Genetic diversity and evolution of H1N1 subtype swine influenza virus in China: a comprehensive analysis from 1977 to 2020

Swine influenza virus (SIV) is a highly contagious respiratory pathogen that causes significant economic losses in the swine industry and poses a potential health risk to humans. This study investigated the genetic diversity and evolution of the H1N1 subtype SIV across different regions of China over the past four decades. Using 959 whole-genome sequences collected between 1977 and 2020 from public databases such as GenBank and the Global Initiative on Sharing Avian Influenza Data (GISAID), we systematically analyzed the epidemiology, phylogenetics, genotypes, and molecular characteristics of the H1N1 subtype SIV. The results revealed marked temporal and geographic heterogeneity in virus distribution, with six major lineages and 25 distinct genotypes identified. The Eurasian avian-like (EA) lineage predominated, reflecting its adaptive advantage in swine populations. Genotypic turnover was evident over time, with certain genotypes (e.g., genotype 2 and genotype 3) exhibiting molecular features associated with adaptation to human hosts, thereby elevating the risk of cross-species transmission and potential pandemics. Amino acid site analysis further identified mutations favoring human-like receptor binding, mammalian adaptation, and antigenic variation. These findings highlight the ongoing evolution of H1N1 subtype SIV in China and underscore the necessity for continuous surveillance and enhanced biosecurity measures in the swine industry to mitigate future pandemic threats.