The complete genome and phylogenetic relatedness of a newly discovered fusagra-like virus infecting Carica papaya in Ecuador

Abstract A new fusagra-like virus infecting papaya (Carica papaya L.) was genetically characterized. The genome of the virus, provisionally named ‘papaya sticky fruit-associated virus (PSFaV)’, comprises a single double-stranded RNA molecule of 9,199 nucleotides (nt) containing two discontinuous open reading frames. Pairwise sequence comparisons based on complete RNA-dependent-RNA-polymerase (RdRp) sequences revealed identities of 79.4% and 83.3% at the nt and amino acid (aa) levels, respectively, with babaco meleira-like virus (BabMelV), an uncharacterized virus sequence discovered in babaco (Vasconcellea x heilbornii) in Ecuador. Additional plant-associated viruses with sequence identities in the 50% range included papaya meleira virus (PMeV) isolates from Brazil. Phylogenetic analysis based on the amino acid sequences of the capsid protein (CP), RdRp, and CP-RdRp fusion protein genes placed PSFaV in a group within a well-supported clade, which shares a recent ancestor with Sclerotium rolfsii RNA virus 2 and Phlebiopsis gigantea mycovirus dsRNA 2, two fungi-associated fusagraviruses. Genomic features and phylogenetic relatedness suggest that PSFaV, along with its closest relative BabMelV, represent a novel plant-associated virus classified within the proposed fusagraviridae family.