Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation

J. Conrad Stack, Pablo R. Murcia, Bryan T. Grenfell, James L.N. Wood, Edward C. Holmes

Research output: Contribution to journalArticlepeer-review

36 Scopus citations


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 showthat some minor, transient alleles can provide evidence of host-to-host transmission and, importantly, can be distinguished from those that cannot.

Original languageEnglish (US)
Article number20122173
JournalProceedings of the Royal Society B: Biological Sciences
Issue number1750
StatePublished - 2013

All Science Journal Classification (ASJC) codes

  • General Immunology and Microbiology
  • General Environmental Science
  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences


  • Evolution
  • Influenza A virus
  • Phylodynamics
  • Phylogeny
  • Transmission


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