Discovery of a Novel Member of the Carlavirus Genus from Soybean (Glycine max L. Merr.).

Thanuja Thekke-Veetil,Kris Lambert,Leslie Domier,Nancy Mccoppin,Glen Hartman,Houston Hobbs,Hyoun-Sub Lim

doi:10.3390/pathogens10020223

Abstract

A novel member of the Carlavirus genus, provisionally named soybean carlavirus 1 (SCV1), was discovered by RNA-seq analysis of randomly collected soybean leaves in Illinois, USA. The SCV1 genome contains six open reading frames that encode a viral replicase, triple gene block proteins, a coat protein (CP) and a nucleic acid binding protein. The proteins showed highest amino acid sequence identities with the corresponding proteins of red clover carlavirus A (RCCVA). The predicted amino acid sequence of the SCV1 replicase was only 60.6% identical with the replicase of RCCVA, which is below the demarcation criteria for a new species in the family Betaflexiviridae. The predicted replicase and CP amino acid sequences of four SCV1 isolates grouped phylogenetically with those of members of the Carlavirus genus in the family Betaflexiviridae. The features of the encoded proteins, low nucleotide and amino acid sequence identities of the replicase with the closest member, and the phylogenetic grouping suggest SCV1 is a new member of the Carlavirus genus.

Highlights

Soybean is one of the most important cash crops in the United States, where it is cultivated on more than 30 million hectares annually [1]
The crop is affected by many pathogens, including a growing number of viruses, of which bean pod mottle virus and soybean vein necrosis orthotospovirus have the highest incidence in most years in North America [2,3]
From RNA-seq analysis of total RNA from soybean leaves, we discovered a putative new member of the Carlavirus genus, tentatively named soybean carlavirus 1 (SCV1)

Summary

Introduction

Soybean is one of the most important cash crops in the United States, where it is cultivated on more than 30 million hectares annually [1]. The crop is affected by many pathogens, including a growing number of viruses, of which bean pod mottle virus and soybean vein necrosis orthotospovirus have the highest incidence in most years in North America [2,3]. The goal of this study was to monitor soybean production fields in the state of Illinois, USA for the relative abundance of previously described and emerging viral pathogens by HTS. Carlavirus genomes typically contain six open reading frames (ORFs) encoding, in order, replicase, triple gene block proteins (TGBps), coat protein (CP) and nucleic acid-binding protein (NABP) [5]. This communication describes the molecular features of SCV1 and its phylogenetic relationship with other recognized members of the family Betaflexiviridae

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Results