Complete genome analysis of a novel iflavirus from a leaf beetle, Aulacophora lewisii
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Complete genome analysis of a novel iflavirus from a leaf beetle, Aulacophora lewisii Zhuang‑Xin Ye1 · Yue‑Hong Li2 · Jian‑Ping Chen1 · Chuan‑Xi Zhang1 · Jun‑Min Li1 Received: 12 August 2020 / Accepted: 15 September 2020 © Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract The leaf beetle Aulacophora lewisii (family Chrysomelidae, order Coleoptera) is a common insect pest of cucurbitaceous vegetables. In this study, the complete genome sequence of a novel virus from a single leaf beetle was determined using metagenomic sequencing and rapid amplification of cDNA ends. A homology search and phylogenetic analysis suggested that the new virus belongs to the genus Iflavirus, family Iflaviridae, and it was tentatively named “Aulacophora lewisii iflavirus 1” (ALIV1). ALIV1 has a single positive-stranded RNA genome of 9655 nucleotides in length (excluding the polyA tail) that is predicted to encode typical conserved domains of iflaviruses, including two picornavirus-like capsid protein domains, a helicase domain, and an RNA-dependent RNA polymerase (RdRp) domain. Sequence comparisons showed that the full genome sequence of ALIV1 is most similar to that of Brevicoryne brassicae picorna-like virus, with 42.4% sequence identity, and it shares 60% sequence identity in the coat protein region with its closest homolog, Watson virus. The average coverage of the ALIV1 sequence was approximately 5000X, suggesting that it might actively replicate in the host. Phylogenetic analysis based on deduced amino acid sequences suggested that ALIV1 is closely related to Dinocampus coccinellae paralysis virus. To the best of our knowledge, ALIV1 is the first virus discovered in A. lewisii and is also the first iflavirus identified in a member of the genus Aulacophora. Iflaviridae is a family of small positive-stranded nonenveloped RNA viruses with a genome of approximately 9-11 kilobases. This family currently has only one genus, Iflavirus. The genome of iflaviruses contains a single large open reading frame (ORF), which is translated directly into a polyprotein to generate the structural and non-structural proteins [1]. All of the iflaviruses identified until now were from arthropods, usually insects. Some of these iflaviruses are insect pathogens, such as deformed wing virus (DWV), Handling Editor: Jesús Navas-Castillo. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04859-1) contains supplementary material, which is available to authorized users. * Jun‑Min Li [email protected] 1
State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‑products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
Jinhua Plant Protection Station, Jinhua 321017, China
2
which causes developmental abnormalities in bees, and sacbrood virus (SBV), which is responsible for behavioral changes
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