Molecular epidemiology of Small ruminant morbillivirus (SRMV) isolates from field outbreaks in Kerala, India based on Fusion (F) and Nucleoprotein (N) gene

Abstract

Abstract Small ruminants contribute significantly to the animal husbandry economy. Peste des petits ruminants (PPR) is one of the major infectious disease of small ruminants caused by Small ruminant morbillivirus (SRMV), a member of the genus Morbillivirus, which cause significant morbidity and mortality in affected population thereby disturb economy of rural poor. The present study describes the molecular characterisation and phylogenetic analysis of SRMV with complete nucleocapsid (N) and Fusion (F) gene sequence. Phylogenetic analysis of the SRMV isolates based on the revealed that, all the isolates shared a common ancestor with Tamil Nadu isolate and were grouped under lineage IV. Phylogenetic analysis also revealed that, there are two genetic groups circulating in Kerala and are 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- 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 F and N gene indicates continuous emergence and circulation of new variants of virus within same geographical area. This is the first report of molecular characterization of PPRV isolates based on full N and F gene from Kerala, India.