Molecular epidemiology of small ruminant morbillivirus (SRMV) isolates from field outbreaks in Kerala, India based on fusion (F) and nucleoprotein (N) gene.

Small ruminants contribute significantly to the animal husbandry economy. Peste des petits ruminants (PPR) is one of the major infectious diseases of small ruminants caused by small ruminant morbillivirus (SRMV) previously known as PPR virus-PPRV, a member of the genus Morbillivirus, which causes significant morbidity and mortality in affected population thereby disturb the economy of rural poor. The present study describes the molecular characterization and phylogenetic analysis of SRMV with complete nucleocapsid (N) and fusion (F) gene sequence. Phylogenetic analysis of the SRMV isolates revealed that, all the isolates shared a common ancestor with Tamil Nadu isolate and were grouped under lineage IV. Phylogenetic analysis also revealed that two genetic groups are circulating in Kerala and have recently evolved. Analysis of the F protein of SRMV showed two unique mutations (A18E and S430I) in Kerala isolates. Amino acid analysis of nucleoprotein revealed that most of the changes were in the C-C-terminal region. Four unique mutations were also observed in the nucleoprotein (NP) of the present SRMV isolates (I153V, A431V, R458M, and G461K). Among the 19 B cell epitopes identified on nucleoprotein, at least one amino acid variation was detected in four epitopes. These changes may affect the monoclonal antibody-based diagnostic assays. These changes in the F and N genes indicate the continuous emergence and circulation of new variants of the virus within the same geographical area. This is the first report on the molecular characterization of PPRV isolates based on full N and F genes from the Kerala state of India.