Inter-Host Reassortment Patterns in Swine Influenza Viruses

Three pandemic influenza strains occurred in the 20 century, in 1918, 1957 and 1968. Influenza pandemic strains are the result of an emerging virus spreading in people which have little or non immunity. At least two of these pandemics strains, in 1957 and in 1968, were the result of reassortments between human and avian viruses. In 1957 three segments, PB1, HA and NA, and in 1968 two segments, PB1 and HA, were of avian origin. Recently new influenza viruses have been isolated in Mexico and the United States. These viruses are found to be a complicated reassortement of swine, avian and human strains. Pigs are frequently found co-infected with human, avian and swine viruses. This observation has led to the conjecture that pigs are the mixing vessel that cause the avian-human reassortments, and hence the pandemics. Understanding the process and the patterns of viral reassortment, especially in pigs, is key to estimate and/or predict the likelihoods and rates of influenza pandemics. In the last few years databases collecting the sequences of influenza viruses in diverse geographical locations since 1918, including swine viruses, have been developed and made publicly available. In this paper, we study the ensemble of the swine influenza viruses to analyze how the reassortments happen in pigs. Inter-host reassortment patterns in pigs confirm similar previous results found in human viruses, both in vitro and in vivo. More interestingly, we have found that one of the polymerases, PB1 reassorts more often than other segments. In the last two pandemics, 1957 and 1968, PB1 was of avian origin. This observation reinforces the hypothesis that pigs constitute the inter-host mixing vessel responsible for at least two of the three pandemics in the 20 century.