Data_Sheet_1_Genetic diversity, distribution, and evolution of chicken anemia virus: A comparative genomic and phylogenetic analysis.PDF

Chicken infectious anemia (CIA) is an immunosuppressive poultry disease that causes aplastic anemia, immunosuppression, growth retardation and lymphoid tissue atrophy in young chickens and is responsible for huge economic losses to the poultry industry worldwide. The disease is caused by the chicken anemia virus (CAV), which belongs to the genus Gyrovirus, family Anelloviridae. Herein, we analyzed the full-length genomes of 243 available CAV strains isolated during 1991–2020 and classified them into two major clades, GI and GII, divided into three and four sub-clades, GI a-c, and GII a-d, respectively. Moreover, the phylogeographic analysis revealed that the CAVs spread from Japan to China, China to Egypt and subsequently to other countries, following multiple mutational steps. In addition, we identified eleven recombination events within the coding and non-coding regions of CAV genomes, where the strains isolated in China were the most active and involved in ten of these events. Furthermore, the amino acids variability analysis indicated that the variability coefficient exceeded the estimation limit of 1.00 in VP1, VP2, and VP3 proteins coding regions, demonstrating substantial amino acid drift with the rise of new strains. The current study offers robust insights into the phylogenetic, phylogeographic and genetic diversity characteristics of CAV genomes that may provide valuable data to map the evolutionary history and facilitate preventive measures of CAVs.

鸡传染性贫血（Chicken Infectious Anemia, CIA）是一种免疫抑制性禽类疾病，可导致雏鸡出现再生障碍性贫血、免疫抑制、生长迟缓及淋巴组织萎缩，给全球养禽业造成巨额经济损失。该病由鸡贫血病毒（Chicken Anemia Virus, CAV）引起，该病毒隶属于环病毒科（Anelloviridae）环转病毒属（Gyrovirus）。本研究对1991年至2020年间分离得到的243株鸡贫血病毒全长基因组进行分析，将其划分为GI、GII两大进化枝（clade），二者分别包含3个亚进化枝（sub-clade）GI a-c与4个亚进化枝GII a-d。此外，系统地理学分析（phylogeographic analysis）显示，鸡贫血病毒经多轮突变演化后，传播路径为从日本传入中国，再由中国传入埃及，随后扩散至全球其他国家。本研究还在鸡贫血病毒基因组的编码区与非编码区中共鉴定出11起重组事件，其中中国分离毒株最为活跃，参与了其中10起事件。氨基酸变异分析表明，VP1、VP2及VP3蛋白编码区的变异系数均超过1.00的阈值，证实随着新毒株的出现，病毒发生了显著的氨基酸漂移。本研究为鸡贫血病毒基因组的系统发育、系统地理学及遗传多样性特征提供了可靠的解析依据，可为阐明该病毒的进化历史、制定防控措施提供极具价值的参考数据。