Characterization of chenopodium trirhavirus 1, a novel tri-segmented virus of the family Rhabdoviridae

A novel tri-segmented virus, tentatively named "Chenopodium trirhavirus 1" (CheTRV1), was identified in Chenopodium album in China using high-throughput sequencing combined with conventional Sanger sequencing after RT-PCR. The genome of CheTRV1 consists of three negative-sense single-stranded RNAs designated as RNA1, RNA2, and RNA3. RNAs 1-3 of CheTRV1 share 57.93-64.41%, 48.16-56.96%, and 38.12-42.22% nucleotide sequence identity with the corresponding segments of previously reported trirhaviruses. The 3'- and 5'-termini of the three segments are similar and exhibit partial inverse complementarity. The ORFs of CheTRV1 are separated by a conserved gene junction region with the consensus motif 3'-AAUUCUUUUGN(N)_nUUC- 5'. RNA1 consists of 6749 nucleotides (nt) and encodes a single putative L protein. RNA2 is 4393 nt in length and contains four genes in the order 3'-N-P2-P3-P4-5'. The smaller RNA3 consists of 3897 nt and has three genes in the order 3'-P6-P7-P8-5'. Phylogenetic analysis and pairwise comparisons suggested that CheTRV1 is most closely related to Medicago trirhavirus 1, with 68.82% amino acid sequence identity in the L protein. This is the first report of the complete genome sequence of a tri-segmented rhabdovirus, and it expands our knowledge of rhabdovirus evolution.