Journal
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
Volume 280, Issue 1750, Pages -Publisher
ROYAL SOC
DOI: 10.1098/rspb.2012.2173
Keywords
influenza A virus; transmission; evolution; phylogeny; phylodynamics
Categories
Funding
- NIH [2 R01 GM080533-06]
- Alborada Trust
- RAPIDD program of the Science and Technology Directorate, Department of Homeland Security
- Fogarty International Center, National Institutes of Health
- MRC [G0801822] Funding Source: UKRI
- Medical Research Council [G0801822, G0801056B] Funding Source: researchfish
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Influenza A viruses (IAVs) cause acute, highly transmissible infections in a wide range of animal species. Understanding how these viruses are transmitted within and between susceptible host populations is critical to the development of effective control strategies. While viral gene sequences have been used to make inferences about IAV transmission dynamics at the epidemiological scale, their utility in accurately determining patterns of inter-host transmission in the short-term-i.e. who infected whom-has not been strongly established. Herein, we use intra-host sequence data from the viral HA1 (hemagglutinin) gene domain from two transmission studies employing different IAV subtypes in their natural hosts-H3N8 in horses and H1N1 in pigs-to determine how well these data recapitulate the known pattern of inter-host transmission. Although no mutations were fixed over the course of either experimental transmission chain, we show that some minor, transient alleles can provide evidence of host-to-host transmission and, importantly, can be distinguished from those that cannot.
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