Complete nucleotide sequence and genome organization of Olive latent virus 3, a new putative member of the family Tymoviridae

Alabdullah, Abdul Kader; Minafra, A.; Elbeaino, Toufic; Saponari, María; Savino, V.; Martelli, G. P.

doi:10.1016/j.virusres.2010.05.010

Cited by 26 publications

(24 citation statements)

References 43 publications

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“…Such failure to identify alternative herbaceous hosts does not rule out grapevine as the original host. Indeed, it has been previously reported that some Tymoviridae display a narrow host range (Dreher, 2004; Alabdullah et al, 2010), up to the extreme situation of having a single identified host [e.g. maize rayado fino virus (MRFV) restricted to corn (Nault et al, 1980) or GFkV to Vitis spp.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…A highly conserved sub-genomic RNA promoter region (“Tymo-box” or “Marafi-box” [ 33 , 34 , 35 ]) was identified immediately prior to the CP ORF ( Figure 1 ). This region is characterized by a highly conserved stretch of 16 nucleotides, eight nucleotides upstream of the putative start of transcription, characterized by another conserved section of three nucleotides.…”

Section: Resultsmentioning

confidence: 99%

“…This region is characterized by a highly conserved stretch of 16 nucleotides, eight nucleotides upstream of the putative start of transcription, characterized by another conserved section of three nucleotides. The putative BeeMLV sub-genomic promoter “box” differs across these two regions by only two nucleotides from the “Marafi-box” and by three nucleotides from the “Tymo-box” ( Figure 1 ), with all variants occurring in positions where this is also tolerated elsewhere among the Tymoviruses and Marafiviruses [ 34 ]. The only unusual aspect is the slight difference between the European and USA variants of BeeMLV, with either a “CAT” (Europe) or a “CAC” (USA), signaling the putative three-nucleotide start of the sub-genomic RNA.…”

Section: Resultsmentioning

confidence: 99%

“…The only unusual aspect is the slight difference between the European and USA variants of BeeMLV, with either a “CAT” (Europe) or a “CAC” (USA), signaling the putative three-nucleotide start of the sub-genomic RNA. Neither the Maculaviruses (including BmMLV) nor the unassigned CuTLV have a typical Tymo-box or Marafi-box [ 25 , 26 , 27 , 34 ], although they may, of course, have alternative means for generating sub-genomic RNAs for translating the 3′ ORFs. A comparison of the main genomic features of BeeMLV with those of the Tymo-, Marafi- and Maculaviruses is found in Supplementary Table S2 .…”

Section: Resultsmentioning

confidence: 99%

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Genome Characterization, Prevalence and Distribution of a Macula-Like Virus from Apis mellifera and Varroa destructor

Miranda

Cornman²,

Evans³

et al. 2015

Viruses

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Around 14 distinct virus species-complexes have been detected in honeybees, each with one or more strains or sub-species. Here we present the initial characterization of an entirely new virus species-complex discovered in honeybee (Apis mellifera L.) and varroa mite (Varroa destructor) samples from Europe and the USA. The virus has a naturally poly-adenylated RNA genome of about 6500 nucleotides with a genome organization and sequence similar to the Tymoviridae (Tymovirales; Tymoviridae), a predominantly plant-infecting virus family. Literature and laboratory analyses indicated that the virus had not previously been described. The virus is very common in French apiaries, mirroring the results from an extensive Belgian survey, but could not be detected in equally-extensive Swedish and Norwegian bee disease surveys. The virus appears to be closely linked to varroa, with the highest prevalence found in varroa samples and a clear seasonal distribution peaking in autumn, coinciding with the natural varroa population development. Sub-genomic RNA analyses show that bees are definite hosts, while varroa is a possible host and likely vector. The tentative name of Bee Macula-like virus (BeeMLV) is therefore proposed. A second, distantly related Tymoviridae-like virus was also discovered in varroa transcriptomes, tentatively named Varroa Tymo-like virus (VTLV).

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“…Search of possible vectors, Euphyllura olivina and Saissetia oleae, was not successful even if OLV-3 was detected by RT-PCR in the psyllid. A survey conducted in the Mediterranean region showed the OLV-3 presence in Italy, Syria, Malta, Tunisia, Portugal, Turkey, Lebanon and Greece with an infection rate average of 30% always in symptomless olive trees (Alabdullah et al, 2010).…”

Section: Strawberry Latent Ringspot Virus (Slrsv)mentioning

confidence: 99%

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Albanese¹,

Saponari²,

Faggioli³

2012

Olive Germplasm - The Olive Cultivation, Table Olive and Olive Oil Industry in Italy

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Complete nucleotide sequence and genome organization of Olive latent virus 3, a new putative member of the family Tymoviridae

Cited by 26 publications

References 43 publications

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

Genome Characterization, Prevalence and Distribution of a Macula-Like Virus from Apis mellifera and Varroa destructor

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