Origins and Evolutionary Genomics of the Novel Swine-Origin Influenza A (H1N1) Virus in Humans —Past and Present Perspectives

Abstract

Swine influenza viruses cause annual epidemics and occasional pandemics claiming the lives of millions from the early history up to the present days. This virus has drawn on a bag of evolutionary tricks to survive in one or another form in both humans and pigs with novel gene constellations through the periodic importation or exportation of viral genes. A prime example is emergence of pandemic novel swine-origin influenza A (H1N1) virus (S-OIV) in 2009 that have transmitted to and spread among humans, resulting in outbreaks internationally. The phylogenetic analysis of sequences of all genes of the S-OIV, showed that its genome contained six gene segments that were similar to ones previously found in triple-reassortant swine influenza viruses circulating in pigs in North America. The genes encoding neuraminidase and M protein were most closely related to those in influenza A viruses circulating in swine populations in Eurasia. This unique genetic combination of influenza virus gene segments leading to the emergence of novel S-OIV that had not been seen before in the world. Here, it has been used evolutionary analysis to estimate the timescale of the origins and the early development of the S-OIV epidemic. This paper shows that it was derived from several viruses circulating in swine and makes a briefly review over the origins and evolutionary genomics of current S-OIV in humans with historical perspectives with a view to exhibition of evolutionary relationship between past and present origins of swine influenza viruses.