Metagenomic Analysis of Plant Virus Occurrence in Common Bean (Phaseolus vulgaris) in Central Kenya

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.

Different Plant Viruses Induce Changes in Feeding Behavior of Specialist and Generalist Aphids on Common Bean That Are Likely to Enhance Virus Transmission

“…Bean-infecting CMV isolates have been associated with major crop losses in the US . In Kenya, metagenomic techniques identified reassortant CMV strains that were of Asian origin and had presumably arrived relatively recently via trade routes (Mutuku et al, 2018). Therefore, control strategies that target the vectoring of CMV are important, as well as measures to prevent the accidental introduction of novel strains into new localities.…”

“…For BCMV (isolate PV-0915, GenBank Number: HG792064), the sequences for the BCMV CP genespecific primers were forward primer 5'-TGA CAA TGG CAC TTC ACC-3' and reverse primer 5'-AACAAACATTGCCGTAGC-3'. The technique used to design these primers is described in an earlier publication (Mutuku et al, 2018). The primers for the CMV CP gene (isolate PV-0473; GenBank number; MH748553.1) were forward primer 5'-ACC ATC TCC TAG GTT TCT TCGG-3' and reverse primer 5'-GTC TCC TTT TGG AGG CCC-3'.…”

“…CMV can cause serious epidemics in common bean crops (Morales, 2006;Jacquemond, 2012), as was seen in Northeastern USA in the early 21 st century . Introduced strains of CMV pose a potential novel threat in East Africa where common bean is a major food security crop, and where bean is already threatened by BCMV and BCMNV (Worrall et al, 2015;Mwaipopo et al, 2017;Mutuku et al, 2018;Wainaina et al, 2019).…”

Metagenomic analyses and genetic diversity of Tomato leaf curl virus complex affecting tomato plants in Kenya

“…Since begomoviruses species and strains cause diseases with similar symptoms in tomato, the use of serological assays has limitations as antibodies are able to cross-react with closelyrelated viruses or virus strains, thus making strain identi cation di cult. Recent advances in sequencing technologies have provided better approaches for identi cation and characterization of plant viruses [26][27][28][29].…”

“…Metagenomics is the analysis of microbial and virus populations in environmental samples through nucleic acid sequencing methods [30]. Motivations for performing plant virus metagenomics include the identi cation of causal organisms associated with virus diseases in crops, screening for speci c viruses when their presence is suspected, detection of asymptomatic or cryptic viruses, and the discovery of novel viruses and other microorganisms [27]. In this study, we used a metagenomics approach to investigate the occurrence of Tomato leaf curl viruses in tomato plants from farmers' elds in Kenya.…”