Analysis of 3′-Terminal Region of Bean common mosaic virus Strains Infecting Common Bean in India

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Abstract
Four strains (NL-1, NL-1n, NL-7 and NL-7n) of Bean common mosaic virus (BCMV) prevalent on common bean (Phaseolus vulgaris) in Himachal Pradesh, a north-western Himalayan state of India were compared at the 3′ terminal region of the viral genome to elucidate variation and relationship among these strains. 3′ terminal region comprising of partial nuclear inclusion b (NIb) (171–233 bp), complete coat protein (CP) (860 bp) and 3′ untranslated region (UTR) (208–244 bp) shared 96–98% nucleotide and 96–99% amino acids identity among various strains of BCMV. Multiple alignment as well as cluster dendrograms of the 3′ terminal region placed the test isolates in BCMV species of genus Potyvirus. Phylogenetic analysis of complete CP as well as 3′ UTR also showed Indian strains to be distinct strains. Sequence homology, multiple alignment and evolutionary divergence of 3′ terminal region could not differentiate the pathogenic strain groups, thereby establishing least role of this region in strain characterization of the virus. Comparisons of CP and 3′ UTR region of BCMV strains and other members of genus Potyvirus clearly indicated the little utility of 3′ terminal region in distinction of virus strains. Implications of coat protein region in viral strain distinction are also discussed.