A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya

James M Wainaina; Elijah Ateka; Timothy Makori; Monica A Kehoe; Laura M Boykin

doi:10.7717/peerj.6465

A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya

PeerJ. 2019 Mar 15:7:e6465. doi: 10.7717/peerj.6465. eCollection 2019.

Authors

James M Wainaina¹, Elijah Ateka², Timothy Makori², Monica A Kehoe³, Laura M Boykin¹

Affiliations

¹ School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia.
² Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
³ Diagnostic Laboratory Service, Plant Pathology, Department of Primary Industries and Regional Development, South Perth, WA, Australia.

Abstract

Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I-III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.

Keywords: Dicistroviridae; Emerging viruses; Potyvirus evolutionary analysis; Smallholder farmer.

Grants and funding

James M. Wainaina is supported by an Australian Award scholarship by the Department of Foreign Affairs and Trade (DFAT), this work forms part of his PhD research. Fieldwork activities were coordinated through Cassava Diagnostic project Kenyan node. Pawsey Supercomputing Centre provided supercomputer resources for data analysis with funding from the Australian Government and the Government of Western Australia. NGS sequencing made possible by The Rising Star Award given by the Faculty of Science Alumni Fund at The University of Western Australia awarded to Laura M. Boykin. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.