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Peer-reviewedCC BY-NC-ND 4.0Virology Journal

Local genetic distance-guided qPCR method for genotyping canine/feline coronaviruses

  • Deming Liu1,2,3
  • Wenwen Yang1,2,3
  • Yi Liu1,2,3
  • Shiyu Zeng1,2,3
  • Di Sun1,2,3
  • Shun Chen1,2,3
  • Mafeng Liu1,2,3
  • Dekang Zhu1,2,3
  • Mingshu Wang1,2,3
  • Renyong Jia1,2,3
  • Shaqiu Zhang1,2,3
  • Ying Wu1,2,3
9 more authors
  • Juan Huang1,2,3
  • Bin Tian1,2,3
  • Qiao Yang1,2,3
  • Xinxin Zhao1,2,3
  • Zhen Wu1,2,3
  • Yu He1,2,3
  • Jingyu Cao4,5
  • Anchun Cheng1,2,3
  • Xumin Ou1,2,3,6
6 affiliations
  1. 1Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Sichuan Agricultural University, Chengdu, China
  2. 2Agricultural Animal Diseases and Veterinary Public Health Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
  3. 3Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
  4. 4Chengdu Institute of Food Inspection, Chengdu, China
  5. 5Key Laboratory of Monitoring and Assessment on Novel Food Raw Materials, State Administration for Market Regulation, Chengdu, China
  6. 6Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu, Sichuan China
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Abstract

Canine coronavirus (CCoV) and feline coronavirus (FCoV) are highly infectious in companion animals. Nevertheless, due to genomic recombination and mutagenesis of the two CoVs, these difficulties dampen their precise diagnosis especially by genotypes. Herein, we addressed these problems and developed a simple real-time quantitative polymerase chain reaction (qPCR) method capable of genotyping major CCoV and FCoV, and partially surveyed the current epidemiological prevalence in dog and cat populations. Exploiting both evolutionary analysis and genome-wide genetic distance analysis, we identified locally conserved genomic regions that are specific to each genotype, including representative CCoV (sub)genotypes (I, IIa, IIb and IIc) and FCoV genotypes (I and II). By targeting these conserved regions, genotype-specific primer pairs were designed and cross-validated by in silico BLAST analysis, PCR melt curve and sequencing analysis. These primer pairs were integrated into the development of a simple qPCR approach and applied for genotyping potential CCoVs and FCoVs in Chengdu, China. We found 62.71% positivity in symptomatic dogs (n = 59) and 66.00% positivity in symptomatic cats (n = 50), with CCoV-I and FCoV-I being major genotypes in their native hosts during 2024–2026. Interestingly, many dogs and cats respectively tested positive for multiple CCoV and FCoV genotypes, with cross-host detection of FCoV RNA in dogs and CCoV RNA in cats. Collectively, we established a genotyping qPCR approach that enables the detection of CCoV and FCoV (sub)genotypes within a single analytical workflow, using one reaction per genotype.

Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12985-026-03263-6.

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Cite

BibTeXRIS
BibTeX
@article{liu2026local,
  title = {{Local genetic distance-guided qPCR method for genotyping canine/feline coronaviruses}},
  author = {Deming Liu and Wenwen Yang and Yi Liu and Shiyu Zeng and Di Sun and Shun Chen and Mafeng Liu and Dekang Zhu and Mingshu Wang and Renyong Jia and Shaqiu Zhang and Ying Wu and Juan Huang and Bin Tian and Qiao Yang and Xinxin Zhao and Zhen Wu and Yu He and Jingyu Cao and Anchun Cheng and Xumin Ou},
  journal = {Virology Journal},
  year = {2026},
  month = aug,
  doi = {10.1186/s12985-026-03263-6},
  url = {https://doi.org/10.1186/s12985-026-03263-6},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - Local genetic distance-guided qPCR method for genotyping canine/feline coronaviruses
AU  - Deming Liu
AU  - Wenwen Yang
AU  - Yi Liu
AU  - Shiyu Zeng
AU  - Di Sun
AU  - Shun Chen
AU  - Mafeng Liu
AU  - Dekang Zhu
AU  - Mingshu Wang
AU  - Renyong Jia
AU  - Shaqiu Zhang
AU  - Ying Wu
AU  - Juan Huang
AU  - Bin Tian
AU  - Qiao Yang
AU  - Xinxin Zhao
AU  - Zhen Wu
AU  - Yu He
AU  - Jingyu Cao
AU  - Anchun Cheng
AU  - Xumin Ou
PY  - 2026
DA  - 2026/08/04
JO  - Virology Journal
DO  - 10.1186/s12985-026-03263-6
UR  - https://doi.org/10.1186/s12985-026-03263-6
AB  - Canine coronavirus (CCoV) and feline coronavirus (FCoV) are highly infectious in companion animals. Nevertheless, due to genomic recombination and mutagenesis of the two CoVs, these difficulties dampen their precise diagnosis especially by genotypes. Herein, we addressed these problems and developed a simple real-time quantitative polymerase chain reaction (qPCR) method capable of genotyping major CCoV and FCoV, and partially surveyed the current epidemiological prevalence in dog and cat populations. Exploiting both evolutionary analysis and genome-wide genetic distance analysis, we identified locally conserved genomic regions that are specific to each genotype, including representative CCoV (sub)genotypes (I, IIa, IIb and IIc) and FCoV genotypes (I and II). By targeting these conserved regions, genotype-specific primer pairs were designed and cross-validated by in silico BLAST analysis, PCR melt curve and sequencing analysis. These primer pairs were integrated into the development of a simple qPCR approach and applied for genotyping potential CCoVs and FCoVs in Chengdu, China. We found 62.71% positivity in symptomatic dogs (n = 59) and 66.00% positivity in symptomatic cats (n = 50), with CCoV-I and FCoV-I being major genotypes in their native hosts during 2024–2026. Interestingly, many dogs and cats respectively tested positive for multiple CCoV and FCoV genotypes, with cross-host detection of FCoV RNA in dogs and CCoV RNA in cats. Collectively, we established a genotyping qPCR approach that enables the detection of CCoV and FCoV (sub)genotypes within a single analytical workflow, using one reaction per genotype.  Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12985-026-03263-6.
SN  - 1743-422X
ER  -