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Izadpanah, K.; Zhang, Yun Ping; Daubert, Steve; Masumi, M.; Rowhani, Adib

doi:10.1023/a:1014516515454

Cited by 26 publications

(7 citation statements)

References 5 publications

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“…ORF1 is a putative replication-associated polyprotein (RP), as it contains the conserved motifs of the viral RNA methyltransferase (MTR), tymovirus endopeptidase (PRO), viral RNA helicase (HEL), and RNA-dependent RNA polymerase domain (RdRP) [1], [2], [12]–[15]. In similarity to GFkV [15], ORF1 lacks the highly conserved 16-nt subgenomic RNA promoter (referred to as tymobox or marafibox) that has been identified near the end of the viral replicases of all sequenced tymoviruses [3] and marafiviruses [4].…”

Section: Resultsmentioning

confidence: 99%

“…The genomic RNA of tymoviruses is 6.0–6.7 kb in size, contains three ORFs, has a 16-nucleotide (nt) sequence known as the “tymobox” which functions as a subgenomic RNA promoter, and has a tRNA-like 3′-terminal structure [1]–[3]. The distinctive feature of the marafivirus genome (6.0–6.5 kb) is the presence of a large single ORF that contains the “marafibox”, which is a conserved 16-nt region comparable to the tymobox, from which it differs by two or three residues and the possession a poly(A) tail at the 3′-terminus [1], [2], [4]. The genomic RNA of maculaviruses (approximately 7.5 kb) is the largest in the family, consisting of four ORFs with a polyadenylated 3′-terminus, and it lacks a conserved sequence comparable to the tymobox or marafibox [1], [2], [5].…”

Section: Introductionmentioning

confidence: 99%

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Genomic Characterization of a Novel Virus of the Family Tymoviridae Isolated from Mosquitoes

Wang¹,

Lv²,

Zhai³

et al. 2012

PLoS ONE

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BackgroundThe family Tymoviridae comprises three plant virus genera, including Tymovirus, Marafivirus, and Maculavirus, which are found in most parts of the world and cause severe agricultural losses. We describe a putatively novel member of the family Tymoviridae, which is isolated from mosquitoes (Culex spp.), referred to as CuTLV.Methods and ResultsThe CuTLV was isolated by cell culture, which replicates and causes cytopathic effects in Aedes albopictus C6/36 cells, but not in mammalian BHK-21 or Vero cells. The complete 6471 nucleotide sequence of CuTLV was determined. The genome of CuTLV is predicted to contain three open reading frames (ORFs). The largest ORF1 is 5307 nucleotides (nt) in length and encodes a putative polypeptide of 1769 amino acids (aa), which contains the conserved motifs for the methyltransferase (MTR), Tymovirus endopeptidase (PRO), helicase (HEL), and RNA-dependent RNA polymerase (RdRp) of the replication-associated proteins (RPs) of positive-stranded RNA viruses. In contrast, the ORF1 sequence does not contain the so-called “tymobox” or “marafibox”, the conserved subgenomic RNA promoter present in all tymoviruses or marafiviruses, respectively. ORF2 and ORF3 putatively encode a 248-aa coat protein (CP) and a proline-rich 149-aa polypeptide. The whole genomic nucleotide identity of CuTLV with other members of family Tymoviridae ranged from 46.2% (ChiYMV) to 52.4% (GFkV). Phylogenetic analysis based on the putative RP and CP genes of CuTLV demonstrated that the virus is most closely related to viruses in the genus Maculavirus.ConclusionsThe CuTLV is a novel virus related to members of the family Tymoviridae, with molecular characters that are distinct from those of tymoviruses, marafiviruses, and other maculaviruses or macula-like viruses. This is the first report of the isolation of a Tymoviridae-like virus from mosquitoes. Further investigations are required to clarify the origin, replication strategy, and the public health or agricultural importance of the CuTLV.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic Characterization of a Novel Virus of the Family Tymoviridae Isolated from Mosquitoes

Wang¹,

Lv²,

Zhai³

et al. 2012

PLoS ONE

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“…Other than members of the genus Maculavirus and the unassigned mycovirus Fusarium graminearum mycotymovirus 1 (FgMTV1) (Li et al, 2016), all other Tymoviridae present a highly conserved 16-nt sequence located at the end of the large coding sequence for the replication-associated polyprotein. Known as the “tymobox” or the “marafibox” (Ding et al, 1990; Izadpanah et al, 2002), it is believed to be an important element for the expression of a subgenomic messenger RNA for subsequent translation.…”

Section: Introductionmentioning

confidence: 99%

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

et al. 2018

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In the past decade, high-throughput sequencing (HTS) has had a major impact on virus diversity studies as well as on diagnosis, providing an unbiased and more comprehensive view of the virome of a wide range of organisms. Rather than the serological and molecular-based methods, with their more “reductionist” view focusing on one or a few known agents, HTS-based approaches are able to give a “holistic snapshot” of the complex phytobiome of a sample of interest. In grapevine for example, HTS is powerful enough to allow for the assembly of complete genomes of the various viral species or variants infecting a sample of known or novel virus species. In the present study, a total RNAseq-based approach was used to determine the full genome sequences of various grapevine fanleaf virus (GFLV) isolates and to analyze the eventual presence of other viral agents. From four RNAseq datasets, a few complete grapevine-infecting virus and viroid genomes were de-novo assembled: (a) three GFLV genomes, 11 grapevine rupestris stem-pitting associated virus (GRSPaV) and six viroids. In addition, a novel viral genome was detected in all four datasets, consisting of a single-stranded, positive-sense RNA molecule of 6033 nucleotides. This genome displays an organization similar to Tymoviridae family members in the Tymovirales order. Nonetheless, the new virus shows enough differences to be considered as a new species defining a new genus. Detection of this new agent in the original grapevines proved very erratic and was only consistent at the end of the growing season. This virus was never detected in the spring period, raising the possibility that it might not be a grapevine-infecting virus, but rather a virus infecting a grapevine-associated organism that may be transiently present on grapevine samples at some periods of the year. Indeed, the Tymoviridae family comprises isometric viruses infecting a wide range of hosts in different kingdoms (Plantae, Fungi, and Animalia). The present work highlights the fact that even though HTS technologies produce invaluable data for the description of the sanitary status of a plant, in-depth biological studies are necessary before assigning a new virus to a particular host in such metagenomic approaches.

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“…The Hel domain showed 57.3–70.7% nt and 50.0–70.2% aa identity levels with those of other related viruses; (iv): the RNA-dependent RNA polymerase domain (4490–5185 nt) shared 63.4–77.6% nt and 63.8–80.7% aa identities with those of other viruses; and (v): the tymovirus coat protein (CP) (5705–6223 nt) shared 39.8–68.2% nt and 22.0–63.4% aa identities with the CP of other tymoviruses. A marafibox-like sequence, CAGGGTGAATTGCTTCA, was found at 5501–5517 nt in the GaMV genome, and it may be the transcriptional promoter that drives the synthesis of a subgenomic RNA encoding only the CP translational reading frame [ 14 ].…”

Section: Resultsmentioning

confidence: 99%

“…The nearly complete genome of GaMV was also determined by multiple 5′-RACE amplifications, which produced the longest obtainable genomic fragments. The genomic sequence included domains homologous to all five common domains found in other marafiviruses, and it also contained a marafibox-like sequence similar to that conserved in viruses belonging to Marafivirus [ 14 ]. Furthermore, the complete genome-based phylogenetic tree revealed that GaMV clustered with other species-related marafiviruses.…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Sequencing Indicates a Novel Marafivirus in Grapevine Showing Vein-Clearing Symptoms

Fan

Zhang

et al. 2021

Plants

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A putative new marafivirus was identified in a ‘Jumeigui’ grapevine exhibitting obvious vein-clearing symptoms by high-throughput sequencing, which tentatively named grapevine-associated marafivirus (GaMV). The nearly complete genomic sequence of GaMV was amplified by reverse transcription PCR, and the terminal sequences were determined using the rapid amplification of cDNA ends method. The nearly complete genome of GaMV is 6346 bp long, excluding the poly(A) tail, and shows 51.2–62.3% nucleotide identity with other members of the genera Marafivirus, Maculavirus and Tymovirus in the family Tymoviridae. Additionally, it includes five functional domains homologous to those found in members of these genera. A phylogenetic analysis showed that GaMV clustered with other species-related marafiviruses. These data support GaMV being a representative member of a novel species in the genus Marafivirus. Furthermore, GaMV was graft-transmissible and 26 of 516 (5.04%) grapevine samples from five provinces in China tested positive by reverse transcription PCR. The coat protein of GaMV isolates shared 91.7–100% and 96.7–100% identities at the nt and aa levels, respectively. The coat protein-based phylogenetic trees revealed three well-defined clusters.

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Cited by 26 publications

References 5 publications

Genomic Characterization of a Novel Virus of the Family Tymoviridae Isolated from Mosquitoes

Genomic Characterization of a Novel Virus of the Family Tymoviridae Isolated from Mosquitoes

High-Throughput Sequencing and the Viromic Study of Grapevine Leaves: From the Detection of Grapevine-Infecting Viruses to the Description of a New Environmental Tymovirales Member

High-Throughput Sequencing Indicates a Novel Marafivirus in Grapevine Showing Vein-Clearing Symptoms

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