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Research Project: Intervention Strategies to Control Endemic and New and Emerging Influenza A Virus Infections in Swine

Location: Virus and Prion Research

Title: Human-to-swine introductions and onward transmission of 2009 H1N1 pandemic influenza viruses in Brazil

item JUNQUEIRA, DENNIS - Universidade Federal De Santa Maria
item Anderson, Tavis
item GAVA, DANIELLE - Embrapa
item HAACH, VANESSA - Federal University Of Rio Grande Do Sul
item CANTAO, MAURICIO - Embrapa
item Baker, Amy
item SCHAEFER, REJANE - Embrapa

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/27/2023
Publication Date: 8/8/2023
Citation: Junqueira, D.M., Tochetto, C., Anderson, T.K., Gava, D., Haach, V., Cantao, M.E., Baker, A.L., Schaefer, R. 2023. Human-to-swine introductions and onward transmission of 2009 H1N1 pandemic influenza viruses in Brazil. Frontiers in Microbiology. 14.

Interpretive Summary: Frequent human-to-swine transmission of the 2009 H1N1 pandemic virus (H1N1pdm09) has contributed to the diversity of influenza A virus (IAV) in swine populations around the globe. We conducted surveillance for IAV in pigs in Brazil during between 2009 and 2020 and isolated and characterized 70 H1N1pdm09 IAVs. Using a comprehensive genetic analysis, we demonstrated 30 introductions of H1N1pdm09 into swine in Brazil, most introductions occurred between 2009 and 2012. Four of the introductions persisted and evolved with diversifying selection from 2012 to 2020 resulting in genetically novel H1N1pdm09 IAV that appear to circulate only in Brazilian swine herds. The identification of these viruses demonstrates the importance of a robust surveillance system for IAV in swine to inform control measures. These data can be used for objective vaccine and diagnostic updates, as well as help identify factors to prevent infection and transmission, such as changes in production practices or on-farm management.

Technical Abstract: Once established in the human population, the 2009 H1N1 pandemic virus (H1N1pdm09) was repeatedly introduced into swine populations globally with subsequent onward transmission among pigs. To identify and characterize human-to-swine H1N1pdm09 introductions in Brazil, we conducted a large-scale phylogenetic analysis of 4,141 H1pdm09 hemagglutinin (HA) and 3,227 N1pdm09 neuraminidase (NA) gene sequences isolated globally from humans and swine between 2009 and 2022. Phylodynamic analysis revealed that during the period between 2009 and 2011, there was a rapid transmission of the H1N1pdm09 virus from humans to swine in Brazil. Multiple introductions of the virus were observed, but most of them resulted in self-limited infections in swine, with limited onward transmission. Only a few sustained transmission clusters were identified during this period. After 2012, there was a reduction in the number of human-to-swine H1N1pdm09 transmissions in Brazil. The virus underwent continuous antigenic drift, and a balance was established between swine-to-swine transmission and extinction, with minimal sustained onward transmission from humans to swine. These results emphasize the dynamic interplay between human-to-swine transmission, antigenic drift, and the establishment of swine-to-swine transmission in shaping the evolution and persistence of H1N1pdm09 in swine populations.