Abstract
Outbreaks of small ruminant morbillivirus (SRMV) are regularly occurring in Pakistan despite vaccine availability. This study was designed to identify substitutions within the immunogenic structural and functional regions of the nucleocapsid, fusion, and hemagglutinin genes of SRMV and their comparison with vaccinal strains of Nigerian and Indian origin. Swabs and tissue samples were collected from diseased animals. RT-PCR was used to characterize selected genes encoded by viral RNA. The study's N, F, and H protein sequences and vaccinal strains were analyzed for B and T cell epitope prediction using ABCpred, Bipred, and IEDB, respectively. Significant substitutions were found on the C terminus of the nucleocapsid, within the fusion motif region of the fusion gene and in the immunoreactive region of the hemagglutinin gene. Our results emphasize the need for the development of effective vaccines that match the existing variants of SRMV strains circulating in Pakistan.
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