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Host-specific lineages of Bean common mosaic virus in Bangladesh, Cambodia and Nepal

Shimul Das: Washington State University

<div><em>Bean common mosaic virus</em> (BCMV; genus <em>Potyvirus</em>, family <em>Potyviridae</em>) infects legume crops worldwide. This study was aimed at characterizing BCMV isolates collected from yardlong beans (<em>Vigna unguiculate</em>) from Bangladesh, Cambodia, and Nepal, and red kidney beans (=common bean, <em>Phaseolus vulgaris</em>) from Nepal. Yardlong bean leaves showing mild mosaic, vein banding, and deformation symptoms and kidney bean leaves exhibiting puckering, mottling and deformation symptoms were analyzed for the presence of viruses. Total RNA from symptomatic samples were subjected to Next-Generation Sequencing using Illumina HiSeq 2000 platform. The quality filtered reads were assembled <em>de novo</em> into contigs using the CLC Genomics workbench 8.0 software and annotated against the viral Ref Seq database in GenBank by BLASTN program to identify viruses present in symptomatic samples. The results indicated the presence of sequences highly similar to BCMV. The coat protein (CP) sequence of BCMV isolates from yardlong beans originating from the three countries were highly identical, but distinct from those obtained from kidney beans. Phylogenetic analysis of the CP sequences differentiated BCMV isolates from Bangladesh, Cambodia, and Nepal into two distinct clades by original host, with Nepalese common bean isolates clustering with those from different countries and legume hosts and yardlong bean isolates forming a distinct clade aligning with cowpea isolates from China.</div>