Expansion of genetic diversity and interspecies transmission dynamics of swine influenza viruses in China

Abstract

Swine influenza viruses (SIVs) pose a continuous threat to agriculture and public health, as indicated by the emergence of 2009 pandemic H1N1 virus (pdm/09). Our previous evolutionary studies of SIVs isolated from long-term surveillance in China during 1998–2010 revealed co-circulation of four major swine lineages, all of which were introduced from North America or Europe. The introduction and reassortment of pdm/09 with these major swine virus lineages have led to the expansion of genetic diversity in the study area. Frequent influenza virus transmission from human to swine also drives evolution of SIVs, facilitating the genesis of novel variants with increased human infectious potentials, as evidenced by the human cases caused by infection of zoonotic H3N2 variants. Repeated transmission of H3 human influenza viruses (huIVs) to pigs has been observed in China since 1998, but their long-term impact on the ecology and development of SIVs were not systematically explored. Using whole-genome sequences of 1,631 SIVs isolated from our influenza surveillance program during 1998–2015, we aim to investigate the following scientific questions: 1) the continuous development of pdm/09-like and huIV-like H3 viruses in pigs; 2) population dynamics of co-circulating swine lineages in China; 3) global migration of SIVs of various origins; 4) viral determinants of increasing diversity and human-to-swine transmissibility. Phylogenetic analyses in this project may provide insights into the risk posed by circulating SIVs and understanding of the mechanism of interspecies transmission.