The Full-length Genome Sequence of a Novel Amalgavirus in Lillium spp. in China

Abstract We report firstly the complete genome sequence of a novel amalgavirus, tentatively designated as ‘Lily amalgavirus 1’(LAV-1), isolated from Lilium spp.in China. LAV-1 is a 3448-nt double-stranded RNA virus. It codes two putative proteins, open reading frame 1(ORF1) is 394 aa in length with unknown function. ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp) of 895 aa. Two ORFs form a ‘1 + 2’ fusion protein translated in ‘+1’ programmed ribosomal frame shift (PRF). BLASTp analysis revealed that the complete genome sequence of LAV-1 shares 48.23%–59.80% sequence identity (query sequence coverage more than 77%) with those of members of the genus Amalgavirus, with the highest nucleotide sequence identity of 59.80% with that of Allium cepa amalgavirus 1 (query sequence coverage 87%). The genome structure, phylogenetic relationships, and sequence similarities to other plant amalgaviruses suggest that LAV-1 is a new member of the genus Amalgavirus.