Evolutionary dynamic of HA gene of swine H1N2 influenza virus in Korea from 2009 to 2022
2023
Shin, G.E. | Lee, E.Y. | Lee, K.K. | Lee, I.S. | Ku, B.K. | Jeoung, H.Y.
Pigs are considered a "mixing vessel" that can produce new influenza strains through genetic reassortments, which threaten public health and cause economic losses worldwide. We performed surveillance of swine influenza virus (SIV) using 114,140 nasal swabs from 11,414 Korean farms from 2009 to 2022, and characterized their genetic evolution at each farm level. A total of 169 farms out of the 11,414 (1.48%) were SIV-positive. The positivity rate for the H1N2 subtype, which is most dominant in the pig population, was 37.87% (64/169). Through hemagglutinin (HA) gene analysis, 64 H1N2-positive farms were classified into Eurasian avian-like (46/64, 71.88%), triple-reassortant (14/64, 21.88%), pdm09 (3/64, 4.69%), and classical swine (1/64, 1.56%) groups. The estimated evolutionary rate of HA in H1N2 from 2009 to 2022 in Korea is 1.5309 × 10⁻³/site/year (95% HPD intervals from 1.0003 × 10⁻³ to 2.1735 × 10⁻³) with an estimated mean growth rate of 0.0114. Estimates of the relative genetic diversity of clades over time suggested that the HA of H1N2 exhibited an increase in population size. The results of this study showed that the Eurasian avian-like-HA of the H1N2 subtype was dominant in the pig population. The continued evolution of the HA of H1N2, which is critical for cell entry, might lead to genetic diversity and the loss of vaccine cross-protection. These results indicate that continus surveillance is imperative for monitoring the evolution of the swine influenza virus.
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