In March and early April 2009, a new swine-origin
influenza A (
H1N1)
virus (S-OIV) emerged in Mexico and the United States. During the first few weeks of
surveillance, the
virus spread worldwide to 30 countries (as of May 11) by human-to-human transmission, causing the World Health Organization to raise its
pandemic alert to level 5 of 6. This
virus has the potential to develop into the first
influenza pandemic of the twenty-first century. Here we use evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV
epidemic. We show that it was
derived from several
viruses circulating in swine, and that the initial transmission to humans occurred several months before recognition of the
outbreak. A
phylogenetic estimate of the gaps in
genetic surveillance indicates a long period of unsampled ancestry before the S-OIV
outbreak, suggesting that the
reassortment of swine lineages may have occurred years before emergence in humans, and that the multiple
genetic ancestry of S-OIV is not indicative of an artificial origin. Furthermore, the unsampled history of the
epidemic means that the nature and location of the
genetically closest swine
viruses reveal little about the immediate origin of the
epidemic, despite the fact that we included a panel of closely related and previously unpublished
swine influenza isolates. Our results highlight the need for systematic
surveillance of
influenza in swine, and provide evidence that the mixing of new
genetic elements in swine can result in the emergence of
viruses with
pandemic potential in humans.
