Complete genome analysis of a novel nyamivirus from the leaf beetle Aulacophora lewisii

Leaf beetles of the subfamily Chrysomelinae are not only herbivorous pests but also potential vectors of plant pathogens. Here, we describe a novel negative-sense virus named "Aulacophora lewisii nyamivirus 1" (ALNyV1), discovered in a leaf beetle (Aulacophora lewisii), a prevalent pest of cucurbitaceous vegetables. Using transcriptome sequencing and rapid amplification of cDNA ends (RACE) techniques, the complete genome sequence of ALNyV1, spanning 10,339 nucleotides (excluding the polyA tail), was determined. A homology search and phylogenetic analysis indicated that ALNyV1 belongs to an unclassified clade in the family Nyamiviridae. This virus contains five open reading frames (ORFs) with typical conserved domains of nyamiviruses. The mean coverage of the ALNyV1 genome was 249, suggesting that active replication had occurred within the leaf beetle host. Furthermore, the virus was found to trigger a small-RNA interference response, with virus-derived small RNAs (vsiRNA) of ALNyV1 displaying a distinct pattern with 21 nucleotides being the most frequent length and exhibiting an A/U bias at the 5' end. This is the first detection of a negative-sense RNA virus in this leaf beetle species, providing important new information about the characteristics of viruses found in leaf beetles.