Identification and Characterization of a Novel Umbra-like Virus, Strawberry Virus A, Infecting Strawberry Plants

Abstract

A novel RNA virus infecting strawberry plants was discovered using high-throughput sequencing. The analyzed plant was simultaneously infected with three different genetic variants of the virus, provisionally named strawberry virus A (StrVA). Although StrVA is phylogenetically clustered with several recently discovered, unclassified plant viruses, it has a smaller genome and several unique features in its genomic organization. A specific and sensitive qPCR system for the detection of identified StrVA genetic variants was designed. A survey conducted in the Czech Republic revealed that StrVA was present in 28.3% of strawberry samples (n = 651) from various origins (plantations, gardens, and propagation material). Sequencing of 48 randomly selected StrVA-positive strawberry samples showed that two or all three StrVA genetic variants were present in 62.5% of the samples in various proportions. StrVA was found in mixed infections with other viruses (strawberry mild yellow edge virus, strawberry crinkle virus, strawberry mottle virus, strawberry polerovirus 1, or strawberry virus 1) in 57.1% of the samples, which complicated the estimation of its biological relevance and impact on the health status of the plants.

New Virus Diagnostic Approaches to Ensuring the Ongoing Plant Biosecurity of Aotearoa New Zealand

“…HTS alongside standard molecular techniques is playing a crucial role in understanding the aetiology of virus diseases in important agronomic crops (i.e., [ 95 ]). In strawberry alone, since 2019 an additional four viruses have been identified including strawberry virus 1 [ 96 ], strawberry-associated virus 1 [ 97 ], Fragaria vesca -associated virus 1 [ 98 ], and strawberry virus A [ 99 ]. The economic significance and biosecurity risks associated with these viruses are yet to be assessed.…”

Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and johnsongrass from Ecuador

“…Although the absence of CP genes is a common characteristic of these viral RNAs, they have unique features that distinguish them from "true" umbraviruses. The term 'umbra-like virus' or 'umbravirus-like associated RNAs (ulaRNAs)' was coined to group these viral RNA entities [6][7][8][9][10][11]. Three classes of ulaRNAs have been categorized based on RdRp analyses and predicted genomic secondary structures [12].…”

“…Class 2 comprises smaller ulaRNAs of ~ 2.7 to 3 kb reported from opuntia (opuntia umbra-like virus, OULV), sugarcane (sugarcane umbra-like virus, SULV), g ( g umbra-like virus, FULV), maize (Ethiopian maize associated virus, EMaV) and citrus yellow vein associated virus (CYVaV) [6,8,10,11]. A recently proposed third class (Class 3), is typi ed by strawberry virus A (StVA), a 3.2 kb ulaRNA sharing a most recent ancestor with those in Class 1 [9].…”

“…Lastly, an important biological feature of "true" umbraviruses is their association with a capsid-assistor virus, typically a member of the Luteoviridae, for genome encapsidation and plant-to-plant transmission by vectors [5]. Luteovirids have been incidentally found (e.g., no formal experiments have been conducted to demonstrate their capsid-lender nature) for SULV, OULV, CYVaV, and StVA [6, [9][10][11]. For the papayainfecting ulaRNAs, an unusual dsRNA totivirus-like virus has been proven to be the capsid assistor of PMeV-2 [14] (Quito-Avila unpublished).…”

Transmission of Diverse Variants of Strawberry Viruses Is Governed by a Vector Species

“…Nearly 30 different viruses have been reported to infect strawberries, which are predominantly transmitted by different aphid species [ 27 , 28 , 29 , 30 , 31 ]. It is recognized that yield losses are affected by frequently observed mixed viral infections [ 32 , 33 ].…”