Abstract
Three human influenza pandemics occurred in the twentieth century, in 1918, 1957, and 1968. Influenza pandemic strains are the results of emerging viruses from non-human reservoirs to which humans have little or no immunity. At least two of these pandemic strains, in 1957 and in 1968, were the results of reassortments between human and avian viruses. Also, many cases of swine influenza viruses have reportedly infected humans, in particular, the recent H1N1 influenza virus of swine origin, isolated in Mexico and the United States. Pigs are documented to allow productive replication of human, avian, and swine influenza viruses. Thus it has been conjectured that pigs are the “mixing vessel” that create the avian-human reassortant strains, causing the human pandemics. Hence, studying the process and patterns of viral reassortment, especially in pigs, is a key to better understanding of human influenza pandemics. In the last few years, databases containing sequences of influenza A viruses, including swine viruses, collected since 1918 from diverse geographical locations, have been developed and made publicly available. In this paper, we study an ensemble of swine influenza viruses to analyze the reassortment phenomena through several statistical techniques. The reassortment patterns in swine viruses prove to be similar to the previous results found in human viruses, both in vitro and in vivo, that the surface glycoprotein coding segments reassort most often. Moreover, we find that one of the polymerase segments (PB1), reassorted in the strains responsible for the last two human pandemics, also reassorts frequently.
Highlights
Pandemics are epidemics that rapidly spread on a worldwide scale, caused by pathogens against which humans have no immunity that infect a large part of the population and lead to associated serious illnesses
From the three influenza pandemics of the twentieth century, the 1918 pandemic was possibly caused by an influenza virus with an avian origin [1,2] and the other two, in 1957 and 1968, were caused by new strains that were combinations of avian and human viruses through the process of reassortment [3,4]
In March 2009, a new human H1N1 influenza A virus of swine origin was isolated in Mexico and the United States [7,8]
Summary
Pandemics are epidemics that rapidly spread on a worldwide scale, caused by pathogens against which humans have no immunity that infect a large part of the population and lead to associated serious illnesses. Since 2003, a highly pathogenic H5N1 avian virus has been successfully infecting more than 400 humans with a mortality rate of 60% [10] It is not clear whether any of these viruses will be the cause of the human influenza pandemic, it is vital to understand the mechanisms behind the genomic evolution of influenza virus and its adaption to new hosts, in particular through the process of reassortment. Multiple strains of influenza virus (with various subtypes such as H1N2, H3N1, H2N3, H4N6, H5N1, etc.) have been isolated in pigs around the world, including both inter-host reassortments and whole genome adaptations of human and/or avian viruses [11,18,19,20,21,22,23,24,25,26]. We find that one of the polymerase segments, PB1, reassorts quite frequently, reiterating similar experimental results from human viruses reported by Downie [30]
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