The overall goal of this project is to develop and validate novel methods to perform joint inference from combined epidemiologic and genetic data. This inference methodology seeks to provide estimates of fundamental transmission parameters, such as RO, as well as provide estimates of unobserved transmission trees and unobserved counts of susceptible, infected and recovered individuals in the population through time. We focus on two common scenarios. In the first, we target densely sampled, but localized, epidemiologic and genetic data, in which the person, place and time are known, and in which pathogen genetic samples are obtained. These sorts of datasets are commonly generated during transmission studies in households, schools, and similar settings, but also in analyses of novel outbreaks such as SARS or H7N9. Our inference framework seeks to estimate host-to-host transmission networks from combined epidemiologic and genetic data. In the second scenario, we target sparsely sampled, but broader in scope, epidemiologic and genetic data, in which we observe a time series of case reports and sparsely sampled pathogen genetic sequences. In this inference framework, we seek to model population-level transmission processes from a relatively small samples of cases. This framework utilizes coalescent theory to extrapolate from sampled genetic sequences to population-level dynamics. In implementation, we plan to utilize sophisticated inference methodology that combines Markov chain Monte Carlo (MCMC) and sequential Monte Carlo (SMC) approaches in what's termed particle MCMC (PMCMC). We plan to utilize these novel inference methods to investigate transmission heterogeneity and local transmission structure in influenza, phenomena that have been difficult to fully analyze without a combined epidemiologic and genetic inference framework in place.

Public Health Relevance

As sequencing becomes increasingly ubiquitous, the ability to combine epidemiologic and genetic data will become increasingly relevant, and appropriate statistical tools will be become increasingly necessary. The methods developed in this project will have direct public health relevance in that they will allow better estimates of critical transmission parameters, such as RO, better reveal risk factors for transmission and provide knowledge of transmission heterogeneity and local transmission structure.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center--Cooperative Agreements (U54)
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Special Emphasis Panel (ZGM1-BBCB-5 (MI))
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Fred Hutchinson Cancer Research Center
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Faulkner, James R; Minin, Vladimir N (2018) Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors. Bayesian Anal 13:225-252
Ma, Mai-Juan; Liu, Cheng; Wu, Meng-Na et al. (2018) Influenza A(H7N9) Virus Antibody Responses in Survivors 1 Year after Infection, China, 2017. Emerg Infect Dis 24:663-672
Lee, Juhye M; Huddleston, John; Doud, Michael B et al. (2018) Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. Proc Natl Acad Sci U S A 115:E8276-E8285
Viboud, Cécile; Sun, Kaiyuan; Gaffey, Robert et al. (2018) The RAPIDD ebola forecasting challenge: Synthesis and lessons learnt. Epidemics 22:13-21
Pavía-Ruz, Norma; Diana Patricia Rojas; Salha Villanueva et al. (2018) Seroprevalence of Dengue Antibodies in Three Urban Settings in Yucatan, Mexico. Am J Trop Med Hyg 98:1202-1208
Massaro, Emanuele; Ganin, Alexander; Perra, Nicola et al. (2018) Resilience management during large-scale epidemic outbreaks. Sci Rep 8:1859
Yang, Yang; Meng, Ya; Halloran, M Elizabeth et al. (2018) Dependency of Vaccine Efficacy on Preexposure and Age: A Closer Look at a Tetravalent Dengue Vaccine. Clin Infect Dis 66:178-184
Ho, Lam Si Tung; Xu, Jason; Crawford, Forrest W et al. (2018) Birth/birth-death processes and their computable transition probabilities with biological applications. J Math Biol 76:911-944
Liu, Quan-Hui; Ajelli, Marco; Aleta, Alberto et al. (2018) Measurability of the epidemic reproduction number in data-driven contact networks. Proc Natl Acad Sci U S A 115:12680-12685
Gallagher, Molly E; Brooke, Christopher B; Ke, Ruian et al. (2018) Causes and Consequences of Spatial Within-Host Viral Spread. Viruses 10:

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