Genetic Characterization of Influenza A Viruses in Japanese Swine in 2015 to 2019

Abstract

To assess the current status of influenza A viruses of swine (IAVs-S) throughout Japan and to investigate how these viruses persisted and evolve on pig farms, we genetically characterized IAVs-S isolated during 2015 to 2019. Nasal swab samples collected through active surveillance and lung tissue samples collected for diagnosis yielded 424 IAVs-S, comprising 78 H1N1, 331 H1N2, and 15 H3N2 viruses, from farms in 21 sampled prefectures in Japan. Phylogenetic analyses of surface genes revealed that the 1A.1 classical swine H1 lineage has evolved uniquely since the late 1970s among pig populations in Japan. During 2015 to 2019, A(H1N1)pdm09 viruses repeatedly became introduced into farms and reassorted with endemic H1N2 and H3N2 IAVs-S. H3N2 IAVs-S isolated during 2015 to 2019 formed a clade that originated from 1999–2000 human seasonal influenza viruses; this situation differs from previous reports, in which H3N2 IAVs-S derived from human seasonal influenza viruses were transmitted sporadically from humans to swine but then disappeared without becoming established within the pig population. At farms where IAVs-S were frequently isolated for at least 3 years, multiple introductions of IAVs-S with phylogenetically distinct hemagglutinin (HA) genes occurred. In addition, at one farm, IAVs-S derived from a single introduction persisted for at least 3 years and carried no mutations at the deduced antigenic sites of the hemagglutinin protein, except for one at the antigenic site (Sa). Our results extend our understanding regarding the status of IAVs-S currently circulating in Japan and how they genetically evolve at the farm level. IMPORTANCE Understanding the current status of influenza A viruses of swine (IAVs-S) and their evolution at the farm level is important for controlling these pathogens. Efforts to monitor IAVs-S during 2015 to 2019 yielded H1N1, H1N2, and H3N2 viruses. H1 genes in Japanese swine formed a unique clade in the classical swine H1 lineage of 1A.1, and H3 genes originating from 1999–2000 human seasonal influenza viruses appear to have become established among Japanese swine. A(H1N1)pdm09-derived H1 genes became introduced repeatedly and reassorted with endemic IAVs-S, resulting in various combinations of surface and internal genes among pig populations in Japan. At the farm level, multiple introductions of IAVs-S with phylogenetically distinct HA sequences occurred, or IAVs-S derived from a single introduction have persisted for at least 3 years with only a single mutation at the antigenic site of the HA protein. Continued monitoring of IAVs-S is necessary to update and maximize control strategies.

Serological and molecular epidemiological study on swine influenza in Zambia

“…Our serological investigation revealed the high seroprevalence of H1 IAV infection in pigs in 2011. The positive rate and neutralization titres for A(H1N1)pdm09 virus were higher than those for the moto et al, 2012;Mine et al, 2020;Ozawa et al, 2015). Since both A(H1N1)pdm09 and human H3N2 viruses were isolated from pigs in Zambia, it might be possible for such a reassortant IAV to emerge in pigs in Zambia.…”

“…Although human seasonal influenza H3N2 viruses were also isolated from pigs in Japan, no descendant strains were subsequently isolated, suggesting that these viruses were sporadically introduced into pigs from humans without establishment of novel IAV lineages (Takemae et al., 2013). On the other hand, H3N2 IAV variants recently generated by the reassortment between A(H1N1)pdm09 and human seasonal H3N2 viruses might be well adapted to swine and have established a novel IAV lineage in pig populations in Asia, including Japan and Thailand (Hiromoto et al., 2012; Mine et al., 2020; Ozawa et al., 2015). Since both A(H1N1)pdm09 and human H3N2 viruses were isolated from pigs in Zambia, it might be possible for such a reassortant IAV to emerge in pigs in Zambia.…”

“…However, these situations were dramatically changed by the emergence of A(H1N1)pdm09 virus in 2009. Since the 2009 pandemic, A(H1N1)pdm09 virus has frequently been transmitted back to pig populations and reassorted with the endemic swine IAVs, further increasing genetic diversity among swine IAVs worldwide (Hiromoto et al., 2012; Mine et al., 2020).…”

Human Infection with a Reassortant Swine-Origin Influenza A(H1N2)v Virus in Taiwan, 2021

“…1), indicating the N2 genes of swine in uenza A viruses in different regions were introduced from human in uenza A viruses at different time points. After the 2009 pandemic, the gene segments of A(H1N1)pdm09 were reintroduced into the swine population, resulting in the circulation of different genotypes in the swine population [8][9][10][11][12]. Humans infected by reassortant swine in uenza viruses with the gene pool of A(H1N1)pdm09 virus have been sporadically detected [13,14,16,23], and it has been reported that Eurasian avian-like swine in uenza A(H1N1) virus with A(H1N1)pdm09 genes has facilitated human infection [24].…”

“…Thereafter, with multiple introductions of human and avian in uenza A viruses into the swine population in different time periods, multiple genotypes and clades of A(H1) and A(H3) viruses have been generated through inter-and intra-subtype reassortment [7]. Later, upon the 2009 pandemic, the viral gene pools of human in uenza A(H1N1)pdm09 viruses were reintroduced into the swine population through reassortment, resulting in the circulation of different genotypes in swine and increasing the threat of the next pandemic [8][9][10][11][12]. Human infections caused by in uenza A(H1)v and A(H3)v viruses with the matrix protein from A(H1N1)pdm09 have been sporadically reported [13][14][15][16].…”