Project Summary
As the highly pathogenic H5N1 avian influenza virus (AIV) continues to spread across Asia, Africa, and Europe, scientists and public health officials are trying to determine where in the world pandemic flu could emerge. A new and innovative approach to answer the “where?” of pandemic AIV employs spatially integrated population, environmental, and genetic information. The influenza virus evolves at different rates in different places, explaining both similarity and dissimilarity of strains isolated worldwide. It is hypothesized that changes in AIV could lead to rapid animal-to-human and then human-to-human transmission and that they are driven by both anthropogenic and environmental factors. In other words, there exist regional ecosystems that encourage or facilitate faster or more radical AIV evolution. To explore this hypothesis, this project uses computational genetics and geographic approaches to build a public, spatially referenced AIV genotype database and then investigate relationships between human-environment factors and AIV evolution.
The specific objectives are to: (1) Classify influenza viral genotypes using their genomic sequence data; (2) Construct an Influenza Genotype-Geographic Database (IGGD) of viruses and hypothesized population-environment drivers; and (3) Analyze the impacts of human-environment ecosystem factors on influenza viral evolution. As a result, this project is generating a systematic description of the spatio-temporal patterns of influenza viral genotypes and enhancing our understanding of ecosystem drivers of influenza viral evolution.
Project Team Members
Michael Emch
Aaron Moody
Margaret Carrel
Publications
Carrel, M; Wan, X-F; Nguyen, T; Emch, M (submitted) H5N1 Avian Influenza Viruses Exhibit Few Barriers to Gene Flow in Vietnam.
Carrel, M; Wan, X-F; Nguyen, T; Emch, M. (2011) Genetic variation of highly pathogenic H5N1 avian influenza viruses in Vietnam shows both species-specific and spatiotemporal associations. Avian Diseases. 55(4): 659-666. link to article
Carrel, M; Emch, M; Jobe, RT; Moody, A; Wan, X-F. (2010) Spatio-temporal structure of molecular evolution of H5N1 highly pathogenic avian influenza in Vietnam. PLoS One. 5(1): e8631. link to article
Wan, X-F; Nguyen, T; Smith, C; Zhao, Z; Carrel, M; Davis, C; Balish, A; Luo, F; Emch, M; Klimov, A; Donis, R. (2008) Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between 2001 and 2007. PLoS One. 3(10): 1-12. link to article
Wan, X-F; Chen, G; Luo, F; Emch, M; Donis, R. (2007) A quantitative genotype algorithm reflecting H5N1 avian influenza niches. Bioinformatics. 23(18): 2368-2375. link to article
Wan, XF; Wu, XM; Lin, G; Holton, SB; Desmone, RA; Shyu, CR; Guan, Y; Emch, M. (2007) Computational identification of reassortments in avian influenza viruses. Avian Diseases. 51: 434-439. link to article
Funding
National Science Foundation, BCS Program, “The geography of avian influenza evolution: Spatio-temporal relationships between virus genes and human-environment factors.” 2007-10.
Collaborating Institutions
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