Phylogenetic analysis of small ruminant morbilli virus in Tamil Nadu: Lineage IV predominance and variability in gene sequences

Abstract

Peste des petits ruminants (PPR), the highly contagious, transboundary disease of small ruminants is caused by PPR virus (PPRV) of the Morbillivirus caprinae species. As a World Organisation for Animal Health (WOAH) listed disease, cases and outbreaks of PPR are to be notified according to the Terrestrial Animal Health Code. Integrated surveillance and monitoring programmes are crucial to evaluation of disease control strategies as India, along with the world, is marching towards a PPRV free status. We have investigated the presence of PPRV in naive, symptomatic ruminants across different agroclimatic zones of Tamil Nadu. Total 88 suspected samples were screened, detection of the partial Nucleocapsid (N) gene by PCR was confirmatory to the presence of virus, nucleotide sequencing of the locus facilitated lineage deduction and phylogenetic analysis. All the isolates from this study belonged to Lineage IV reiterating the predominance of this lineage in India. Phylogenetic analysis revealed the isolates to be distinct from the outbreak strains of 2004 and 2011 in Tamil Nadu but similar to those from recent incidents in the country. Samples from different agroclimatic zones clustered within a single subclade indicative of an overall closeness, however they were segregated on account of relatedness to isolates from other regions. Virus from Timiri and Tirunelveli, the Northeastern (NE) and Southern zones respectively, were similar to Karnataka, 2023 and Pondicherry, 2022 outbreak strains. Chengalpattu sample, from the NE zone, grouped with isolates from Northern parts of India, whereas Cauvery delta zone PPRV was similar to a Northeastern isolate.