Pathogenic Seedborne Viruses Are Rare but Phaseolus vulgaris Endornaviruses Are Common in Bean Varieties Grown in Nicaragua and Tanzania

We surveyed seedborne viruses in new common bean varieties (Phaseolus vulgaris) introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Beans harvested from Nicaragua and Tanzania were grown in a greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30–36 samples per pool), and small RNAs were subjected to deep sequencing (Illumina). Assembly of the reads (21, 22 and 24 nt) to contiguous sequences and searches for homologous viral sequences in databases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. The small-RNA reads from each pool of samples were mapped to the complete PvEV-1 and PvEV-2 sequences characterized in Brazil (genome lengths ca. 14 kb and 16 kb, respectively). The average depth of coverage was 14–328 times, depending on the pool. No pathogenic, seedborne viruses were detected in the samples from Nicaragua, but Cowpea mild mosaic virus was detected in one region in Tanzania.