Aphis Glycines Virus 2, a Novel Insect Virus with a Unique Genome Structure

Abstract

The invasive soybean aphid, Aphis glycines, is a major pest in soybeans, resulting in substantial economic loss. We analyzed the A. glycines transcriptome to identify sequences derived from viruses of A. glycines. We identified sequences derived from a novel virus named Aphis glycines virus 2 (ApGlV2). The assembled virus genome sequence was confirmed by reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing, conserved domains were characterized, and distribution, and transmission examined. This virus has a positive sense, single-stranded RNA genome of ~4850 nt that encodes three proteins. The RNA-dependent RNA polymerase (RdRp) of ApGlV2 is a permuted RdRp similar to those of some tetraviruses, while the capsid protein is structurally similar to the capsid proteins of plant sobemoviruses. ApGlV2 also encodes a larger minor capsid protein, which is translated by a readthrough mechanism. ApGlV2 appears to be widespread in A. glycines populations and to persistently infect aphids with a 100% vertical transmission rate. ApGlV2 is susceptible to the antiviral RNA interference (RNAi) pathway. This virus, with its unique genome structure with both plant- and insect-virus characteristics, is of particular interest from an evolutionary standpoint.

Discovery of Known and Novel Viral Genomes in Soybean Aphid by Deep Sequencing

“…An unrelated sequence submitted previously to GenBank was named AGV1 (accession number KF360262). AGV2 was found in all samples of U.S. soybean aphids, and partial sequences were found in the Chinese sample, extending previous observations that no soybean aphids have been found without this virus (Liu et al 2016). There were insufficient reads of AGV2 from the Chinese soybean aphid sample to assemble a genome, but overall this sample was highly enriched in other viral sequences, possibly because the sample was stored at room temperature, causing selective degradation of less stable viruses and nonviral RNA, whereas the Iowa, Michigan, and Ohio virions were isolated from live aphid colonies.…”

“…The other three segments (S1, S3, and S6) shared low amino acid identity with the top BLASTx hits. S1 is the genome of AGV2 which is described in detail by Liu et al (2016). The top BLAST hit for S1 (AGV2) was Euprosterna elaeasa virus (EeV) with 33% amino acid identity in ORF1.…”

“…Segment S1. S1 is the genome of a novel virus recently described as AGV2 (Liu et al 2016). An unrelated sequence submitted previously to GenBank was named AGV1 (accession number KF360262).…”

“…These viruses do not replicate in the aphid. Only a recently discovered novel RNA virus, Aphis glycines virus 2 (AGV2), is known to replicate in soybean aphid (Liu et al 2016). An unrelated viral sequence called Aphis glycines virus 1 (AGV1), isolated from soybean aphid, has been deposited in Gen-Bank (accession number KF360262), but whether this RNA actually infects soybean aphid has not been reported.…”

Topical dsRNA delivery induces gene silencing and mortality in the pea aphid

“…The RNAi pathway has a major role in antiviral immunity in insects, protecting them from viral infections or maintaining hemostasis with viral infections . Next‐generation sequencing has provided evidence that insects harbor a wide range of insect‐specific RNA viruses, and these viruses are often restricted by the RNAi pathway . Aphids feed on plant phloem, therefore, their viral infections occur mainly through two routes, digestive system and/or body wall.…”