Genetic diversity of influenza A viruses in swine in southeast Mexico

Authors: NELSON, MARTHA - Fogarty International Center; SOUZA, CARINE - Orise Fellow; TROVÃO, NÍDIA - Fogarty International Center; DIAZ, ANDRES - University Of Minnesota; MENA, IGNACIO - The Icahn School Of Medicine At Mount Sinai; ROVIRA, ALBERT - University Of Minnesota; Baker, Amy; TORREMORELL, MONTSERRAT - University Of Minnesota; MARTHALER, DOUGLAS - Kansas State University; CULHANE, MARIE - University Of Minnesota

Submitted to: Emerging Infectious Diseases
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/7/2018
Publication Date: 2/7/2019
Citation: Nelson, M.I., Souza, C., Trovão, N.S., Diaz, A., Mena, I., Rovira, A., Vincent, A.L., Torremorell, M., Marthaler, D., Culhane, M.R. 2019. Human-origin influenza A (H3N2) reassortant viruses in swine, southeast Mexico. Emerging Infectious Diseases. 25(4):691-700. https://doi.org/10.3201/eid2504.180779.
DOI: https://doi.org/10.3201/eid2504.180779

Interpretive Summary: Influenza A viruses (IAVs) that circulate in swine have the potential to infect humans and may cause pandemics, such as in 2009. The 2009 H1N1 pandemic was shown to originate in swine in Mexico, yet the level of surveillance for IAV in swine in Mexico is relatively low. Available data suggested that some IAV in swine in Mexico may be similar to those in the United States, but some may be unique to Mexico. Producers attempt to control IAVs in their herds through ongoing monitoring and vaccination, but vaccines should be matched to the circulating strains. We characterized IAVs collected from swine from multiple regions in Mexico and identified extensive viral genetic and antigenic diversity, including strains that are highly divergent from those circulating in US herds. As such, vaccine intervention for IAV in swine herds in Mexico would need to be tailored specifically to the country’s strains. This information is important for effective control of IAV in swine.

Technical Abstract: The genetic diversity of influenza A viruses circulating in swine (IAV-S) presents a threat to humans and complicates eradication efforts in animals. The origin of the century’s first influenza pandemic in Mexico was unexpected, but recently explained by the exceptionally diverse IAV-S populations identified in west and central Mexico, including Eurasian viruses never previously identified in the Americas. To further understand the evolution of IAV-S in Mexico, and to evaluate strains for the development of new influenza vaccines for pigs in Mexico, we sequenced the entire genomes of 59 viruses collected from two major regions of swine production and performed antigenic cartography on select strains. We find that the genetic and antigenic diversity of IAV-S in southeast Mexico is particularly high, including human-origin H3 viruses that are antigenically distinct from all known US swine lineages. Commercially available vaccines developed for US swine herds are therefore unlikely to protect against all viruses circulating in swine in Mexico, requiring the development of new influenza vaccines, particularly for pigs in the southeast region. Further understanding of the extensive genetic and antigenic diversity of IAV-S circulating in Mexico’s large swine herds is greatly needed.