Genomic Analysis of Nucleocapsid and Fusion Genes of Small Ruminant Morbillivirus in Pakistan
Genomic Analysis of Nucleocapsid and Fusion Genes of Small Ruminant Morbillivirus in Pakistan
Hafiz Muhammad Imran Javed* and Mushtaq Ahmed
ABSTRACT
Small ruminant morbillivirus (SRMV) is the most contagious viral disease of sheep and goats. The present study compared the select genetic markers of the vaccine and field strains originating from the field outbreaks for phylogenetic analysis, nucleotide and deduced amino acid sequence analyses, and a comparison of three-dimensional protein structures. The N gene ORF was 1578 nucleotide long with a single open reading frame encoding 526 amino acids. Similarly, the ORF of F gene was 1641 nucleotide long which encoded 547 amino acids. Upon phylogenetic analysis of the country isolates with the vaccine strains, it was revealed that isolates were clustered within lineage IV (Asian Lineage) closer to Indian isolates. On the other hand, a number of substitutions were observed at sites considered important for the structural and functional integrity of the N and F protein. All of the conserved regions were same regardless of the gene while the substitutions were seen at different residues other than the conserved domains. However, the analysis based upon the three-dimensional protein structures revealed that the study isolates showed mutation at C-terminus region of N protein. Such a study helps to improve our understanding towards evolution of emerging and re-emerging strains of SRMVs in the country.
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