Complete genome sequence of ramie marafivirus 1, a novel marafivirus infecting ramie (Boehmeria nivea)

High-throughput sequencing (HTS) combined with reverse transcription-polymerase chain reaction (RT-PCR) revealed a novel marafivirus, tentatively named “ramie marafivirus 1” (RaMaraV1), infecting ramie (Boehmeria nivea (L.) Gaudich.) plants in China. The complete genome of RaMaraV1 consists of 6,607 nucleotides (nt) and shares the highest nt sequence identity (65.4%) with Artemisia argyi albinism-associated virus (AAAaV), a recently identified marafivirus. The RaMaraV1 genome structure is typical of marafiviruses, containing a conserved 16-nt marafibox motif and a large open reading frame (ORF) encoding a polyprotein with five predicted domains. The coat protein (CP) of RaMaraV1 shares 23.9–65.4% amino acid (aa) sequence identity with those of reported marafiviruses, which is below the species demarcation threshold for the genus Marafivirus. Phylogenetic analyses based on the sequences of the complete genome and polyprotein revealed that RaMaraV1 clustered closely with viruses of the genus Marafivirus. Collectively, these results suggest that RaMaraV1 is a novel virus in the genus Marafivirus.