Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses