Department of Veterinary Medicine, Institute of Applied Science, Ho Chi Minh City University of Technology (HUTECH), 475A Dien Bien Phu Street, Ward 25, Binh Thanh District, Ho Chi Minh City 700000, Viet Nam.
NTT High-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh City 700000, Viet Nam.
Comp Immunol Microbiol Infect Dis. 2021 Jun;76:101654. doi: 10.1016/j.cimid.2021.101654. Epub 2021 Apr 24.
Feline- and canine-derived coronaviruses (FCoVs and CCoVs) are widespread among dog and cat populations. This study was to understand the route of disease origin and viral transmission in veterinary animals and in human through comparative pan-genomic analysis of coronavirus sequences, especially retrieved from genomes of FCoV and CCoV. Average nucleotide identity based on complete genomes might clustered CoV strains according to their infected host, with an exception of type II of CCoV (accession number KC175339) that was clustered closely to virulent FCoVs. In contrast, the hierarchical clustering based on gene repertories retrieved from pan-genome analysis might divided the examined coronaviruses into host-independent clusters, and formed obviously the cluster of Alphacoronaviruses into sub-clusters of feline-canine, only feline, feline-canine-human coronavirus. Also, functional analysis of genomic subsets might help to divide FCoV and CCoV pan-genomes into (i) clusters of core genes encoding spike, membrane, nucleocapsid proteins, and ORF1ab polyprotein; (ii) clusters of core-like genes encoding nonstructural proteins; (iii) clusters of accessory genes encoding the ORF1A; and (iv) two singleton genes encoding nonstructural protein and polyprotein 1ab. Seven clusters of gene repertories were categorized as common to the FCoV and/or CCoV genomes including pantropic and high virulent strains, illustrating that distinct core-like genes/accessory genes concerning to their pathogenicity should be exploited in further biotype analysis of new isolate. In conclusion, the phylogenomic analyses have allowed the identification of trends in the viral genomic data, especially in developing a specific control measures against coronavirus disease, such as the selection of good markers for differentiating new species from common and/or pantropic isolates.
猫冠状病毒（FCoV）和犬冠状病毒（CCoV）广泛存在于犬猫群体中。本研究旨在通过对冠状病毒序列进行比较泛基因组分析，尤其是从 FCoV 和 CCoV 基因组中检索到的序列，了解兽医动物和人类疾病的起源和病毒传播途径。基于完整基因组的平均核苷酸同一性可能会根据其感染的宿主对 CoV 株进行聚类，CCoV 类型 II（登录号 KC175339）是一个例外，它与高致病性 FCoV 聚类密切。相反，基于泛基因组分析中从基因库检索到的基因谱的层次聚类可能会将检查的冠状病毒分为宿主独立的聚类，并且明显地将α冠状病毒聚类为猫科-犬科、仅猫科、猫科-犬科-人冠状病毒的亚聚类。此外，基因组子集的功能分析可能有助于将 FCoV 和 CCoV 泛基因组分为 (i) 编码刺突、膜、核衣壳蛋白和 ORF1ab 多蛋白的核心基因簇；(ii) 编码非结构蛋白的核心样基因簇；(iii) 编码 ORF1A 的辅助基因簇；和 (iv) 编码非结构蛋白和多蛋白 1ab 的两个单基因。七个基因库聚类被归类为 FCoV 和/或 CCoV 基因组所共有，包括泛嗜性和高致病性株，这表明与它们的致病性有关的不同核心样基因/辅助基因应在新分离株的生物型分析中进一步利用。总之，系统基因组分析允许识别病毒基因组数据中的趋势，特别是在制定针对冠状病毒病的特定控制措施方面，例如选择区分新物种与常见和/或泛嗜性分离株的良好标记。
