Virome analysis of Capsicum spp. and the potential aphid vector Aphis gossypii through next-generation sequencing

Chili peppers (Capsicum spp.), an important export crop for the agroindustry of southwestern Colombia, face phytosanitary problems that are presumably attributable to viral infections. To date, virus detection in these crops has primarily relied on ELISA, PCR, and RT-PCR techniques. To characterize the virome of commercial Capsicum spp. crops and identify potential virus vectors, an ecogenomic analysis was conducted using total RNA extracted from symptomatic leaf tissues of cayenne pepper (Capsicum annuum) and tabasco pepper (Capsicum frutescens), as well as from the dominant aphid species present in the cultivated area of the inter-Andean valley of the Cauca River, Colombia. Analysis of the RNA libraries from C. annuum and C. frutescens revealed the presence of cryptic viruses, including bell pepper endornavirus (BPEV; Alphaendornavirus capsici), pepper cryptic virus 1 (PCV1; Deltapartitivirus unocapsici, and pepper cryptic virus 2 (PCV2; Deltapartitivirus duocapsici); as well as symptomatic viruses transmitted by vectors, such as cucumber mosaic virus (CMV; Cucumovirus CMV), pepper vein yellows virus (PeVYV; Polerovirus PEVYV), and pepper severe mottle virus (PepSMoV); and the symptomatic, mechanically transmitted pepper mild mottle virus (PMMoV; Tobamovirus capsici). The RNA library from A. gossypii revealed the presence of CMV and PEVYV. These results suggest that A. gossypii, which often occurs at high population densities in commercial crops, may serve as a vector transmitting these symptomatic viruses. The current study presents the first report of mechanically transmitted symptomatic viruses from Colombia.