Abstract
Previous human influenza pandemics were the results of emerging viruses from non-human reservoirs, with at least two caused by strains of mixed human and avian origin. Also, many cases of swine influenza viruses have reportedly infected humans, including the recent human H1N1 strain, isolated in Mexico and the United States. Pigs are documented to get infected with human, avian, and swine viruses and allow productive replication, thus it has been conjectured that they are the “mixing vessel” that create reassortant strains, causing the human pandemics. In this paper, we apply several statistical techniques to an ensemble of publicly available swine viruses to study the reassortment phenomena. The reassortment patterns in swine viruses confirm previous results found in human viruses that the glycoprotein coding segments reassort most often. Moreover, one of the polymerase segments (PB1), reassorted in the strains responsible for the last two human pandemics of 1957 and 1968, 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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