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. 2024 Sep 26;11(10):456.
doi: 10.3390/vetsci11100456.

Genetic and Evolutionary Analysis of Canine Coronavirus in Guangxi Province, China, for 2021-2024

Kaichuang Shi  1   2   3 , Yandi Shi  2 , Yuwen Shi  2 , Yi Pan  1 , Shuping Feng  3 , Zhuo Feng  2 , Yanwen Yin  3 , Yang Tang  2 , Zongqiang Li  2 , Feng Long  3
Affiliations

Genetic and Evolutionary Analysis of Canine Coronavirus in Guangxi Province, China, for 2021-2024

Kaichuang Shi et al. Vet Sci. .

Abstract

Canine coronavirus (CCoV) is an important gastrointestinal pathogen that causes serious harm to pet dogs worldwide. Here, 1791 clinical samples were collected from pet dogs in different pet hospitals in Guangxi Province, southern China, for the 2021-2024 period and detected for CCoV by a multiplex RT-qPCR. The results showed that 8.43% (151/1791) of samples were positive for CCoV. Sixty-five positive samples were selected to amplify, sequence, and analyze S, M, and N genes. A sequence comparison revealed that the nucleotide and amino acid similarities of the S, M, and N genes were 94.86% and 94.62%, 96.85% and 97.80%, and 96.85% and 97.80%, respectively. Phylogenetic analysis indicated that 65 CCoV strains obtained in this study belonged to the CCoV-II genotype, of which 56 CCoV strains belonged to the CCoV-IIa subtype and 9 CCoV strains belonged to the CCoV-IIb subtype. A potential recombination event analysis of S gene sequences indicated that two CCoV strains, i.e., GXBSHM0328-34 and GXYLAC0318-35, have recombination signals. A Bayesian analysis indicated that the evolutionary rates of the S, M, and N genes were 1.791 × 10-3, 6.529 × 10-4, and 4.775 × 10-4 substitutions/site/year, respectively. The population size grew slowly before 1980 and then began to shrink slowly; it then shrank rapidly in 2005 and expanded sharply in 2020, leveling off thereafter. These results indicated the CCoV strains prevalent in Guangxi Province, southern China, showed a high level of genetic diversity and maintained continuous variation among clinical epidemic strains.

Keywords: M gene; N gene; S gene; canine coronavirus (CCoV); genetic diversity; phylogenetic analysis.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Genetic evolutionary relationships of different species of coronaviruses.
Figure 2
Figure 2
The prevalence of CCoV infection in China in 2014–2023.
Figure 3
Figure 3
Distribution of CCoV in Guangxi Province, China.
Figure 4
Figure 4
The CCoV S gene phylogenetic tree. The 65 CCoV strains obtained in this study were marked with black circles (●).
Figure 5
Figure 5
The CCoV M gene phylogenetic tree. The obtained 65 CCoV strains from Guangxi Province in this study were marked with black circles (●).
Figure 6
Figure 6
The CCoV N gene phylogenetic tree. The obtained 65 CCoV strains from Guangxi Province in this study are marked with black circles (●).
Figure 7
Figure 7
Maximum clade credibility (MCC) tree of CCoV-II S gene sequences.
Figure 8
Figure 8
The demographic history of the CCoV-II strains. The blue line indicates the median estimate of the effective population size, and the shaded regions indicate the corresponding 95% confidence interval.
Figure 9
Figure 9
Mutations of amino acids encoded by CCoV S gene. (A,B) CCoV-IIa strain; (C,D) CCoV-IIb strain.
Figure 9
Figure 9
Mutations of amino acids encoded by CCoV S gene. (A,B) CCoV-IIa strain; (C,D) CCoV-IIb strain.
Figure 9
Figure 9
Mutations of amino acids encoded by CCoV S gene. (A,B) CCoV-IIa strain; (C,D) CCoV-IIb strain.
Figure 10
Figure 10
Recombination analysis of CCoV S gene sequences. (A) GXBSHM0328-34 strain; (B) GXYLAC0318-35 strain. 1: minor parent; 2: major parent.
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References

    1. Woo P.C.Y., de Groot R.J., Haagmans B., Lau S.K.P., Neuman B.W., Perlman S., Sola I., van der Hoek L., Wong A.C.P., Yeh S.H. ICTV virus taxonomy profile: Coronaviridae 2023. J. Gen. Virol. 2023;104:001843. doi: 10.1099/jgv.0.001843. - DOI - PubMed
    1. Liu Y., Deng Y., Niu S., Zhu N., Song J., Zhang X., Su W., Nie W., Lu R., Irwin D.M., et al. Discovery and identification of a novel canine coronavirus causing a diarrhea outbreak in Vulpes. Sci. Bull. 2023;68:2598–2606. doi: 10.1016/j.scib.2023.09.011. - DOI - PubMed
    1. Li N., Bai Y., Liu R., Guo Z., Yan X., Xiang K., Liu F., Zhao L., Ge J. Prevalence and genetic diversity of canine coronavirus in northeastern China during 2019–2021. Comp. Immunol. Microbiol. Infect. Dis. 2023;94:101956. doi: 10.1016/j.cimid.2023.101956. - DOI - PubMed
    1. Licitra B.N., Duhamel G.E., Whittaker G.R. Canine enteric coronaviruses: Emerging viral pathogens with distinct recombinant spike proteins. Viruses. 2014;6:3363–3376. doi: 10.3390/v6083363. - DOI - PMC - PubMed
    1. Duijvestijn M., Mughini-Gras L., Schuurman N., Schijf W., Wagenaar J.A., Egberink H. Enteropathogen infections in canine puppies: (Co-)occurrence, clinical relevance and risk factors. Vet. Microbiol. 2016;195:115–122. doi: 10.1016/j.vetmic.2016.09.006. - DOI - PMC - PubMed

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