Discovery of a novel member of the Carlavirus genus from Soybean (Glycine max L. Merr.)

Authors: THEKKE-VEETIL, THANUJA - University Of Illinois; McCoppin, Nancy; HOBBS, HOUSTON - University Of Illinois; Hartman, Glen; LAMBERT, KRIS - University Of Illinois; LIM, HYOUN-SUB - Chungnam National University; Domier, Leslie

Submitted to: Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2021
Publication Date: 2/18/2021
Citation: Thekke-Veetil, T., McCoppin, N.K., Hobbs, H.A., Hartman, G.L., Lambert, K.N., Lim, H., Domier, L.L. 2021. Discovery of a novel member of the Carlavirus genus from Soybean (Glycine max L. Merr.). Pathogens. 10(2). Article 223. https://doi.org/10.3390/pathogens10020223.
DOI: https://doi.org/10.3390/pathogens10020223

Interpretive Summary: Soybean is cultivated on more than 30 million hectares in the United States annually, provides essential nutrients for both humans and food animals and is an important source of bioenergy. The crop is affected by many pathogens including a growing number of viruses that can significantly reduce yields and seed quality. To identify and quantify viruses infecting commercial Illinois soybean fields, surveys were conducted during the 2008 through 2014 growing seasons by high-throughput sequencing. The surveys identified a new soybean-infecting virus that was named soybean carlavirus 1. The virus was detected in 2008, 2009, and 2014 from soybean leaf samples and in 2018 from soybean thrips captured by the Midwest Suction Trap Network. The symptoms produced by the virus and its biological vectors remain to be determined. The virus identified in this study adds to the biological diversity of viruses naturally infecting soybean plants. This information will be useful to scientists interested in studying virus-host interactions and synergistic diseases caused by infection of soybean plants by multiple viruses.

Technical Abstract: A novel member of the Carlavirus genus, provisionally named soybean carlavirus 1 (SCV1), was discovered by high-throughput sequencing of total RNA from soybean leaves. The SCV1 genome contains six open reading frames that encode viral replicase, triple gene block proteins, coat protein (CP) and a nucleic acid binding protein. These proteins showed highest amino acid sequence identities with the corresponding proteins of red clover carlavirus A (RCCVA). The RNA dependent RNA polymerase (RdRP) sequence of SCV1 was only 60% identical with the RdRP of RCCVA, which is far below the demarcation criteria for a new species in the family Betaflexiviridae. In phylogenetic analyses with the RdRP and CP sequences of members of the Betaflexiviridae, SCV1 consistently grouped with members of the Carlavirus genus. The molecular features of the encoded proteins, low identity of the RdRP sequence with the closest member, and the phylogenetic grouping suggest SCV1 is a new member of the Carlavirus genus and may represent the first of this taxon identified from soybean.