College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, China.
Agricultural Development Service Center of Hunnan District, Shenyang 110000, China.
Biomed Res Int. 2022 Apr 13;2022:9627961. doi: 10.1155/2022/9627961. eCollection 2022.
To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV.
Anal swab samples were collected from 35 foxes to detect the presence of CoV and obtain the virus sequence. Phylogenetic analysis was conducted using MrBayes. The possibility of recombination within these sequences was assessed using GARD. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Data Monkey platforms.
Of the 35 samples, two were positive, and complete genome sequences for the viruses were obtained. Phylogenetic analysis, using Bayesian methods, of these sequences, together with other CoV sequences, revealed that the fox CoV sequences clustered with canine coronavirus (CCoV) sequences, with sequences from other carnivores more distantly related. In contrast to the feline, ferret and mink CoV sequences that clustered into species-specific clades, the fox CoV fell within the CCoV clade. Minimal evidence for recombination was found among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes, respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively.
The complete genome sequence of fox CoV has been obtained for the first time. The results suggest that the genome sequence of fox CoV may have experienced adaptive evolution in the genes replication, entry, and virulence. The number of sites in each gene that experienced negative selection is far greater than the number that underwent positive selection, suggesting that most of the sequence is highly conserved and important for viral survive. However, positive selection at a few sites likely aided these viruses to adapt to new environments.
报道首个通过全基因组扩增获得的完整狐狸冠状病毒（CoV）基因组序列，并了解狐狸 CoV 的适应性进化。
从 35 只狐狸中采集肛门拭子样本，以检测 CoV 的存在并获得病毒序列。使用 MrBayes 进行系统发育分析。使用 GARD 评估这些序列内重组的可能性。使用 PAML 和 Data Monkey 平台上的方法评估这些序列经历的选择压力水平。
35 个样本中，有 2 个为阳性，获得了病毒的完整基因组序列。使用贝叶斯方法对这些序列和其他 CoV 序列进行的系统发育分析表明，狐狸 CoV 序列与犬冠状病毒（CCoV）序列聚类，而与其他食肉动物的序列关系较远。与聚类到种特异性分支的猫、雪貂和水貂 CoV 序列不同，狐狸 CoV 属于 CCoV 分支。在这些序列中未发现明显的重组证据。在 M、N、S 和 7B 基因中分别鉴定出 7、3、14 和 2 个正选择位点，在 M、N 和 S 基因中分别鉴定出 99、111 和 581 个负选择位点。
首次获得了狐狸 CoV 的完整基因组序列。结果表明，狐狸 CoV 的基因组序列在基因复制、进入和毒力方面可能经历了适应性进化。每个基因中经历负选择的位点数量远远大于经历正选择的位点数量，表明大多数序列高度保守，对病毒的存活至关重要。然而，少数位点的正选择可能有助于这些病毒适应新环境。
