Survey for virus diversity in common bean (Phaseolus vulgaris L.) fields and the detection of a novel strain of cowpea polerovirus 1 in Zambia

The production of common bean (Phaseolus vulgaris L.) is adversely affected by virus-like diseases globally, but little is known about the occurrence, distribution, and diversity of common bean-infecting viruses in Zambia. Consequently, field surveys were conducted during 2018 season in 128 fields across six provinces of Zambia and 640 common bean leaf tissue samples were collected with (n=585) or without (n=55) symptoms. The prevalence of symptomatic fields was 100%, but incidence of symptomatic plants ranged from 32% to 67.5%. Metagenomic analyses of nine composite samples and a single plant sample of interest revealed the occurrence of isolates of Bean common mosaic necrosis virus, Bean common mosaic virus, Cowpea aphid-borne mosaic virus, Peanut mottle virus, Southern bean mosaic virus (SBMV), Cucumber mosaic virus, Phaseolus vulgaris alphaendornavirus 1 (PvEV-1), PvEV-2, Ethiopian tobacco bushy top virus, and a novel strain of cowpea polerovirus 1 (CPPV1-Pv) of 5,902 nt in length. While CPPV1-Pv was consistently detected in mixed infection with ETBTV and its satellite RNA (satRNA) molecule, it does not appear to be involved in disease etiology based on results of mechanical transmission assays, suggesting that its role may be limited to being a helper virus for the umbravirus. Screening of the survey samples by RT-PCR for the viruses detected by high throughput sequencing revealed the prevalence of single (65.2% or 417/640) over mixed (1.9% or 12/640) infections in the samples. SBMV was the most frequently detected virus, occurring in ~29.4% (188/640) of the samples and at a prevalence rate of 58.6% (75/128) across fields. The results showed that diverse virus species are present in Zambian common bean fields and the information will be useful for the management of common bean viral diseases.