Research Article
Year 2020,
Volume: 67 Issue: 3, 265 - 271, 03.06.2020
Abstract
References
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- 18. Jeoung SY, Ann SY, Kim HT, et al (2014): M gene analysis of canine coronavirus strains detected in Korea. J Vet Sci, 15, 495-502.
- 19. King AM, Lefkowitz E, Adams MJ, et al (2011): Virus Taxonomy. In: AM King, E Lefkowitz, MJ Adams, EB Carstens (Eds), 9th Report of the International Committee on Taxonomy of Viruses. Elsevier, UK.
- 20. Kumar S, Stecher G, Li M, et al (2018): MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol, 35, 1547-1549.
- 21. Lai MM, Holmes KV (2001): Coronaviridae: the viruses and their replication. 1163–1185. In: DM Knipe, PM Howley (Ed). Fields Virology. Lippincott Williams and Wilkins, Philadelphia.
- 22. Ma G, Wang Y, Lu C (2008): Molecular characterization of the 9.36 kb C-terminal region of canine coronavirus 1-71 strain. Virus Genes, 36, 491-497.
- 23. Pratelli A, Tempesta M, Greco G, et al (1999): Development of a nested PCR assay for the detection of canine coronavirus. J Virol Methods, 80, 11-15.
- 24. Pratelli A, Martella V, Pistello M, et al (2003): Identification of coronaviruses in dogs that segregate separately from the canine coronavirus genotype. J Virol Methods, 107, 213-222.
- 25. Pratelli A, Decaro N, Tinelli A, et al (2004): Two genotypes of canine coronavirus simultaneously detected in the fecal samples of dogs with diarrhea. J Clin Microbiol, 42, 1797-1799.
- 26. Pratelli A (2011): The evolutionary processes of canine coronaviruses. Adv Virol, 2011, 1-10.
- 27. Saitou N, Nei M (1987): The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol, 4, 406-425.
- 28. Stavisky J, Pinchbeck G, Gaskell RM, et al (2012): Cross sectional and longitudinal surveys of canine enteric coronavirus infection in kennelled dogs: a molecular marker for biosecurity. Infect Genet Evol, 12, 1419-1426.
- 29. Tamura K (1992): Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol Biol Evol, 9, 678-687.
- 30. Yeşilbağ K, Yılmaz Z, Torun S, et al (2004): Canine coronavirus infection in Turkish dog population. J Vet Med, Series B, 51, 353-355.
Phylogenetic analysis of partial transmembrane protein gene of canine coronaviruses detected in Turkey
Abstract
Canine coronaviruses (CCoVs), a member of the family Coronaviridae, are the causative agents of acute gastroenteritis and are genetically divided into two groups, CCoV type I and CCoV type II. The aim of this study was to detect and characterize CCoV strains in fecal samples from six dogs exhibited gastrointestinal system symptoms. To determine the presence of the CCoV RNA, samples were tested by the reverse transcription-polymerase chain reaction (RT-PCR) assay targeting the partial M gene and then sequenced. Among six samples tested, two were found positive for CCoV RNA. Phylogenetic analysis was performed by Maximum-Likelihood (ML) method and revealed that one of the obtained field sequences was classified into CCoV-I genotype; and the other positive sample grouped in CCoV-II genotype. Both genogroups demonstrated broad genetic diversity. Phylogenetic analysis of amino acid sequences shows that our CCoV field strains was closely related to Italy and Brazil strains and placed on different genogroup clades in the CCoV cluster. Sequence comparison of the partial M gene revealed nucleotide identity of 71–100% and 68–100% similarity among the 25 coronavirus strains. TR/Ccv2 (MK636864) and TR/Ccv6 (MK636865) obtained in this study demonstrated 78.5-97.5% and 71–99% nucleotide identity with other CCoV strains around the world respectively. The results of the study demonstrate, CCoV strains from different genogroups are circulating in Turkey and this is a report on the phylogenetic analysis of a CCoV in Turkey, which there is limited information.
Keywords
References
- 1. Appel MJ (1987): Canine Coronavirus. 115–122. In: MJ Appel (Ed), Virus Infections of Carnivores. Elsevier Science Publishers, The Netherlands.
- 2. Avci O, Bulut O, Yapici O, et al (2016): Canine coronavirus infection in dogs in Turkey: Virological and serological evidence. Indian J Anim, 50, 565-568.
- 3. Beaudette FR, Hudson CB (1937): Cultivation of the virus of infectious bronchitis. J Am Vet Med A, 90, 51-60.
- 4. Campanella JJ, Bitincka L, Smalley J (2003): MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. BMC bioinformatics, 4, 29.
- 5. Chomczynski P, Sacchi, N (1987): Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem, 162, 156-159.
- 6. Costa EM, de Castro TX, de Oliveira Bottino F, et al (2014): Molecular characterization of canine coronavirus strains circulating in Brazil. Vet Microbiol, 168, 8-15.
- 7. Decaro N, Buonavoglia C (2008): An update on canine coronaviruses: viral evolution and pathobiology. Vet Microbiol, 132, 221-234.
- 8. Decaro N, Mari V, Campolo M, et al (2009): Recombinant canine coronaviruses related to transmissible gastroenteritis virus of swine are circulating in dogs. J Virol, 83, 1532-1537.
- 9. Decaro N, Buonavoglia C (2011): Canine coronavirus: not only an enteric pathogen. Vet Clin N Am-Small, 41, 1121-1132.
- 10. Decaro N, Mari V, Elia G, et al (2015a): Full-length genome analysis of canine coronavirus type I. Virus Res, 210, 100-105.
- 11. Decaro N, Martella V, Elia G, et al (2015b): U.S. Patent No. 9,200,259. U.S. Patent and Trademark Office. Washington, D.C.
- 12. Erles K, Brownlie J (2008): Canine respiratory coronavirus: an emerging pathogen in the canine infectious respiratory disease complex. Vet Clin N Am-Small, 38, 815-825.
- 13. Erles K, Brownlie J (2009): Sequence analysis of divergent canine coronavirus strains present in a UK dog population. Virus Res, 141, 21-25.
- 14. Felsenstein J (1985): Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783-791.
- 15. Gibbs AJ, Gibbs MJ, Armstrong JS (2004): The phylogeny of SARS coronavirus. Arch Virol, 149, 621-624.
- 16. Gür S, Gençay A, Doğan N (2008): A serologic investigation for canine corona virus infection in individually reared dogs in central Anatolia. Erciyes Üniv Vet Fak Derg, 5, 67-71.
- 17. Herrewegh AA, Smeenk I, Horzinek MC, et al (1998): Feline coronavirus type II strains 79-1683 and 79-1146 originate from a double recombination between feline coronavirus type I and canine coronavirus. J Virol, 72, 4508-4514.
- 18. Jeoung SY, Ann SY, Kim HT, et al (2014): M gene analysis of canine coronavirus strains detected in Korea. J Vet Sci, 15, 495-502.
- 19. King AM, Lefkowitz E, Adams MJ, et al (2011): Virus Taxonomy. In: AM King, E Lefkowitz, MJ Adams, EB Carstens (Eds), 9th Report of the International Committee on Taxonomy of Viruses. Elsevier, UK.
- 20. Kumar S, Stecher G, Li M, et al (2018): MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol, 35, 1547-1549.
- 21. Lai MM, Holmes KV (2001): Coronaviridae: the viruses and their replication. 1163–1185. In: DM Knipe, PM Howley (Ed). Fields Virology. Lippincott Williams and Wilkins, Philadelphia.
- 22. Ma G, Wang Y, Lu C (2008): Molecular characterization of the 9.36 kb C-terminal region of canine coronavirus 1-71 strain. Virus Genes, 36, 491-497.
- 23. Pratelli A, Tempesta M, Greco G, et al (1999): Development of a nested PCR assay for the detection of canine coronavirus. J Virol Methods, 80, 11-15.
- 24. Pratelli A, Martella V, Pistello M, et al (2003): Identification of coronaviruses in dogs that segregate separately from the canine coronavirus genotype. J Virol Methods, 107, 213-222.
- 25. Pratelli A, Decaro N, Tinelli A, et al (2004): Two genotypes of canine coronavirus simultaneously detected in the fecal samples of dogs with diarrhea. J Clin Microbiol, 42, 1797-1799.
- 26. Pratelli A (2011): The evolutionary processes of canine coronaviruses. Adv Virol, 2011, 1-10.
- 27. Saitou N, Nei M (1987): The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol, 4, 406-425.
- 28. Stavisky J, Pinchbeck G, Gaskell RM, et al (2012): Cross sectional and longitudinal surveys of canine enteric coronavirus infection in kennelled dogs: a molecular marker for biosecurity. Infect Genet Evol, 12, 1419-1426.
- 29. Tamura K (1992): Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol Biol Evol, 9, 678-687.
- 30. Yeşilbağ K, Yılmaz Z, Torun S, et al (2004): Canine coronavirus infection in Turkish dog population. J Vet Med, Series B, 51, 353-355.
There are 30 citations in total.
Details
| Primary Language | English |
|---|---|
| Subjects | Veterinary Surgery |
| Journal Section | Research Article |
| Authors | |
| Publication Date | June 3, 2020 |
| Published in Issue | Year 2020Volume: 67 Issue: 3 |