Whole genome sequence analysis of canine parvovirus reveals pan-Indian replacement with Novel CPV-2c strain

Abstract

Canine parvovirus (CPV) infection causes severe gastroenteritis in canines with high mortality in puppies. This virus evolved from FPV by altering its transferrin receptor (TfR) followed by emergence of CPV-2 variants in subsequent years by altering the immunodominant VP2 amino acid residues. Though the previous studies analysed VP2 gene, there are limited studies on non-structural protein (NS1 & NS2) genes. In this study, comparative whole genomic analysis was performed with the CPV suspected clinical samples collected Pan-India in 2023 with the repository CPV strains (2009–2019 isolates) and the current Indian CPV vaccine strain. The present pan-Indian study showed that the CPV-2c (N426E) had almost completely replaced the previously dominant CPV-2a variant (N426) in India. The Q370R mutation of VP2 was the most common change in the recent CPV-2c strain (CPV-2c 370Arg variant). Phylogeny showed the existence of three clades among the recent CPV-2c strains. The study identified several new positive selection sites in VP1 (N terminus), VP2, NS1 and NS2 genes in the recent CPV strains indicating emergence of new CPV-2c variants with varied antigenic and replication properties. The predominant ‘CPV-2c 370Arg variants’ were grouped along with the Chinese and Nigerian CPV-2c strains away from the CPV vaccine strain and repositories. VP2 epitope analysis predicted nine amino acid variations (includes 2 new variations) at four potential linear B-cell epitopes in the ‘CPV-2c 370Arg variants’ underlying chance of vaccine failure. This pan-Indian study, laid the foundation for further research concerning the dynamics of virus evolution and understanding genetic mutations.