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.

Keywords: cucumovirus; endornavirus; insect vectors; maize lethal necrosis; plant-virus interactions; potyvirus; vertical transmission; viral metagenomics.

Figure 1

Sampling sites in Kenya showing locations in Kirinyaga County and the location of the University of Nairobi Research Farm in Kabete.

Figure 2

Phylogenetic analysis of six bean common mosaic necrosis virus (BCMNV) isolates from Kabete (Nairobi University Research Farm) and farms in Kirinyaga County with other BCMNV isolates and strains. The phylogeny was based on aligning 312 amino acid bases of the P1 protein. The evolutionary history was inferred by using the Maximum likelihood method based on the Jones-Taylor-Thornton matrix based model with 1,000 bootstraps in MEGA version 6. Viral isolates identified in this study are indicated by ^*.

Figure 3

Phylogenetic analysis of Phaseolus vulgaris alphaendornavirus 1 (PvEV1) and PvEV2 isolates from farms in Kirinyaga County and Nairobi University Research Farm, Kabete with other endornavirus strains using the viral helicase (Hel-1) protein. The phylogeny was based on aligning 235 amino acids of the viral Hel-1 helicase sequence. The evolutionary history was inferred by the Maximum Likelihood Method based on the WAG substitution model (Whelan and Goldman, 2001) with 1,000 bootstraps in MEGA version 6. PaEv, Persea americana alphaendornavirus 1; CmEV, Cucumis melo alphaendornavirus; OrEV, Oryza sativa alphaendornavirus; BpEV, bell pepper alphaendornavirus; HpEV, hot pepper alphaendornavirus. Endornavirus sequences identified in this study are indicated by ^*.

Figure 4

(A–C) Phylogenetic analysis of cucumber mosaic virus (CMV) RNAs 1, 2, and 3 of the Kenyan strain with other CMV strains and isolates from diverse plant hosts. The phylogeny was based on aligning 2,994 nucleotide bases of the RNA1, 2,079 nucleotide bases of the RNA2 and for RNA3, an alignment of 657 nucleotide bases of the coat protein gene. The evolutionary history was inferred by the Maximum likelihood method based on the Tamura Nei model with 1,000 bootstraps in MEGA version 6. Placement of the three isolates from samples obtained at Kirinyaga is indicated by asterisks.