The genomic landscape of swine influenza A viruses in Southeast Asia

Abstract

Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza virus (swIAV). Effective surveillance is essential to uncover emerging virus strains, however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. By collecting more than 4,000 nasal swabs and 4,000 sera from pigs in Cambodia, we unmasked the co-circulation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swine reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two to 15 years ago, indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.

Ingrained: Rice farming and the risk of zoonotic spillover, examples from Cambodia

“…The expansion and intensification of pig husbandry can increase the risk of a number of zoonotic viruses, including the emergence and spread of novel influenza subtypes, African swine fever, Japanese encephalitis, Nipah, and coronaviruses [ 56 ]. Intensification of pig farming and increased demand for pork are also linked with the zoonotic risk of swine influenza A virus (swIAV) and the transmission and circulation of multiple classical swine influenzas [ 57 ]. At the same time, wild hogs exist in rice fields as destructive pests, carrying diseases that spread to other livestock and damaging crops.…”