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. 2016 Nov 19;8(11):315.
doi: 10.3390/v8110315.

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

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

Sijun Liu et al. Viruses. .
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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.

Keywords: insect virus; plant virus; readthrough domain; small RNA virus; soybean aphid.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Aphis glycines virus 2 (ApGlV2) morphology and genomic structure. (A) Virions of ApGlV2 viewed using a transmission electron microscope. Arrows indicate ApGlV2 icosahedral virions with a diameter of ~30 nm. (B) Schematic representation of the ApGlV2 genome. The virus genome likely has a 5′-linked viral protein genome-linked (VPg) with the putative RNA-dependent RNA polymerase (RdRp; 125.3 kDa) encoded by the 5′ open reading frame (ORF). The putative ApGlV2 VPg is encoded at nucleotides 544 to 580 (amino acids 155–167 within the replicase ORF; shown in orange). The capsid protein (CP, 24.3 kDa) is encoded toward the 3′ end along with a putative readthrough domain (RTD, 30.3 kDa). ApGlV2 may encode a subgenomic RNA for the expression of CP and CP-RTD. An additional two potential ORFs (in gray) are located between 705–938 nt (78 aa) and 1528–1719 nt (64 aa). (C) The ApGlV2 genome has a conserved VPg domain at the 5′ end. Clustal W sequence alignment of N-terminal sequences of Euprosterna elaeasa virus (EEV), Thosea asigna virus (TAV), Aphis glycines virus 2 (AGV), and Drosophila A virus (DAV). The sequence alignment shows conservation of amino acid sequences (highlighted) for the VPg at the 5′ end of the virus genome.
Figure 2
Figure 2
ApGlV2 has a non-canonical (C-A-B) RdRp, similar to those of some other insect viruses. (A) The conservation of the amino acid residues between ApGlV2, the tetraviruses; Thosea asigna virus (TAV) and Euprosterna elaeasa virus (EEV); Drosophila A virus (DAV) and birnaviruses; Infectious pancreatic necrosis virus (IPNV) and Infectious bursal disease virus (IBDV) are highlighted. Yellow highlights show conservation between EEV, TAV, and DAV but not ApGlV2 while blue highlights show conservation of EEV, TAV, and DAV with ApGlV2. Red highlights show conservation of residues between all viruses. All highlighted amino acids are key RdRp motifs. (B) Phylogenetic tree of ApGlV2 RdRp with closely related viruses and other viruses with permuted RdRp based on BLAST results of amino acid identity. Phylogenetic trees were constructed using MEGA 6.06 with the maximum likelihood method. Thosea asigna virus (TAV, accession AAQ14329.1) and EEV (AF461742_1) are closely related to but phylogenetically distinct from DAV (YP003038595.1) and ApGlV2 (AGV). The RdRps of these insect viruses are clustered with Birnaviruses, e.g., Infectious pancreatic necrosis virus (IPNV; AAV48847.1), Infectious bursal disease virus (IBDV; ACS44343.1), and Blotched snakehead virus (BSNV; YP052864). In contrast, the RdRps of negeviruses with permuted RdRps, Dezidougou virus (DEZV, AFI24669.1), Santana virus (SANV, AFI24675.1), Wallerfield virus (WALV, AIS40860.1), and Tanay virus (TANNV, YP_009028558.1) are close to a plant virus, Grapevine fleck virus (GFV, CAC84400.1), forming a distinct branch and indicating that the RdRps of negeviruses are distinct from that of ApGlV2; (C) The predicted RdRp structures for ApGlV2 (AGV), DAV, and EEV are similar. Homology modeling of tertiary protein structures of RdRp from ApGlV2, Drosophila A virus (DAV), and Euprosterna elaeasa virus (EEV). Images were generated using the LOMETS server.
Figure 3
Figure 3
ApGlV2 capsid proteins. (A) The predicted structures of ApGlV2 (AGV) and tobacco necrosis virus (TNV) capsid proteins are similar. Homology modeling of tertiary protein structures of viral capsid protein for ApGlV2 and TNV (PBD:1C8N). Merge shows superimposed images of the two predicted CP structures with signature jelly-roll-like symmetric antiparallel β sheets. The images were generated using the LOMETS server. (B) Identification of ApGlV2 structural proteins. Purified virions (V; ~5 µg) were subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) (15% gel) and bands cut from the Coomassie brilliant blue-stained gel. The seven bands (1–7) were isolated for peptide sequencing. M, molecular mass markers.
Figure 4
Figure 4
Virus-derived small interfering RNA (vsRNA) sequences derived from the sense (blue) and anti-sense (red) genome of ApGlV2. Reads were extracted from a small RNA sequencing dataset of A. glycines (Iowa) infected with ApGlV2 and an ALPV-like virus. The majority of the ApGlV2 vsRNAs are 22 nt, characteristic of double-stranded RNA processing by Dicer2.

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