Investigation of known and novel geminiviruses in the Mediterranean area through vector-enabled metagenomics (VEM) approach

Cucurbits and tomatoes, the major cultivated crops in the Mediterranean area, are frequently infected by geminiviruses, a family of monopartite or bipartite circular single-stranded DNA viruses, which cause noteworthy agricultural losses with high economic impacts. Geminiviruses are highly invasive since they are transmitted by several insects belonging to the suborder of homopterans and show high recombination levels that can potentially originate new resistance-breaking strains. These premises led us to investigate the “circulating geminiviroma” in the Mediterranean area using a vector-enabled metagenomics (VEM). Collections campaigns of Bemisia spp. complex, leafhoppers, aphids, and mirids were conducted for three years (2020-2021-2022) in two Italian and three Tunisian eco-agrosystems. After extraction and enrichment of circular DNAs, samples were pooled and sent to a specialized company for high-throughput sequencing. Viruses belonging to different genera inside Geminiviridae family, along with new species belonging to Genomoviridae family were detected and will be subjected to validation. Overall, the VEM approach may be valuable to monitor the presence of already known viruses as well as new invasive geminiviruses (NIGs) and can be considered a useful tool for preventing new epidemics.