Molecular characterization of a novel amalgavirus infecting Lilium spp. in China

Abstract

Abstract A novel plant virus with a double-stranded (ds) RNA genome was detected in Lilium spp. in China by high-throughput sequencing, tentatively named “Lily amalgavirus 2” (LAV2). The genomic RNA of LAV2 is 3432 nucleotides (nt) and encodes a large fusion protein with 1053 amino acids (aa). It encodes two open reading frames (ORFs). The two ORFs putatively encode a ‘1 + 2’ fusion protein generated by a ‘+1’ programmed ribosomal frameshift (PRF). ORF1 encodes a 386-aa protein with unknown function, ORF2 overlaps ORF1 by 350 nt and encodes a 783-aa protein consists of a conserved sequence, which is RNA-dependent RNA polymerase (RdRp). The ‘+1’ ribosomal frameshifting motif sequence, UUU_CGN, which was highly conserved among known Amalgaviruses, was also found in LAV2. Sequence analysis suggested that it shared 46.04%-51.59% complete nucleotide sequence identity with those members of the genus Amalgavirus and had the highest identity (51.59%) to Lily amalgavirus 1 (accession no. OM782323). Phylogenetic analysis based on the RdRp amino acid sequences showed that LAV2 clustered with Amalgavirus. Overall, our data suggest that LAV2 is a new member of the genus Amalgavirus.