Genetic characterization and phylogenetic analysis of Peste des Petits Ruminants virus (PPRV) from an outbreak in Puducherry region, India
Genotyping of PPR virus in India
DOI:
https://doi.org/10.70964/avr.7Keywords:
Peste des Petits Ruminants, RT-PCR, N gene, Sequencing, Phylogenetic analysisAbstract
Peste des petits ruminants (Goat plague) is an acute, highly contagious, and lethal viral disease of goats and sheep. It causes high morbidity and mortality and is considered a significant constraint on the productivity of small ruminants. Four genetic lineages of the PPR virus (Genotype I to IV) have been identified globally. The study was planned to genetically characterize the circulating PPR virus lineages/genotypes in a suspected outbreak in goats from the Puducherry region (Southern India). Fifty-nine nasal/faecal swabs were collected from the goats with the history of profuse diarrhoea, nasal and ocular discharges, stomatitis, and high mortality during the outbreak. A total of 44 out of 59 (74.5%) nasal/faecal swabs were found positive by Reverse Transcriptase PCR targeting the N gene of the PPR virus, with an amplicon size of 359 bp. Based on sequence analysis of three representative samples, the Indian vaccine strain and various global genotypes, forty-one non-synonymous amino acid variations were identified from 110 amino acids. These amino acid variations specific to the study sequences are characteristic of the Genotype IV lineage. Though the vaccine virus (Sungri 96 strain) also had amino acid relatedness with the Genotype IV lineage, nine non-synonymous mutations were repeatedly identified in the field strains, indicating that the virus is under serious positive selection in these regions. In addition, three new mutations were identified at the positions Lys/Gln458→Pro, Thr469→Pro, and Met507→Thr of the N gene. Thus, it could be concluded that the genotype IV lineage of PPRV is circulating in India with three new mutations at the N gene. As the PPRV strains were found to be under immense selection pressure and realizing the constant mutations happening in the field strains, monitoring of circulating genotypes in wider geographical regions of India would be of utmost importance.
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