Metagenomic analysis of plant virus occurrence in common bean (Phaseolus vulgaris) in central Kenya

Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.