Abstract
The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus. To describe evolution of swine influenza A viruses in Mexico and evaluate strains for vaccine development, we sequenced the genomes of 59 viruses and performed antigenic cartography on strains from 5 regions. We found that genetic and antigenic diversity were particularly high in southeast Mexico because of repeated introductions of viruses from humans and swine in other regions in Mexico. We identified novel reassortant H3N2 viruses with genome segments derived from 2 different viruses that were independently introduced from humans into swine: pandemic H1N1 viruses and seasonal H3N2 viruses. The Mexico swine viruses are antigenically distinct from US swine lineages. Protection against these viruses is unlikely to be afforded by US virus vaccines and would require development of new vaccines specifically targeting these diverse strains.
Highlights
The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm09 virus
Genetic Diversity of Swine influenza A viruses (IAV) in Mexico Phylogenetic analysis of the 59 swine IAV whole-genome sequences generated for this study showed that extensive genetic diversity is circulating in the northwest and southeast regions of Mexico
The recent characterization of the origins of the influenza A(H1N1)pdm09 virus in swine in Mexico underscored the need for efforts to control the unexpectedly diverse swine IAV populations circulating in large swine herds in this country [1]
Summary
The genetic diversity of influenza A viruses circulating in swine in Mexico complicates control efforts in animals and presents a threat to humans, as shown by influenza A(H1N1)pdm virus. Diverse influenza A viruses (IAV) circulate in swine globally, complicating efforts to control the virus and increasing the threat that a novel virus will emerge in pigs with the capacity to infect humans. This threat was exemplified by the influenza A(H1N1)pdm virus, which originated in swine in Mexico, most likely in the west or central–north regions [1]. During the 1990s, ≈100,000 live hogs were transported annually, on average, from the United States to Mexico (Figure 1, panel B), facilitating establishment of 2 major North American swine IAV lineages in Mexico by the end of the decade: triple reassortant swine H3N2 (TRswH3N2) viruses and classical swine H1N1 (CswH1N1) viruses [1] (referred to as lineage 1A according to recently proposed H1 nomenclature [3]). Lifting of internal movement controls during 2009 provided new opportunities for swine IAV to migrate between regions in Mexico
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