Viral pathogens are the primary cause of canine gastroenteritis. However, few structured comprehensive studies on the viral etiology of canine gastroenteritis have been conducted. In this study, 475 rectal swabs collected over three years (2018-2021) from clinical canine gastroenteritis cases were screened for the presence of six major enteric viruses – canine parvovirus 2 (CPV-2), canine distemper virus (CDV), canine adenovirus 2 (CAdV-2), canine coronavirus (CCoV), canine astrovirus (CaAstV), and canine rotavirus (CRV) – by real-time PCR. The most frequently detected virus was CPV-2, which was present in 64.8% of the samples (subtype 2a, 21.1%; 2b, 77.4%; 2c, 1.5%), followed by CDV (8%), CaAstV (7.2%), CCoV (5.9%), and CAdV-2 (4.6%). Two to four of these viruses in different combinations were found in 16.8% of the samples, and CRV was not detected. The complete genome sequences of Indian isolates of CDV, CCoV, and CaAstV were determined for the first time, and phylogenetic analysis was performed. This study highlights the need for routine prophylactic vaccination with the appropriate vaccines. Notably, 70.3% of animals vaccinated with DHPPiL were found to be positive for at least one virus. Hence, regular molecular analysis of the prevalent viruses is crucial for addressing vaccination failures. Supplementary Information The online version contains supplementary material available at 10.1007/s00705-022-05674-6.

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Viral pathogens account for major aetiology of canine gastroenteritis in India. However, till date, there was no structured comprehensive study reported on the viral aetiology of canine gastroenteritis in India. To elucidate this, 475 rectal swabs collected over a period of three years (2018-2021) from clinical canine gastroenteritis cases were screened by real-time PCR for the presence of six majorly known enteric viruses (Canine parvovirus -2 (CPV-2), canine distemper virus (CDV), canine adenovirus-2 (CAdV-2), canine corona virus (CCoV), canine astrovirus (CaAstV), canine rotavirus (CRV)). 71.6% of the samples were found to harbour at least one of the five viruses tested (CPV-2/2a/2b/2c, CDV, CAdV-2, CCoV and CaAstV), whereas, there was no evidence of CRV. The overall incidence rate for each virus was found highest at 64.8% for CPV-2/2a/2b/2c (2a: 21.1%, 2b: 77.4%, 2c: 1.5%), followed by 8% for CDV, 7.2% for CaAstV, 5.9% for CCoV and 4.6% for CAdV-2 with 16.8% incidence for coinfections ranging from two to four viruses in different combinations. Further, for the first time we report the whole genome sequences of CDV, CCoV and CaAstV Indian isolates from canine gastroenteritis cases. Phylogenetic analysis of whole genome revealed that CDV clustered with Asia-1 lineage, CaAstV clustered with group III that consists of China and Brazil isolates, and CCoV clustered with group II that consists of China and Taipei isolates. This study adds to our knowledge on the prevalence of these pathogens in the Indian subcontinent and highlights the need for relevant and routine vaccine prophylactic measures. It is alarming to note that 70.3% of animals vaccinated with DHPPIL were found positive for at least one virus. Hence, regular molecular analysis of the prevalent viruses is crucial to address vaccination failures.

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Viral pathogens account for the major aetiology of canine gastroenteritis. However, structured comprehensive studies on viral aetiology of canine gastroenteritis are sparse. To this end, 475 rectal swabs collected over a period of three years (2018–2021) from clinical canine gastroenteritis cases were screened for the presence of six majorly known enteric viruses (CPV-2, CDV, CAdV-2, CCoV, CaAstV, CRV), by real-time PCR. The overall incidence rate for each virus was found highest at 64.8% for CPV-2/2a/2b/2c (2a: 21.1%, 2b: 77.4%, 2c: 1.5%), followed by 8% for CDV, 7.2% for CaAstV, 5.9% for CCoV and 4.6% for CAdV-2 with 16.8% incidence for coinfections ranging from two to four viruses in different combinations; no incidence of CRV was reported. The whole-genome sequences of CDV, CCoV and CaAstV Indian isolates were reported for the first time and phylogenetic analysis was performed. This study highlights the need for relevant and routine vaccine prophylactic measures. It is alarming to note that 70.3% of animals vaccinated with DHPPIL were found positive for at least one virus. Hence, regular molecular analysis of the prevalent viruses is crucial to address vaccination failures.