Complete genome sequence of a novel alphanucleorhabdovirus infecting cassava (Manihot esculenta Crantz) in Brazil.

The genus Alphanucleorhabdovirus comprises plant-infecting viruses with an unsegmented, negative-sense, single-stranded RNA genome. Here, we report the complete genome sequence of a novel alphanucleorhabdovirus infecting cassava (Manihot esculenta Crantz), identified in accession BGM-1275 from the germplasm collection at Embrapa Mandioca e Fruticultura (Cruz das Almas, Bahia, Brazil). The viral genome is 13,625 nucleotides (nt) in length and displays the typical organization of alphanucleorhabdoviruses, with six predicted open reading frames. Pairwise comparisons of its whole genome sequence with those of other known alphanucleorhabdoviruses revealed nt sequence identity values in the range of 31.0-67.8%, which is below the species demarcation threshold (75%). Phylogenetic analysis based on the L gene confirmed placement of the novel virus within the genus Alphanucleorhabdovirus, with cassava alphanucleorhabdovirus 1 as the closest relative. Reverse transcription polymerase chain reaction assays detected the virus in symptomatic (cassava frogskin disease) and asymptomatic cassava samples collected in fields in Northeast Brazil (Paraíba and Rio Grande do Norte) and in other Embrapa accessions, suggesting widespread occurrence. The name "cassava alphanucleorhabdovirus 2" (CsRV2) is proposed for the newly discovered virus.