Complete nucleotide sequence of a new carlavirus in chrysanthemums in China

A new virus causing a serious stunt disease of chrysanthemum was identified in China by high-throughput sequencing (HTS) and named chrysanthemum virus R (CVR). The complete sequence of CVR was determined by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The genomic RNA of CVR consists of 8,874 nucleotides (nt), excluding the poly(A) tail, contains six putative open reading frames (ORFs), and has a genomic organization typical of members of the genus Carlavirus. BLAST analysis of the full genome sequence showed low similarity (38%–56% sequence identity) to other members of the genus Carlavirus. BLAST analysis and phylogenetic analysis based on the amino acid (aa) sequences of the CVR replicase and coat protein (CP) confirmed that CVR is a distinct member of the genus Carlavirus.