Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

The H3N2 canine influenza virus (CIV) originated from an avian species. Since its emergence, it has circulated in multiple states and has caused pandemics among dog populations; however, no comprehensive studies have explored the causes driving these ongoing cases. The study of the codon usage patterns of viruses can reveal the genetic changes required for the viruses to adapt to new hosts and the external environment. Here we performed a thorough genetic, evolutionary, and codon usage analysis. We identified three evolutionary H3N2 CIV clades from a timescaled phylogenetic tree, namely, Origin, China, and Korea/USA, by principal component analysis (PCA). Additionally, we found a low codon usage bias and that mutation pressure, natural selection, and dinucleotide abundance shape the codon usage bias of H3N2 CIVs, with natural selection being more crucial than the others. Moreover, the human codon adaptation index was similar to that of dogs (the natural host) and cats. In addition, the H3N2 CIV similarity index values were higher than those of the avian influenza virus (AIV), suggesting viral adaptation to the host. Therefore, H3N2 CIVs may pose a potential risk to public health in the future, and further epidemiologic, evolutionary, and pathogenetic studies are required.H3N2犬流感病毒（H3N2 canine influenza virus, CIV）起源于禽类宿主。自被发现以来，该病毒已在多个区域传播，并在犬群中引发大流行；然而目前尚无全面研究阐明驱动这些持续暴发的具体原因。对病毒密码子使用模式的研究，可揭示病毒适应新宿主与外部环境所需的遗传变化。本研究开展了全面的遗传、进化及密码子使用模式分析。通过主成分分析（principal component analysis, PCA），本研究从时间标度系统发育树中鉴定出三个H3N2 CIV进化分支，分别为始祖分支、中国分支以及韩国与美国分支。此外，研究发现H3N2 CIV的密码子使用偏倚程度较低，突变压力、自然选择及二核苷酸丰度共同塑造了其密码子使用偏倚，其中自然选择的作用相较于其他因素更为关键。另外，人类密码子适应指数（codon adaptation index）与犬（天然宿主）及猫的该指数相近。H3N2 CIV的相似性指数高于禽流感病毒（avian influenza virus, AIV），提示该病毒已实现对宿主的适应。综上，H3N2 CIV未来或对公共卫生构成潜在风险，亟需开展进一步的流行病学、进化及致病机制相关研究。