Genome characterization of a begomovirus isolated from Brazilian Carica papaya plants

Papaya (Carica papaya L.) plants are susceptible to several viral pathogens. However, information regarding papaya-associated DNA viruses in Latin America is limited. In this study, we collected symptomatic papaya plants in Baraúna, Rio Grande do Norte, Brazil, and screened for begomovirus infection. Three of ten samples tested positive through PCR using universal primers, and were further analyzed using rolling circle amplification and Oxford Nanopore sequencing. This approach allowed us to recover complete circular viral genomes with the typical DNA-A segment organization of begomoviruses. We named this newly identified viral agent papaya mottle virus (PaMoV). No DNA-B component was detected in the samples, suggesting that PaMoV is a monopartite begomovirus. The sequences from the three isolates shared over 95% nucleotide identity. Pairwise sequence identity along with phylogenetic analyses supported the classification of PaMoV as a member of a novel begomovirus species, for which we propose the name "Begomovirus papayavariati". This is the first report of a begomovirus associated with C. papaya in Brazil.