病毒宏基因组学揭示了实验大鼠粪便中的两种新型环状病毒。
Viral metagenomics reveals two novel anelloviruses in feces of experimental rats.
机构信息
Joint Institute of Molecular Etiology Diagnosis, Donghai County People's Hospital, Jiangsu University, Donghai, 222300, Jiangsu, China.
School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China.
出版信息
Virol J. 2021 Dec 20;18(1):252. doi: 10.1186/s12985-021-01723-9.
BACKGROUND
Rodents are widely distributed and are the natural reservoirs of a diverse group of zoonotic viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Rodents are commonly used in animal testing, particularly mice and rats. Experimental rats are important animal models, and a history of pathogenic infections in these animals will directly affect the animal trial results. The pathogenicity of Anellovirus (AV) remains poorly understood due to the lack of a suitable model cell line or animal to support the viral cycle. This study aimed to discover possible anelloviruses from the virome in feces of experimental rats by viral metagenomic technique.
METHODS
Fecal samples were collected from 10 commercial SD rats and pooled into a sample pool and then subjected to libraries construction which was then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline and two novel anelloviruses (AVs) were identified from fecal sample of experimental rats. The prevalence of these two viruses was investigated by conventional PCR.
RESULTS
The complete genomic sequence of these two AVs were determined and fully characterized, with strain name ratane153-zj1 and ratane153-zj2. The circular genomes of ratane153-zj1 and ratane153-zj2 are 2785 nt and 1930 nt in length, respectively, and both include three ORFs. Ratane153-zj1 closely clustered with members within the genus Wawtorquevirus and formed a separate branch based on the phylogenetic tree constructed over the amino acid sequence of ORF1 of the two AVs identified in this study and other related AVs. While the complete amino acid sequences of ORF1 of ratane153-zj2 (nt 335 to 1390) had the highest sequence identity with an unclassified AV (GenBank No. ATY37438) from Chinchilla lanigera, and they clustered with one AV (GenBank No. QYD02305) belonging to the genus Etatorquevirus from Lynx rufus. Conventional PCR with two sets of specific primers designed based on the two genomes, respectively, showed that they were detectable at a low frequency in cohorts of experimental rats.
CONCLUSION
Our study expanded the genome diversity of AVs and provided genetic background information of viruses existed in experimental rats.
背景
啮齿动物分布广泛，是多种人畜共患病毒的天然宿主。因此，分析啮齿动物所携带的病毒多样性有助于预测和降低人畜共患病毒性疾病未来出现的风险。啮齿动物通常用于动物实验，尤其是老鼠和大鼠。实验大鼠是重要的动物模型，这些动物的致病性感染史将直接影响动物试验结果。由于缺乏合适的模型细胞系或动物来支持病毒周期，因此对细小病毒（Anellovirus，AV）的致病性仍了解甚少。本研究旨在通过病毒宏基因组技术从实验大鼠粪便中的病毒组中发现可能的细小病毒。
方法
收集 10 只商用 SD 大鼠的粪便样本，将其混合为样本池，然后进行文库构建，然后在 Illumina MiSeq 平台上进行测序。使用病毒宏基因组分析流程对测序结果进行分析，从实验大鼠粪便样本中鉴定出两种新型细小病毒（AVs）。通过常规 PCR 调查这两种病毒的流行情况。
结果
确定并充分表征了这两种 AV 的完整基因组序列，其病毒株名称分别为 ratane153-zj1 和 ratane153-zj2。ratane153-zj1 和 ratane153-zj2 的圆形基因组分别长 2785 个核苷酸和 1930 个核苷酸，均包含三个 ORF。ratane153-zj1 与属内的 Wawtorquevirus 成员密切聚类，并基于本研究中鉴定的两种细小病毒和其他相关细小病毒的 ORF1 氨基酸序列构建的系统进化树，形成了一个单独的分支。而 ratane153-zj2 的 ORF1 全长氨基酸序列（nt 335 至 1390）与 Chinchilla lanigera 中一种未分类的细小病毒（GenBank No. ATY37438）具有最高的序列同一性，并且它们与 Lynx rufus 中的一种细小病毒（GenBank No. QYD02305）聚类，属于 Etatorquevirus 属。基于两个基因组分别设计的两套特异性引物的常规 PCR 显示，它们在实验大鼠的队列中以低频率检测到。
结论
本研究扩展了细小病毒的基因组多样性，并提供了实验大鼠中存在的病毒的遗传背景信息。
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