Aphis glycines virus 1, a new bicistronic virus with two functional internal ribosome entry sites, is related to a group of unclassified viruses in the Picornavirales

Authors: YASMIN, TUBA - University Of Illinois; THEKKE-VEETIL, THANJUJA - University Of Illinois; HOBBS, HOUSTON - University Of Illinois; NELSON, BERLIN - North Dakota State University; McCoppin, Nancy; Lagos-Kutz, Doris; Hartman, Glen; LAMBERT, KRIS - University Of Illinois; Walker, David; Domier, Leslie

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/2/2019
Publication Date: 11/26/2019
Citation: Yasmin, T., Thekke-Veetil, T., Hobbs, H.A., Nelson, B.D., McCoppin, N.K., Lagos-Kutz, D.M., Hartman, G.L., Lambert, K.N., Walker, D.R., Domier, L.L. 2019. Aphis glycines virus 1, a new bicistronic virus with two functional internal ribosome entry sites, is related to a group of unclassified viruses in the Picornavirales. Journal of General Virology. 101(1):105-111. https://doi.org/10.1099/jgv.0.001355.
DOI: https://doi.org/10.1099/jgv.0.001355

Interpretive Summary: The soybean aphid (Aphis glycines) is an invasive pest that has spread throughout soybean growing regions in North America. In seasons when soybean aphid populations are large, soybean yields can be reduced directly by the feeding of aphids and indirectly from the growth of sooty mold on honeydew excreted by the aphids. Soybean genes have been identified for resistance to soybean aphids, but aphid populations can adapt to overcome the resistance. Properly timed applications of insecticides can help reduce yield losses but represent an added cost to soybean producers. In this study, a new virus, Aphis glycines virus 1, was identified that infects soybean aphids that has the potential to be used as a biological control agent to help manage soybean aphid populations. The virus was found in aphids and soybean plants from Illinois, Iowa and North Dakota and has molecular properties that differentiate it from previously identified animal and invertebrate viruses. The results of this study will be of interest to researchers working to limit the impacts of soybean aphids on soybean production or studying viruses that infect aphids and other invertebrates.

Technical Abstract: A novel picorna-like virus with distinct molecular features was discovered by high-throughput sequencing of RNA from soybean leaf samples and independently detected in soybean aphids (Aphis glycines) was provisionally named as Aphis glycines virus 1 (ApGlV1). The single-stranded positive-sense RNA genome of ApGlV1 contained two large open reading frames (ORFs) predicted to encode proteins that have similarity to structural and nonstructural proteins of members of the Picornavirales. The genome organization resembled those of the members of Dicipivirus genus in the Picornaviridae where the 5’ proximal ORF encodes structural proteins while the 3’ proximal ORF codes for nonstructural proteins. Like members of the Dicistroviridae and Dicipivirus, each ORF in ApGlV1 was preceded by an internal ribosome entry site (IRES), one in the 5’ noncoding region and the second in the intergenic region (IGR) both predicted to initiate translation at AUG codons. The 5’ IRES was more active in dual luciferase activity assays than the IGR IRES. ApGlV1 proteins had very low amino acid sequence identities with those of confirmed members of the Picornavirales, and the virus was predicted to encode a serine instead of cysteine protease. In phylogenetic analyses of capsid protein and RdRp amino acid sequences, ApGlV1 consistently clustered with a group of unclassified bicistronic picorna-like viruses that may represent a novel family in the order Picornavirales.