H3N2 feline influenza virus (FIV) and canine influenza virus (CIV) are very common in cats and dogs. Due to the ability of the influenza virus to spread across hosts and frequent contact between pets and people, there exist huge public health problems. In this study, we collected H3N2 CIV and FIV genomes from 2006 to 2019 from NCBI and analyzed the evolutionary dynamics and molecular variation using a series of phylogenetic analysis methods. Results indicated that H3N2 FIVs were closely related to CIVs with high posterior probability and CIVs and FIVs have certain regional characteristics. However, compared with previous studies, the significance of geographical structure correlation decreased. Furthermore, we also found that the intrasubtypic reassortment between FIVs and CIVs were common during epidemics. The integrated analysis was also performed for different selection pressure acting on HA (566 codons), NA (469 codons), M1 (252 codons), and M2 (97 codons) proteins. One HA, two NA, three M1, and two M2 sites were found under positive selection. We subsequently performed the evolutionary dynamics of H3N2 CIV. The results indicated that the time of the most recent common ancestor of CIV H3N2 may have occurred earlier than indicated in a previous study. The Bayesian skyline plot analysis in this study showed the period of divergence of major H3N2 CIVs segments occurred between 2008 and 2010. Notably, according to our research, the PB1 has experienced two divergence periods (2006–2008 and 2009–2011).

中文翻译：

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2006-2019年H3N2犬猫流感病毒株系统发育分析及进化动态

H3N2 猫流感病毒 (FIV) 和犬流感病毒 (CIV) 在猫和狗中非常常见。由于流感病毒具有跨宿主传播的能力以及宠物与人之间的频繁接触，存在巨大的公共卫生问题。在本研究中，我们从NCBI收集了2006年至2019年的H3N2 CIV和FIV基因组，并利用一系列系统发育分析方法分析了进化动力学和分子变异。结果表明，H3N2 FIV 与 CIV 密切相关，后验概率较高，且 CIV 和 FIV 具有一定的区域特征。但与以往的研究相比，地理结构相关性的显着性有所下降。此外，我们还发现FIV和CIV之间的亚型内重配在流行期间很常见。还对作用于HA（566个密码子）、NA（469个密码子）、M1（252个密码子）和M2（97个密码子）蛋白质的不同选择压力进行了整合分析。在正选择下发现了 1 个 HA、2 个 NA、3 个 M1 和 2 个 M2 位点。我们随后进行了 H3N2 CIV 的进化动力学研究。结果表明，CIV H3N2 最近的共同祖先出现的时间可能早于之前研究中指出的时间。本研究中的贝叶斯天际线图分析表明，H3N2 CIV 主要细分市场的分化期发生在 2008 年至 2010 年之间。值得注意的是，根据我们的研究，PB1 经历了两个分化期（2006-2008 年和 2009-2011 年）。