The goal of this research is to develop a quantitative understanding of the dynamics of pathogens such as influenza and dengue that exhibit strain variation. We will use this understanding to design strategies for vaccination and control of these infections. The evolution of these pathogens is affected by two factors. The first is the generation of variation in the virus. This is determined by the molecular constraints that limit the mutations tolerated by the virus. The second is the selection that operates on the generated variation. This is determined by both the fitness of the virus and the immune status of individuals in the population. Understanding the selective forces on the virus is complicated by population heterogeneity which arises from previous exposure of individuals to different numbers of strains and their antigenic composition. Consequently we will take a multi-scale approach that integrates key processes at three scales: (i) Evolutionary changes in the virus. At the molecular level we will use computational models to predict how mutations in the key proteins of the influenza virus affect its fitness. In doing so we will determine the extent to which molecular constraints limit virus evolution. (ii) Within-host dynamics of influenza infections. We will develop models for the dynamics of infection and immunity in an individual. These models will allow us to determine how infection with influenza changes the level of immunity and how this impacts the dynamics of infection following exposure to new virus strains. These models will be applied to understanding the generation of immunity following vaccination with the killed subunit vaccine as well as the live attenuated virus. In doing so we hope to optimize the choice of strains to include in annual influenza vaccination programs and in the longer term help design universal influenza vaccines that provide protection against all strains. (iii) Epidemiological models that track the generation and spread when multiple virus strains in the population of individual with different and changing levels of immunity.

Public Health Relevance

This project develops computational models for understanding and predicting the dynamics of pathogens such as influenza and dengue that exhibit strain variation. This will help the public health community with the design and choice of vaccines and other control measures for these pathogens. This project will integrate with the other proposed Center activities for predicting and controlling evolving pathogens.

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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Feldstein, Leora R; Matrajt, Laura; Elizabeth Halloran, M et al. (2016) Extrapolating theoretical efficacy of inactivated influenza A/H5N1 virus vaccine from human immunogenicity studies. Vaccine 34:3796-802
Bento, Ana I; Rohani, Pejman (2016) Forecasting Epidemiological Consequences of Maternal Immunization. Clin Infect Dis 63:S205-S212
Xue, Katherine S; Hooper, Kathryn A; Ollodart, Anja R et al. (2016) Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. Elife 5:e13974
Koepke, Amanda A; Longini Jr, Ira M; Halloran, M Elizabeth et al. (2016) PREDICTIVE MODELING OF CHOLERA OUTBREAKS IN BANGLADESH. Ann Appl Stat 10:575-595
Ngwa, Moise C; Liang, Song; Kracalik, Ian T et al. (2016) Cholera in Cameroon, 2000-2012: Spatial and Temporal Analysis at the Operational (Health District) and Sub Climate Levels. PLoS Negl Trop Dis 10:e0005105
Chao, Dennis L; Dimitrov, Dobromir T (2016) Seasonality and the effectiveness of mass vaccination. Math Biosci Eng 13:249-59
Neher, Richard A; Bedford, Trevor; Daniels, Rodney S et al. (2016) Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Proc Natl Acad Sci U S A 113:E1701-9
Chen, Wan-Jun; Lai, Sheng-Jie; Yang, Yang et al. (2016) Mapping the Distribution of Anthrax in Mainland China, 2005-2013. PLoS Negl Trop Dis 10:e0004637
Fang, Li-Qun; Yang, Yang; Jiang, Jia-Fu et al. (2016) Transmission dynamics of Ebola virus disease and intervention effectiveness in Sierra Leone. Proc Natl Acad Sci U S A 113:4488-93
Magpantay, F M G; Domenech DE Cellès, M; Rohani, P et al. (2016) Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity. Parasitology 143:835-49

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