Epidemiology, risk factors and molecular characterization of small ruminant morbillivirus in Haryana, India

Peste des petitis ruminants is an economically important transboundary and notifiable viral disease of sheep and goats. In this study, 14 PPR suspected outbreaks among sheep and goats were investigated in four districts of Haryana, India, during July 2020 to October, 2021. The causative agent of the disease; small ruminant morbillivirus was detected by Reverse Transcription Polymerase Chain Reaction targeting full gene sequences of fusion protein gene and confirmed by sequencing. The overall morbidity and cumulative mortality in these outbreaks were 37.56% and 12.09%, respectively. Risk factor analysis identified significant difference in mortality based on age with higher mortality in young ones; 21% as compared to adults; 7.55%. Analysis of the vaccination status revealed significant difference in morbidity and mortality with higher morbidity and mortality in un-vaccinated animals as compared to vaccinated ones. The sequencing and phylogenetic analysis of representative samples revealed that the strains of the present study fall in lineage IV (96.6–99.1%) along with other Indian isolates but made a separate cluster (sub-lineage). The comparison of deduced amino acid (aa) sequence analysis of fusion protein of circulating field strains with reference vaccine strain and other lineage IV strains revealed four N-linked glycosylation sites instead of three. The findings of the present study revealed changes in fusion protein of some of the circulating field strains of SRMV in Haryana, India. Further detailed studies are warranted to delineate the molecular details of these circulating field strains and to evaluate the effectiveness of currently used vaccine against these mutated strains. •Fourteen PPR suspected outbreaks among sheep and goats were investigated in Haryana, India, during July 2020 to October 2021.•Characterization of SRMV strains based on fusion gene protein revealed that they fall in lineage IV but made a separate cluster (sub-lineage).•Risk factor analyses revealed age and immune status of the population as important risk factors for the occurrence of disease.•The amino acid sequence analysis of fusion protein of circulating field strains revealed four N-linked glycosylation sites instead of three.