Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family Phenuiviridae

Diaz‐Lara, Alfredo; Navarro, Beatriz; Serio, Francesco Di; Stevens, Kristian; Hwang, Min Sook; Kohl, Joshua B.; Vu, Sandra; Falk, Bryce W.; Golino, Deborah A.; Rwahnih, Maher Al

doi:10.3390/v11080685

Cited by 31 publications

(28 citation statements)

References 47 publications

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“…In addition, other two viruses in the same clades were associated with wood diseases in apple [45,46]. Recently two new viruses belonging to the family Phenuiviridae were reported in grapevine and fully described [47]. It is interesting to note that, in our samples only the esca symptomatic vines displayed the presence of GaClV4.…”

Section: Discussionmentioning

confidence: 58%

Two New Putative Plant Viruses from Wood Metagenomics Analysis of an Esca Diseased Vineyard

Bertazzon

Chitarra

Angelini

et al. 2020

Plants

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The concept of plant as a holobiont is now spreading among the scientific community and the importance to study plant-associated microorganisms is becoming more and more necessary. Along with bacteria and fungi, also viruses can play important roles during the holobiont-environment interactions. In grapevine, viruses are studied mainly as pathological agents, and many species (more than 80) are known to be able to replicate inside its tissues. In this study two new viral species associated with grape wood tissues are presented, one belongs to the Potyviridae family and one to the Bunyavirales order. Due to the ability of potyviruses to enhance heterologous virus replication, it will be important to assess the presence of such a virus in the grapevine population to understand its ecological role. Furthermore, the association of the cogu-like virus with esca symptomatic samples opens new questions and the necessity of a more detailed characterization of this virus.

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Section: Discussionmentioning

confidence: 58%

Two New Putative Plant Viruses from Wood Metagenomics Analysis of an Esca Diseased Vineyard

Bertazzon

Chitarra

Angelini

et al. 2020

Plants

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“…Most phenuiviruses have enveloped particles with helical morphology, except tenuiviruses that have non-enveloped filamentous particles, and their genomes are comprised of two to four single-stranded, linear RNA segments. As of 2019, the family Phenuiviridae includes 19 ICTV-recognized genera (Figure 1) (Navarro et al, 2018b;Diaz-Lara et al, 2019). Phylogenetic relationships with other phenuiviruses support their classification within this family (Diaz-Lara et al, 2019).…”

Section: Phenuiviridaementioning

confidence: 95%

“…As of 2019, the family Phenuiviridae includes 19 ICTV-recognized genera (Figure 1) (Navarro et al, 2018b;Diaz-Lara et al, 2019). Phylogenetic relationships with other phenuiviruses support their classification within this family (Diaz-Lara et al, 2019).…”

Section: Phenuiviridaementioning

confidence: 95%

“…This is exemplified by the recently discovered coguviruses and rubodviruses, where the host assignment based on their phylogenetic relationships is only preliminary. Thus, further biological studies will be required to determine if they are plant, plant-associated, or insect viruses (Navarro et al, 2018b;Diaz-Lara et al, 2019;Chiapello et al, 2020).…”

Section: High-throughput Sequencing To Uncover the Negative-sense Simentioning

confidence: 99%

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The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

2020

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The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our 'new eyes,' are unraveling in real time the richness and magnitude of the plant RNA virosphere.

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“…The development of Next Generation Sequencing (NGS) has provided a powerful tool for plant pathogens diagnosis, especially for the novel virus identification. Many plant viruses have been discovered by the NGS method, such as grapevine Muscat rose virus (GMRV) [2], Apple rubbery wood virus (ARWV) [3], Tea plant necrotic ring blotch virus (TPNRBV) [4] and Areca palm necrotic ringspot virus…”

Section: Introductionmentioning

confidence: 99%

Complete Genomic Sequence of <em>Noni mosaic virus</em> (NoMV), a Novel Potyvirus Associated with a Mosaic Disease in <em>Morinda citrifolia L.</em>

Yu¹,

Cai²,

Zhou³

et al. 2019

Preprint

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An outbreak of a virus-like disease has caused severe damage to noni plants (Morinda citrifolia L.) in Xishuangbanna area of China's southwestern Yunnan province since 2015. The diseased plants displayed typical mosaic symptom with light and dark green patches on leaves. Flexuous filamentous virus particles of about 800 nm in length were observed from the leaf saps by transmission electron microscope. Illumina transcriptomic sequencing further revealed the presence of a potyvirus and its near complete genome was obtained from de novo assembly. The complete genome of 9,659 nts was obtained by Sanger sequencing of eight amplicons generate by RT-PCR and 5’ and 3’ RACE. BLASTp analysis of the polyprotein sequence showed that the virus was most closely related to Tobacco vein banding mosaic virus (TVBMV), but these two viruses only shared 50.7% amino acid sequence similarity. Both phylogenetic analyses of the polyprotein and CP amino acid sequences indicated that this virus is a member of genus Potyvirus. However, the low sequence homology with all known potyviruses established this virus as a new species in the genus, tentatively named as Noni mosaic virus (NoMV). Our field surveys showed that 100% of the symptomatic samples and 28.57% of the asymptomatic samples were infected with this novel potyvirus. Aphids collected from diseased leaves were also detected carrying the virus. In summary, our data indicated that a novel species of potyvirus, NoMV, is prevalent in Yunnan, China and is associated with an emerging mosaic disease on M. citrifolia.

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Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family Phenuiviridae

Cited by 31 publications

References 47 publications

Two New Putative Plant Viruses from Wood Metagenomics Analysis of an Esca Diseased Vineyard

Two New Putative Plant Viruses from Wood Metagenomics Analysis of an Esca Diseased Vineyard

The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes

Complete Genomic Sequence of <em>Noni mosaic virus</em> (NoMV), a Novel Potyvirus Associated with a Mosaic Disease in <em>Morinda citrifolia L.</em>

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