Genotyping of Canine Distemper Virus Lineage in Clinically Infected Dogs in Puducherry, Southern India

Abstract

Aims: This study aimed to determine the Canine Distemper Virus (CDV) lineage circulating in the Puducherry region (Southern India) and how they are genetically and antigenically related to the vaccine and other known CDV lineages around the world. Study Design: The study involved genetic characterization of the canine distemper virus strains/lineages circulating in the clinically suspected dogs in the field. Place and Duration of Study: Department of Veterinary Clinical Complex, Animal Husbandry Department, Private Veterinary Clinics, NGOs like Bark India, People for Animals organization, Puducherry between January 2018 and December 2019. Methodology: The ocular and nasal swabs were collected from 40 dogs suspected for canine distemper from Puducherry state (Southern India). Following viral RNA Extraction and cDNA synthesis; the cDNAs were screened for virus by targeting the CDV Nucleocapsid (N) gene using Reverse Transcriptase PCR. Further, the N gene positive cDNAs were genetically characterized for sequence analysis of the CDV hemagglutinin (H) gene. Results: A total of 15 (37.5%) out of 40 ocular/ nasal swabs were found to be CDV positive by RT-PCR targeting the N gene. The sequence analysis of the H gene revealed forty-nine non-synonymous and thirty-three synonymous mutations (out of 356 amino acids) in comparison with vaccine strain. The vaccine virus (Onderstepoort strain), which is related to the America 1 lineage, possessed high level of (30 – 35 i.e. more than 10%) amino acid divergence with the CDV sequences analysed in this study. The Phylogenetic analysis revealed that the present CDV sequences formed a separate monophyletic group with the CDV sequences of other Indian dogs and the Indian wildlife (Lion) and is clustered away from the vaccine strain. The CDV sequences were closer to the CDVs of Africa - 2 lineage than the other Asian lineages.  The Recombination analysis revealed no potential breakpoints and recombination events. Conclusion: Together, these findings highlighted the possible existence of the novel Indian CDV lineage/s distinct from the vaccine strain and from other known Asian lineages.