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. 2018 Aug 3;10(8):406.
doi: 10.3390/v10080406.

A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

Thanuja Thekke-Veetil  1 , Thien Ho  2 , Joseph D Postman  3 , Robert R Martin  4 , Ioannis E Tzanetakis  5
Affiliations

A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

Thanuja Thekke-Veetil et al. Viruses. .

Abstract

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.

Keywords: Betaflexiviridae; Ribes americanum virus A; blackcurrant; characterization; detection.

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Conflict of interest statement

The authors declare no conflict of interest. The funding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, and in the decision to publish the results.

Figures

Figure 1
Figure 1
Symptoms observed on American blackcurrant infected with Ribes americanum virus A. Infected Ribes americanum cultivar Gall (PI 617879, left) showing ragged leaf margins and crinkled leaf surface compared to healthy plant (right).
Figure 2
Figure 2
Genome organization of Ribes americanum virus A (RAVA) in comparison to the genomes of members of Tymovirales with triple gene block (TGB) movement proteins. M—methyltransferase, A—AlkB, O—OTu-like peptidase, P—papain-like protease, H—helicase, and R—RNA-dependent RNA polymerase. Boxes represent open reading frames. Size of the proteins encoded in the ORFs is indicated. Abbreviations: ASPV—apple stem pitting virus, CRMaV—cherry rusty mottle associated virus, PVM—potato virus M, ICRSV—Indian citrus ringspot virus, LoLV—lolium latent virus, PVX—potato virus X, BanMMV—banana mild mosaic virus.
Figure 3
Figure 3
Phylogenetic relationship of Ribes americanum virus A (RAVA) with members of the order Tymovirales. Phylogenetic analysis was performed using the conserved domains of RNA-dependent RNA polymerase (RdRp; 3A) and methyl transferase (MTR; 3B). The trees were generated by the maximum likelihood method using MEGA 7 and bootstrap values (indicated for each branch node) were estimated using 1000 bootstrap replicates. The branches with bootstrap values less than 70% are collapsed. The details of virus isolates used for the studies are provided in Table 1.
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