Complete genome sequence of citrus yellow spot virus, a newly discovered member of the family Betaflexiviridae

A novel plant virus with a positive single-stranded (+ss) RNA genome was detected in Taibei pomelo (Citrus grandis (L.) Osbeck cv. Taibeiyou) in China by high-throughput sequencing (HTS). Tentatively named “citrus yellow spot virus” (CiYSV), it has 8,061 nucleotides (nt) excluding the poly(A) tail and contains three open reading frames (ORFs). ORF1 is predicted to encode a replicase polyprotein (RP) with conserved domains typical of members of the family Betaflexiviridae. ORF2 encodes a protein sharing the highest sequence identity with the putative movement protein (MP) found in the negative-stranded RNA virus Trifolium pratense virus B (TpVB, MH982249, genus Cytorhabdovirus). ORF3 overlaps ORF2 by 137 nt and encodes a predicted coat protein (CP) that is distantly related to those of betaflexiviruses. Phylogenetic analysis based on the MP amino acid sequence showed that the CiYSV clustered with cytorhabdoviruses rather than betaflexiviruses, whilst trees based on the whole genome, RP, and CP showed it to belong to the family Betaflexiviridae but to be distinct from any other known betaflexiviruses. These results suggest that the CiYSV should be considered the first member of a tentative new genus in the family Betaflexiviridae.