Molecular characterization of horse nettle virus A, a new member of subgroup B in the genus Nepovirus

Abstract A new RNA virus was discovered from a horse nettle plant using high throughput sequencing (HTS) and its full genome was characterized consisting of two molecules: RNA1 and RNA2 which are 7522 and 4710 nucleotides in length, respectively. Each molecule encodes a single open reading frame flanked by 5’ and 3’ untranslated regions (UTRs) followed by a poly(A) tail at the 3’ end. Genome organization and the phylogenetic analysis revealed its close relationship with subgroup B of nepoviruses, sharing minimal similarity with any known nepoviruses, and the recombination analysis also revealed its evolutionary history within the same subgroup. These results suggest the new virus, provisionally named as horse nettle virus A, represents a new species within the genus Nepovirus.