This work aimed to study the epidemiology and molecular detection of existing canine coronavirus (CCoV) strain circulating in Egypt. A total number of 86 dogs with clinical signs suggestive for CCoV infection was subjected to clinical examination and quick immunochromatography (IC) on faecal swabs to detect viral antigen. To identify CCoV viral RNA and S protein gene in blood and faeces, conventional PCR and quantitative RT-PCR were used. All examined dogs showed clinical signs suggestive of CCoV infection. Only 32 out of 86 dogs were positive for IC. Of all samples, 36 showed positive results in PCR and the amplification products from these 36 samples were confirmed as CCoV-S protein partial gene by the analysis of nucleotide sequence. However, the qRTPCR analysis detected 45 positive samples e.g. more than those of IC or conventional polymerase chain reaction. Statistical evaluation of IC and conventional PCR to the results of qRT-PCR performance showed sensitivity, specificity, accuracy, positive and negative predictive values of 71%, 100%, 84.9%, 100%, 75.9% for IC and 80%, 100%, 89.5%, 100%, 82% for PCR, respectively. Sex and age had no effects on IC and PCR results. The prevalence of CCoV infection among the population of this study was 52.3%. Sequence analysis results proved that CCoV strain 59/08 was the strain, circulating in Egypt among dog populations. PCR products of the CCoV cDNA were closely identical to published CCoV-S partial gene. The NCBI Genbank accession number of sequence of the studied gene (CCoV-S partial gene) in this study was KY655745.
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