Metagenomic Analysis of Groundnut (Arachis Hypogaea L.) RNA Viruses in Gem and Matayos Sub-counties, Western Kenya

Abstract

Groundnut or peanut (Arachis hypogaea L.) is one of the most valuable legume grown throughout the tropical and subtropical regions in almost 100 countries on six continents. Viruses are the most important pathogens causing several diseases among cultivated legumes including groundnut. The most abundant category of viruses causing most economic losses is the RNA viruses although only a few viruses in this diverse group have been studied. Previous studies have in most cases dealt with single species but not diverse species simultaneously. These previous approaches have relied on availability of sequence information and could not detect variety of groundnut viruses. In this study, NGS for metagenomics analysis was used to detect the presence and relative abundances of RNA viruses in symptomatic and asymptomatic groundnut leaf samples collected from farmers’ fields in Western Kenya. Total RNA was extracted from groundnut leaves collected from the fields and sequenced on the Illumina HiSeq 2500 platform. Partial genomes of GRV, satRNA, PCSV, CPPV1 and CPPV2 were detected. Co-infections were established between two sets, GRV- satRNA and CPPV1 - CPPV2. This is the first report of CPPV 1 and CPPV 2 viruses outside Burkina Faso and on groundnut as a host. Overall, PCSV was the most prevalent virus detected at 50% of all samples. Gem Sub-county in Siaya reported higher incidence and severity than Matayos Sub-county but with similar viral distribution. In conclusion, the results establish a universal platform for simultaneous detection of several groundnut RNA viruses. The use of viral metagenomics diagnostic procedures offers capability of generic use in groundnut seed system development, exchange and breeding programmes.