Data from: Expansion of genotypic diversity and establishment of 2009 H1N1 pandemic-origin internal genes in pigs in China

‘Two-way' transmission of influenza viruses between humans and swine
has been frequently observed and the occurrence of the 2009 H1N1 pandemic
influenza (pdm/09) demonstrated that swine-origin viruses could facilitate
the genesis of a pandemic strain. Although multiple introductions to and
reassortment in swine of the pdm/09 virus have been repeatedly reported in
both Eurasia and the Americas, its long-term impact on the development of
swine influenza viruses (SIVs) has not been systematically explored. Our
comprehensive evolutionary studies on the complete genomes of 387 SIVs
obtained from 2009 to 2012 in influenza surveillance in China revealed 17
reassortant genotypes with pdm/09-origin genes. Even though the entire
2009 pandemic virus and its surface genes cannot persist, its internal
genes have becoming established and are now the predominant lineages in
pigs in the region. The main persistent pdm/09-origin reassortant forms
had at least 5 pdm/09-origin internal genes and their surface genes
primarily of European avian-like (EA) or human H3N2-like SIV origin. These
findings represent a marked change to the evolutionary patterns and
ecosystem of SIVs in China. It is possible that the pdm/09-origin internal
genes may be in the process of replacing EA- or triple reassortant-like
internal genes. These alterations to the SIV gene pool need to be
continually monitored to assess changes in the potential for SIVs to
transmit to humans. Importance: Shortly after the emergence of the 2009
pandemic H1N1 (pdm/09) influenza virus, it was transmitted from humans to
pigs and this continues to occur around the world. Many reassortants
between pdm/09-origin viruses and enzootic swine influenza viruses (SIVs)
have been detected. However, the long-term impact of pdm/09-origin viruses
on the SIV gene pool, which could lead to the generation of influenza
viruses with the potential to infect humans, has not been systematically
examined. From extensive surveillance of SIVs over a 38-month period in
southern China, it was found that, although neither complete pdm/09
viruses nor their surface genes could persist in pigs, their internal
genes did persist. Over the survey period, these internal genes became
predominant, potentially replacing those of the enzootic SIV lineages. The
altered diversity of the SIV gene pool needs to be closely monitored for
changes in the potential of SIVs to transmit to humans.