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

Abstract

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about the immediate origin of the epidemic, despite the fact that we included a panel of closely related and previously unpublished swine influenza isolates.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.

Against the new H1N1 influenza (swine influenza): Vaccinate or don’t vaccinate (all)? That is currently the question!

“…Several analyses have shown that the new pandemic H1N1 (2009) virus in domestic pigs emerged from genetic elements of the old human H1N1 and H3N2 viruses as well as from North American and European porcine H1N1 viruses, probably as ''reassortment'' of successive double infection. These results actualize what the influenza virologist has long feared: not birds (avian influenza) but rather mammals, such as swine, represent, as in the past (H2N2, H3N3), the greatest threat for spreading zooanthroponotic influenza infections to humans [2].…”

Multiple Reassortment between Pandemic (H1N1) 2009 and Endemic Influenza Viruses in Pigs, United States

“…During 1998–2009, reassortment of influenza viruses in US pigs occurred relatively frequently ( 37 ). The genotypes of the viruses generated through these reassortments typically contained different swine or human influenza virus HA and NA genes in combination with the TRIG cassette ( 13 – 20 ).…”

Vietnamese chickens: a gate towards Asian genetic diversity

“…Smith et al . [29] showed that virus from the H2N2/1957 and H3N2/1968 pandemics seemed to have originated from avian hosts, probably in Asia. Wild relatives may represent a host population where the virus can evolve and where control measures such as vaccination are not possible to use.…”