犬圆环病毒从野生到家养食肉动物的进化动力学及系统地理学分析

圆环病毒是相对较新的病原体，新的圆环病毒不断被发现，宿主范围越来越广。最近，据报道，犬圆环病毒（CanineCV）感染了猫和獾，进一步扩大了其宿主范围。以前关于CanineCV进化和传播的研究是零散的。在这里，在对收容所犬进行宏基因组分析时，我们确定了犬圆环病毒阳性率为 32.4%，并获得了三种新的病毒株。此外，我们整合了公开可用的病毒序列，并采用多种生物信息学软件工具来分析CanineCV的进化、密码子使用偏倚、重组、起源、时空分布和宿主适应性。本研究将CanineCV分为5个不同的系统发育分支，根据其地理分布特征系统地命名为China-I、China-II、Cosmopolitan、EA和SEA分支。观察到广泛的分支间重组，在病毒进化中起重要作用，而根据现有序列信息，CanineCV最有可能起源于 <i>秃鹫 vulpes vulpes</i> 1950.7年（1919.4-1975.3,95%HPD）的Vulpes vulpes（PP=0.51），进化速率=2.95×10-3-3^-3亚点/年（2.12-3.85×10-3-3^-3subs/site/year）。值得注意的是，与先前报道的宿主相比，CanineCV对人类宿主表现出更高的适应性，正如宿主适应性指数所表明的那样，表明该病毒可能是一种潜在的人畜共患病原体。总之，我们的研究揭示了犬类CV的系统地理学和进化动力学，并强调了研究犬类CV的人畜共患潜力的必要性。

Circoviruses are relatively novel pathogens, with new circoviruses continuously discovered and their host range expanding increasingly. Recently, Canine circovirus (CanineCV) was reported to infect cats and badgers, further broadening its host range. Previous studies on the evolution and transmission of CanineCV were fragmented. Here, through metagenomic analysis of shelter dogs, we determined a 32.4% positivity rate for CanineCV and obtained three novel viral strains. Additionally, we integrated publicly available viral sequences and employed multiple bioinformatics software tools to analyze the evolution, codon usage bias, recombination, origin, spatiotemporal distribution, and host adaptation of CanineCV. In this study, CanineCV was divided into five distinct phylogenetic clades, systematically named China-I, China-II, Cosmopolitan, EA, and SEA clades based on their geographic distribution characteristics. Extensive inter-clade recombination was observed, which plays a critical role in viral evolution. Based on existing sequence information, CanineCV most likely originated from *Vulpes vulpes* (PP=0.51) approximately 1950.7 years ago (1919.4–1975.3, 95% HPD), with an evolutionary rate of 2.95 × 10^-3 subs/site/year (95% HPD: 2.12–3.85 × 10^-3 subs/site/year). Notably, compared with previously reported hosts, CanineCV exhibits higher adaptation to human hosts, as indicated by the host adaptation index, suggesting that this virus is a potential zoonotic pathogen. Collectively, our study reveals the phylogeography and evolutionary dynamics of CanineCV and emphasizes the necessity of researching the zoonotic potential of CanineCV.