Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

A phylogenetic analysis of swine-origin H1N1 influenza A virus provides evidence that the virus is a reassortment possessing genes from avian, swine and human origin viruses. The pandemic virus appears to have evolved in way typical of swine flu sequences prior to entering humans, and is derived from several viruses circulating in swine. Initial transmission to humans appears to have occurred several months before recognition of the outbreak. An estimate of the gaps in genetic surveillance points to a period of years between the reassortment of swine lineages and the transfer to humans and the multiple genetic ancestry is inconsistent with an artificial origin for the virus. The gaps in out knowledge revealed…

• DA
  David and Lucile Packard Foundation
• RS
  Royal Society
• UG
  University Grants Committee

  Award: AoE/M-12/06
• NI
  National Institutes of Health

  Award: HHSN266200700005C
• DF
  Directorate for Biological Sciences
• BA
  Biotechnology and Biological Sciences Research Council

  Award: BB/E009670/1
• NI
  National Institute of Allergy and Infectious Diseases

  Award: HHSN266200700005C