REJMANEK D, Hosseini PR, Mazet JA, Daszak P, et al. Evolutionary dynamics and global diversity of influenza A virus. J Virol. 2015 Aug 26. pii: JVI.01573-15.
The increasing number of zoonotic infections caused by influenza A virus (IAV) subtypes of avian origin in recent years (e.g. H5N1 and H7N9) underscores the need to better understand the factors driving IAV evolution and diversity. To evaluate the current feasibility of global analyses to contribute to this aim, we evaluated information in the public domain to explore IAV evolutionary dynamics including, nucleotide substitution rates and selection pressures, using 14 IAV subtypes in 32 different countries over a 12-year period (2000 - 2011). Using geospatial information from 39,785 IAV strains, we examined associations between subtype diversity and socio-economic, biodiversity, and agricultural indices. Our analyses showed that nucleotide substitution rates for 11 of the 14 evaluated subtypes tended to be higher in Asian countries, particularly those in East Asia, compared to Canada and the United States. Similarly at a regional level, subtypes H5N1, H5N2, and H6N2 exhibited significantly higher substitution rates in East Asia compared to North America. In contrast, the selection pressures (measured as dN/dS ratios) acting on individual subtypes showed little geographic variation. We found that the strongest predictors for the detected subtype diversity at the country level were reporting effort and healthcare spending (an indicator of economic development). Our analyses also identified major global gaps in IAV reporting (including lack of sequences submitted from large portions of Africa and South America, and lack of geolocation information) and broad subtype testing which, until addressed, will continue to hinder efforts to track the evolution and diversity of IAV around the world.
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