Genetic and Evolutionary Analysis of Canine Coronavirus in Guangxi Province, China, for 2021–2024
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Clinical Sample Collection and Test
2.2. PCR Amplification of Samples
2.2.1. Primer Design
2.2.2. Sequencing of Target Fragments
2.3. CCoV Prevalence
2.3.1. CCoV Time Distribution Analysis in China
2.3.2. Investigation of CCoV in Guangxi Province
2.4. Phylogenetic and Recombination Analyses
2.5. Estimation of the Evolutionary Rates
3. Results
3.1. Analysis of Temporal Distribution of CCoV in China
3.2. Test Results of Clinical Samples
3.3. Prevalence Analysis of CCoV in Guangxi Province
3.4. Sequence Similarity Analysis
3.5. Phylogenetic Trees Based on CCoV S, M, and N Genes
3.5.1. Phylogenetic Trees of S Gene Sequences
3.5.2. Phylogenetic Trees of M Gene Sequences
3.5.3. Phylogenetic Trees of N Gene Sequences
3.6. Bayesian Temporal Dynamics Analysis
3.7. Analysis of Amino Acid Variations in CCoV S Gene
3.8. Analysis of Recombination in S Gene
3.9. Evolutionary Rates Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene | Primer | Sequence (5′→3′) | Tm (°C) | Product/bp |
---|---|---|---|---|
M | CCoV-M-F | CCTGATGAAGCACTCCTTGTT | 58.7 | 911 |
CCoV-M-R | GGCCACGAGAATTGGAAAGA | 54.5 | ||
N | CCoV-N-F | TCAACAGACGCAAGAACTGATA | 55.9 | 1225 |
CCoV-N-R | TCGTTTAGTTCGTCACCTCATC | 57.4 | ||
S | CCoV-S1-F | ATGGTCGTTGGATTACTAAG | 50.9 | 1180 |
CCoV-S1-R | GCACCCATGCCAGATTGTAC | 58.7 | ||
CCoV-S2-F | GTTAATTGYTTRTGGCCAGT | 54.5 | 1154 | |
CCoV-S2-R | CAGGAGTCTAAGTGTARCACTGAC | 57.2 | ||
CCoV-S3-F | TGGTGCCAACTGYAAGTTTGATG | 58.5 | 1190 | |
CCoV-S3-R | GTGCACCTAATGTTATACCACCTGC | 60.7 | ||
CCoV-S4-F | TACCTGGTGTGGCTAATGATGAC | 58.5 | 901 | |
CCoV-S4-R | GGTATAATACTAGGCAAGTCAATTAC | 54.5 | ||
CCoV-S5-F | GACTCCCAGAACTATGTATCAGCC | 59.9 | 638 | |
CCoV-S5-R | CCATACAAGACCTGTAATGACTC | 57.0 |
Variables | Number of Dogs (n = 1791) | CCoV-Positive Dogs (n = 151) | CCoV-Negative Dogs (n = 1640) | p Value | |
---|---|---|---|---|---|
Sex | Female | 1052 | 96 (9.13%) | 956 (90.87%) | >0.05 |
Male | 739 | 55 (7.44%) | 684 (92.56%) | ||
Age | <6 months | 776 | 107 (13.79%) | 674 (86.86%) | <0.05 |
6–24 months | 560 | 27 (4.82%) | 533 (95.18%) | ||
>2 years | 455 | 17 (3.74%) | 438 (92.26%) | ||
Clinical status | Asymptomatic | 831 | 20 (2.41%) | 811 (97.59%) | <0.05 |
Sick | 960 | 131 (13.65%) | 829 (86.35%) | ||
Season | Spring (Mar–May) | 431 | 59 (13.69%) | 372 (86.31%) | <0.05 |
Summer (Jun–Aug) | 515 | 26 (5.05%) | 489 (94.95%) | ||
Autumn (Sep–Nov) | 473 | 47 (9.94%) | 426 (90.06%) | ||
Winter (Dec–Feb) | 372 | 19 (5.11%) | 353 (94.89%) |
Gene | Evolutionary Rate (s/s/y) | 95% HPD (s/s/y) |
---|---|---|
S | 1.791 × 10−3 | 1.013 × 10−3–2.458 × 10−3 |
M | 6.529 × 10−4 | 4.817 × 10−4–8.2772 × 10−4 |
N | 4.775 × 10−4 | 3.607 × 10−4–5.8693 × 10−4 |
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Shi, K.; Shi, Y.; Shi, Y.; Pan, Y.; Feng, S.; Feng, Z.; Yin, Y.; Tang, Y.; Li, Z.; Long, F. Genetic and Evolutionary Analysis of Canine Coronavirus in Guangxi Province, China, for 2021–2024. Vet. Sci. 2024, 11, 456. https://doi.org/10.3390/vetsci11100456
Shi K, Shi Y, Shi Y, Pan Y, Feng S, Feng Z, Yin Y, Tang Y, Li Z, Long F. Genetic and Evolutionary Analysis of Canine Coronavirus in Guangxi Province, China, for 2021–2024. Veterinary Sciences. 2024; 11(10):456. https://doi.org/10.3390/vetsci11100456
Chicago/Turabian StyleShi, Kaichuang, Yandi Shi, Yuwen Shi, Yi Pan, Shuping Feng, Zhuo Feng, Yanwen Yin, Yang Tang, Zongqiang Li, and Feng Long. 2024. "Genetic and Evolutionary Analysis of Canine Coronavirus in Guangxi Province, China, for 2021–2024" Veterinary Sciences 11, no. 10: 456. https://doi.org/10.3390/vetsci11100456