and May (1991): mixing patterns age age age age class class class class 1→ 2→ 3→ 4→ age class 1 ↓ β1 β1 β3 β4 age class 2 ↓ β1 β2 β3 β4 age class 3 ↓ β3 β3 β3 β4 age class 4 ↓ β4 β4 β4 β4 Mathematical modeling the dynamics of infection Who acquires infection from whom? How it all started . . . The Traditional ‘WAIFW’ approach Anderson and May (1991): mixing patterns → disadvantages: low dimensional matrices non-realistic discontinuities choice age classes: ad hoc Farrington and Whitaker (2005): continuous contact surface → both methods rely on strong parametric assumptions Wallinga et al. (2006): use data on social contacts to inform estimation of age-dependent transmission rates 20/47 Mathematical modeling the dynamics of infection 21/47 Who acquires infection from whom? The social contact approach Social Contact hypothesis Social contact hypothesis (Wallinga et al., 2006) β(a, a0 ) @ @ R @ c(a, a0 ) k k proportionality constant contact rate @ estimation R @ serological survey social contact survey q · Mathematical modeling the dynamics of infection Who acquires infection from whom? The social contact approach Social Contact Approach Alternative approach: Using data on social contacts to estimate age-specific transmission parameters for respiratory-spread infectious agents. Objectives Disentangle contact behaviour from transmission process Get insights in predictiveness of social contact data Get new insights in the transmission process 22/47 Mathematical modeling the dynamics of infection 23/47 Who acquires infection from whom? The social contact approach Social Contact Survey Wallinga et al. (2006): Utrecht POLYMOD pilot study: Beutels et al. (2006) main study: Mossong et al. (2008) PLoS MEDICINE Social Contacts and Mixing Patterns Relevant to the Spread of Infectious Diseases Joël Mossong1,2*, Niel Hens3, Mark Jit4, Philippe Beutels5, Kari Auranen6, Rafael Mikolajczyk7, Marco Massari8, Stefania Salmaso8, Gianpaolo Scalia Tomba9, Jacco Wallinga10, Janneke Heijne10, Malgorzata Sadkowska-Todys11, Magdalena Rosinska11, W. John Edmunds4 1 Microbiology Unit, Laboratoire National de Santé, Luxembourg, Luxembourg, 2 Centre de Recherche Public Santé, Luxembourg, Luxembourg, 3 Center for Statistics, Hasselt University, Diepenbeek, Belgium, 4 Modelling and Economics Unit, Health Protection Agency Centre for Infections, London, United Kingdom, 5 Unit Health Economic and Modeling Infectious Diseases, Center for the Evaluation of Vaccination, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium, 6 Department of Vaccines, National Public Health Institute KTL, Helsinki, Finland, 7 School of Public Health, University of Bielefeld, Bielefeld, Germany, 8 Istituto Superiore di Sanità, Rome, Italy, 9 Department of Mathematics, University of Rome Tor Vergata, Rome, Italy, 10 Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands, 11 National Institute of Hygiene, Warsaw, Poland Funding: This study formed part of POLYMOD, a European Commission project funded within the Sixth Framework Programme, Contract number: SSP22-CT-2004–502084. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ABSTRACT (WoK: 400 citations) Competing Interests: The authors have declared that no competing interests exist. Background Mathematical modelling of infectious diseases transmitted by the respiratory or close-contact route (e.g., pandemic influenza) is increasingly being used to determine the impact of possible interventions. Although mixing patterns are known to be crucial determinants for model outcome, researchers often rely on a priori contact assumptions with little or no empirical basis. We conducted a population-based prospective survey of mixing patterns in eight European countries using a common paper-diary methodology. Mathematical modeling the dynamics of infection 24/47 Who acquires infection from whom? The social contact approach Social Contact Survey Belgian Contact Survey Part of POLYMOD project Period March - May 2006 750 participants, selected through random digit dialing Diary-based questionnaire Two main types of contact: non-close and close contacts Hens et al. (2009a,b) Total of 12775 contacts (≈ 16 contacts per person per day) Mathematical modeling the dynamics of infection 25/47 Who acquires infection from whom? The social contact approach 0 e ag t ac nt pa rti co ci pa e ag nt 20 te ct ra age contact ta con 40 60 Mixing Patterns 0 20 40 age participant Assortative mixing with clear (grand)parent-(grand)child components Divergence for work contacts 60 Mathematical modeling the dynamics of infection Who acquires infection from whom? The social contact approach EU mixing patterns common structure note the converging off-diagonals: parents get older 26/47 Mathematical modeling the dynamics of infection 27/47 Who acquires infection from whom? Research based on social contact data Serology and social contacts Modeling Infectious Disease Parameters Based on Serological and Social Contact Data A Modern Statistical Perspective Mathematical epidemiology of infectious diseases usually involves describing the flow of individuals between mutually exclusive infection states. One of the key parameters describing the transition from the susceptible to the infected class is the hazard of infection, often referred to as the force of infection. The force of infection reflects the degree of contact with potential for transmission between infected and susceptible individuals. The mathematical relation between the force of infection and eff ective contact patterns is generally assumed to be subjected to the mass action principle, which yields the necessary information to estimate the basic reproduction number, another key parameter in infectious disease epidemiology. It is within this context that the Center for Statistics (CenStat, I-Biostat, Hasselt University) and the Centre for the Evaluation of Vaccination and the Centre for Health Economic Research and Modelling Infectious Diseases (CEV, CHERMID, Vaccine and Infectious Disease Institute, University of Antwerp) have collaborated over the past 15 years. This book demonstrates the past and current research activities of these institutes and can be considered to be a milestone in this collaboration. This book is focused on the application of modern statistical methods and models to estimate infectious disease parameters. We want to provide the readers with software guidance, such as R packages, and with data, as far as they can be made publicly available. Varicella Ogunjimi et al. (2009) Statistics / Life Sciences, Medicine, Health Sciences ISBN 978-1-4614-4071-0 9 781461 440710 SBH 1 Modeling Infectious Disease Parameters Based on Serological and Social Contact Data Hens et al. (2012) −→ Statistics for Biology and Health Niel Hens · Ziv Shkedy · Marc Aerts · Christel Faes · Pierre Van Damme · Philippe Beutels Hens · Shkedy · Aerts Faes · Van Damme · Beutels Using social contact surveys in statistical and mathematical models Statistics for Biology and Health Niel Hens · Ziv Shkedy Marc Aerts · Christel Faes Pierre Van Damme · Philippe Beutels Modeling Infectious Disease Parameters Based on Serological and Social Contact Data A Modern Statistical Perspective Goeyvaerts et al. (2010) 5.64 4.21 4.79 5.37 6.07 • ( • • × • 6 W4 6 6 M1 gL MA 66 M2 g MA 6 ) 6 MA gR MA 8.26 8.68 • • 14.08 • 15.69 • M3 C3 SA C1 6 6 6 6 Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data School Closure most effective social distancing measure previous analyses were based on assumptions or sentinel data (see e.g. Cauchemez et al., 2008) use contact data to quantify the reduction in R0 POLYMOD data use the holiday period as a proxy for school closure: 17% reduction use the weekend as a proxy for social distancing: 21% reduction Hens et al. (2009a) school closure: huge economic impact Keogh-Brown et al. (2010a,b) 28/47 Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data School Closure global school closure and its impact on the health care system Cauchemez et al. (2009) Could reactive school closure alleviate the burden upon the NHS critical care capacity during the H1N1 influenza pandemic? mathematical influenza model UK contact data (holiday pattern as a proxy) timing is crucial! in the most realistic situation 12% over maximum capacity House et al. (2011) 29/47 Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data Contact patterns during illness Van Kerckhove et al. (2013): study in the UK people were asked to record their contacts when ill (H1N1-diagnosis - lab-confirmed) when healthy (few weeks later) 30/47 Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data Contact patterns during illness 31/47 Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data Contact patterns during illness assuming 1/3-2/3 asymptomatic individuals (Carrat et al., 2008) 32/47 Inc Inc Mathematical modeling the dynamics of infection 33/47 Who acquires infection from whom? 20 20 Research based on social contact data Contact patterns during illness 0 0−3 4−10 11−21 22−45 46−64 Age, years ≥65 0−3 4−10 11−21 22−45 46−64 Age, years ≥65 Figure 3. Age distribution of cases in the early stages of the 2009 A/H1N1pdm influenza epidemic as predicted by asymptomatic contact pat- terns (left; n = 140) and symptomatic contact patterns (right; n = 140) in the paired data set, assuming full susceptibility in the population, England, fitted to age-specific relative ILI incidence during exponential phase 2009–2010. The indicated 95% confidence intervals (T-shaped bars) were obtained using a nonparametric bootstrap. Because of the skewness of the underlying distributions, the mean values are not in the middle of the intervals. 2009 A/H1N1pandemic in the UK results: them continued to engage in normal social activities, there would have been a large increase in transmission. work and social distancing for persons with symptoms. It appears that during the A/H1N1pdm epidemic, symptomatic persons were, in general, sufficiently unwell that they moderated their social behavior; had a substantial fraction of symptomatic individuals are 3 to 12R istimes asmeasure infectious a common of viral fitness (26). Using this 0 measure, we have demonstrated that there is a considerable symptomatic individuals cause 66% of all infections 80 80 φ =0 φ = 0.5 φ =1 60 Incidence, % Incidence, % 60 All Contacts Skin-to-Skin Contacts Long-Duration Contacts 40 20 40 20 0 0 0 20 40 Age, years 60 80 0 20 40 60 80 Age, years Figure 4. Theory (left) and fit (right) of a model to the observed age distribution from general practitioners’ consultation data from England and Wales for the early phase of the 2009 A/H1N1pdm influenza pandemic (black dots), England, 2009–2010. The left-hand panel shows different φ values (assuming q = 1, for illustration) leading to different age distributions. The right-hand panel shows the fit obtained using the best-fitting Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data Preferential transmission Account for pre-clinical subclinical infectious period subclinical/asymptomatic infections Investigate the role of carrying over high viral loads viral load ∼ infectiousness (intranasal dose: Keitel et al., 1990) viral load ∼ symptoms (Carrat et al., 2008) transfer? supported indirectly by challenge studies & empirical evidence for other infections Simplistic approach: compartmental models (a)symptomatic infections (Ejima et al., 2013) preferential transmission 34/47 asymptomatic and moves into the ! compartment at rate (1 − !)!! . Finally, asymptomatic Mathematical modeling the dynamics of infection 35/47 acquires to infection whom? casesWhomove the from ! compartment at rate ! ! and symptomatic cases become recovered at rate Research based on social contact data ! ! . Figure 2 shows a schematic diagram of the preferential transmission model. The corresponding system of ODEs is available in Appendix. Preferential transmission !! !! # !! !!! # !!! !!# !! (1 − !)!! S# R# (1 − !)!! !! !!! # !! # !! !!# !! !!! Figure 2. Schematic diagram of the preferential compartmental transmission model. Superscripts indicate clinical status of the infectee: symptomatic (s) or asymptomatic (a). Subscripts indicate whether the infector was symptomatic (s) or not (a). In this paper it is assumed that !! = !! = ! and !! = !! = !. Under these assumptions, the preferential transmission model simplifies to the non-preferential transmission model if ! = 1 − !. In Section 2.2, a social contact network between different age groups is introduced which allows using social contact data of ill and healthy people to describe the Mathematical modeling the dynamics of infection 36/47 Who acquires infection from whom? Research based on social contact data Preferential transmission: results Non-preferential transmission if φ = 1 − φ̃ φ̃ = 0.4209 (95% CI : 0.3258, 0.5222) 1 − φ = 0.1618 (95% CI : 0.1227, 0.2103) Sensitivity analysis 12 scenarios (estimated - referenced values) best scenario (γ, θ, σ a , σ s ) = {(1.5, 0.5, 1, 5.6)days}−1 φ̃ = 0.5706 (95% CI : 0.4784, 0.6583) 1 − φ = 0.2664 (95% CI : 0.2187, 0.3203) Outcome rel. trans. of symptomatic individuals is 2.87 (95% CI: 2.20, 3.73) evidence suggests preferential transmission is possible Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data Preferential transmission: control strategies Isolation (at home) 37/47 Mathematical modeling the dynamics of infection 38/47 Who acquires infection from whom? Research based on social contact data Susceptibility patterns for H1N1 in Vietnam household-based survey in rural Vietnam 80 80 264 households 3.0 1.2 60 1.0 60 2.5 0.8 0.6 40 contact's age 40 1.5 0.4 20 20 1.0 0.2 0 0.5 0 contact's age 2.0 0 20 40 participant's age 60 80 0 20 40 participant's age 60 80 Mathematical modeling the dynamics of infection 39/47 Who acquires infection from whom? Research based on social contact data Susceptibility patterns for H1N1 in Vietnam 0.8 0.8 0.8 1.0 H1N1 incidence 1.0 Seroprevalence post−H1N1 1.0 Seroprevalence pre−H1N1 20 40 ● ● 60 80 0.6 0.6 incidence ● 0.4 ●● 0 ● ● 20 40 60 age eigenvector (susc) eigenvector ● ● 80 0 0.20 60 80 ratio of incidence and eigenvector → q(a) 8 q(a) ● 6 ● ● 0 ● 20 40 age 60 80 0 ● ● 2 ● 20 40 age 60 80 ● 0 ● 0.05 ● 0 serial seroprevalence → H1N1 incidence estimate q(a) ● ● 4 incidence 40 0.10 ● ● ● ● 0.15 0.20 0.15 ● 0.10 incidence ● 20 ● age 10 age ● ●● 0.2 ● 0.0 ● 0.4 seroprevalence ● ● 0 ● 0.0 ●● 0.2 0.6 0.4 0.0 0.2 seroprevalence ● ● 20 ● ● 40 age ● 60 ● 80 Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data Comparative analysis of the spread of H1N1 in Europe relative incidence example UK: 40/47 Mathematical modeling the dynamics of infection Who acquires infection from whom? Research based on social contact data Comparative analysis of the spread of H1N1 in Europe based on the European contact data estimating the relative susceptibility meta-analysis over countries 41/47 Mathematical modeling the dynamics of infection 42/47 Who acquires infection from whom? Research based on social contact data Inferring networks from egocentric data households of size 4 egocentric data latent network 64 possible networks 63 parameters 4 × 23 = 32 observations penalized likelihood approach Potter and Hens (2013) Mathematical modeling the dynamics of infection Epilogue Further research Further research Serology-contact papers Goeyvaerts et al. (2011): immunological processes for B19 Santermans et al. (2014): inferring infectivity from serology Hens et al. (2009c); Abrams et al. (2014): frailty models Other contact-related work Willem et al. (2012): Weather & contacts Grijalva et al. (2014): Contact Patterns in Peru Goeyvaerts et al. (in prep): Household contact survey in Flanders Van Kerckhove et al. (in prep): Spatial networks of social contacts Luca et al. (in prep): A spatio-temporal model of social contacts Béraud et al. (in prep): Social contacts in France: temporal effects ... 43/47 Mathematical modeling the dynamics of infection Epilogue Discussion Discussion Infectious disease dynamics mass action principle contact data prove to be useful new epidemiological hypotheses Bruges 2015: 7-11 September 2015: 2nd network course by Martina Morris and colleagues 6th SIMID course (www.simid.be; Hens et al. (2012)) 44/47 Mathematical modeling the dynamics of infection Epilogue Discussion Acknowledgements All colleagues @CenStat and Vaxinfectio All collaborating centres nationally and internationally John Edmunds, Ken Eames, Stefan Flasche (London School of Hygiene and Tropical Medicine, UK) Peter Horby (Oxford University, UK) Thomas House (University of Warwick, UK) Gail Potter (University of Washington, US) Chair in evidence-based vaccinology 45/47 Mathematical modeling the dynamics of infection Epilogue Discussion Selected references I Abrams, S., Beutels, P., and Hens, N. (2014). Assessing mumps outbreak risk in highly vaccinated populations using spatial seroprevalence data. Am J Epidemiol, 179(8):1006–1017. Anderson, R. and May, R. (1991). Infectious Diseases of Humans: Dynamics and Control. Oxford University Press, Oxford. Bailey, N. (1975). The Mathematical Theory of Infectious Diseases and its Applications. Charles Griffin and Company, London. Carrat, F., Vergu, E., and Ferguson, N. e. a. (2008). Time lines of infection and disease in human influenza: a review of volunteer challenge studies. Am, 167(7):775–785. Cauchemez, S., Ferguson, N. M., Wachtel, C., Tegnell, A., Saour, G., Duncan, B., and Nicoll, A. (2009). Closure of schools during an influenza pandemic. Lancet Infect Dis, 9(8):473–481. Cauchemez, S., Valleron, A.-J., Boëlle, P.-Y., Flahault, A., and Ferguson, N. M. (2008). Estimating the impact of school closure on influenza transmission from sentinel data. Nature, 452(7188):750–754. Daley, D. and Gani, J. (1999). Epidemic Modelling: An Introduction. Cambridge University Press. Ejima, K., Aihara, K., and Nishiura, H. (2013). The impact of model building on the transmission dynamics under vaccination: observable (symptom-based) versus unobservable (contagiousness-dependent) approaches. PLoS One, 8(4):e62062. Farrington, C. and Whitaker, H. (2005). Contact surface models for infectious diseases: estimation from serologic survey data. Journal of the American Statistical Association, 100:370 – 379. Goeyvaerts, N., Hens, N., Aerts, M., and Beutels, P. (2011). Model structure analysis to estimate basic immunological processes and maternal risk for parvovirus B19. Biostatistics, 12(2):283–302. Goeyvaerts, N., Hens, N., Ogunjimi, B., Aerts, M., Shkedy, Z., Van Damme, P., and Beutels, P. (2010). Estimating infectious disease parameters from data on social contacts and serological status. Journal of the Royal Statistical Society Series C, 59:255–277. Grenfell, B. and Dobson, A. (1995). Ecology of Infectious Disease in Natural Populations. Cambridge, UK: Cambridge University Press. Hens, N., Ayele, G. M., Goeyvaerts, N., Aerts, M., Mossong, J., Edmunds, J. W., and Beutels, P. (2009a). Estimating the impact of school closure on social mixing behaviour and the transmission of close contact infections in eight European countries. BMC Infectious Diseases, 9:187. Hens, N., Goeyvaerts, N., Aerts, M., Shkedy, Z., Damme, P. V., and Beutels, P. (2009b). Mining social mixing patterns for infectious disease models based on a two-day population survey in Belgium. BMC Infectious Diseases, 9:5. Hens, N., Shkedy, Z., Aerts, M., Faes, C., Van Damme, P., and Beutels, P. (2012). Modeling Infectious Disease Parameters Based on Serological and Social Contact Data. A Modern Statistical Perspective. Statistics for Biology and Health. Springer, New York. 46/47 Mathematical modeling the dynamics of infection Epilogue Discussion Selected references II Hens, N., Wienke, A., Aerts, M., and Molenberghs, G. (2009c). The correlated and shared gamma frailty model for bivariate current status data: an illustration for cross-sectional serological data. Stat Med, 28(22):2785–2800. Hethcote, H. (2000). The mathematics of infectious diseases. SIAM REview, 42(4):599–653. House, T., Baguelin, M., Hoek, A. J. V., White, P. J., Sadique, Z., Eames, K., Read, J. M., Hens, N., Melegaro, A., Edmunds, W. J., and Keeling, M. J. (2011). Modelling the impact of local reactive school closures on critical care provision during an influenza pandemic. Proc Biol Sci. Keitel, W. A., Couch, R. B., Cate, T. R., Six, H. R., and Baxter, B. D. (1990). Cold recombinant influenza b/texas/1/84 vaccine virus (crb 87): attenuation, immunogenicity, and efficacy against homotypic challenge. J Infect Dis, 161(1):22–26. Keogh-Brown, M. R., Smith, R. D., Edmunds, J. W., and Beutels, P. (2010a). The macroeconomic impact of pandemic influenza: estimates from models of the united kingdom, france, belgium and the netherlands. Eur J Health Econ, 11(6):543–554. Keogh-Brown, M. R., Wren-Lewis, S., Edmunds, W. J., Beutels, P., and Smith, R. D. (2010b). The possible macroeconomic impact on the uk of an influenza pandemic. Health Econ, 19(11):1345–1360. Ogunjimi, B., Hens, N., Goeyvaerts, N., Aerts, M., Damme, P. V., and Beutels, P. (2009). Using empirical social contact data to model person to person infectious disease transmission: an illustration for varicella. Mathematical Biosciences, 218(2):80–87. Van Kerckhove, K., Hens, N., Edmunds, W. J., and Eames, K. T. D. (2013). The impact of illness on social networks: implications for transmission and control of influenza. Am J Epidemiol, 178(11):1655–1662. Wallinga, J., Teunis, P., and Kretzschmar, M. (2006). Using data on social contacts to estimate age-specific transmission parameters for respiratory-spread infectious agents. American Journal of Epidemiology, 164:936–944. Willem, L., Van Kerckhove, K., Chao, D. L., Hens, N., and Beutels, P. (2012). A nice day for an infection? weather conditions and social contact patterns relevant to influenza transmission. PLoS One, 7(11):e48695. 47/47