Abstract
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.
Highlights
In Eastern and Central Africa, common bean (Phaseolus vulgaris L.) is a vital crop that naturally enriches the soil with nitrogen, providing natural fertilizer for other important crops such as maize and cassava (Allen, 1995; Broughton et al, 2003; Mucheru-Muna et al, 2010)
Our results show that bean common mosaic necrosis virus (BCMNV), PvEV1 and 2, and cucumber mosaic virus (CMV) sequences were present (Table 3)
Sequence signatures of other viruses including Grapevine leafrollassociated virus 1, Citrus exocortis viroid, Hardenbergia mosaic virus, and Rice ragged stunt virus, were detected when the sequences were applied to a general BLAST database but not followed up in detail because these signatures disappeared when an e-value threshold of 1e-20 was applied to the virus database
Summary
In Eastern and Central Africa, common bean (Phaseolus vulgaris L.) is a vital crop that naturally enriches the soil with nitrogen, providing natural fertilizer for other important crops such as maize and cassava (Allen, 1995; Broughton et al, 2003; Mucheru-Muna et al, 2010). In a more recent study, they were detected in western Kenyan counties immediately adjacent to the Ugandan border and Lake Victoria (Mangeni et al, 2014) These studies, were dependent upon immunological methods to identify BCMV and BCMNV based on their coat protein (CP) antigenic properties and the use of differential indicator hosts. The cucumovirus, cucumber mosaic virus is (like BCMV and BCMNV) vectored non-persistently by aphids (horizontal transmission) and transmitted vertically through seed (Morales, 2006), and can cause serious disease epidemics in common bean (Gildow et al, 2008; Thompson et al, 2015) Perhaps more importantly, such focused methods will not reveal the presence of unsuspected or novel viruses infecting the crop or the presence of co-infecting viruses in the same plant (Syller, 2012)
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