White yam (Dioscorea rotundata) plants exhibiting virus-like symptoms are co-infected with a new potyvirus and a new crinivirus in Ethiopia.

White yam (Dioscorea rotundata) plants collected from farmers' fields and planted at the Areka Agricultural Research Center, Southern Ethiopia, displayed mosaic, mottling, and chlorosis symptoms. To determine the presence of viral pathogens, an investigation for virome characterization was conducted by Illumina high-throughput sequencing. The bioinformatics analysis allowed the assembly of five viral genomes, which according to the ICTV criteria were assigned to a novel potyvirus (3 genome sequences) and a novel crinivirus (2 genome sequences).

Mycoviruses Increase the Attractiveness of for Fungivores and Suppress Production of the Mycotoxin Deoxynivalenol.

RNA viruses of the genera , , , and were found in a single isolate of . The genomes of the mitovirus, sclerotimonavirus, and partitivirus were assigned to previously described viruses, whereas the ambivirus genome putatively represents a new species, named 1 (FgAV1). To investigate the effect of mycoviruses on the fungal phenotype, the spontaneous loss of mycoviruses during meiosis and the transmission of mycoviruses into a new strain via anastomosis were used to obtain isogenic strains both with and without mycoviruses.

First report of strawberry polerovirus 1 in strawberry in Italy.

Strawberry (Fragaria × ananassa Duch.) was introduced in Sicily (Italy) in the 1930s in the small town of Maletto, on the slopes of Etna volcan, where it's currently cultivated in a total area of 30 ha. The French cv.

Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.

We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones.

Molecular characterization of two new alternaviruses identified in members of the fungal family Nectriaceae.

Since the first report in 2009, at least ten additional viruses have been identified and assigned to the proposed virus family Alternaviridae. Here we report two new mycoviruses tentatively assigned to this family, both identified as members of the fungal family Nectriaceae, which were isolated from surface-disinfected apple roots (Malus x domestica, Borkh.) affected by apple replant disease (ARD).

First report of a chrysovirus infecting a member of the fungal genus Ilyonectria.

The fungus Ilyonectria pseudodestructans belongs to the family Nectriaceae and was found to be part of the endophytic microbiome of apple trees (Malus x domestica, Borkh.) with apple replant disease (ARD). After dsRNA extraction, a mycoviral infection became evident.

High molecular diversity of full-length genome sequences of zucchini yellow fleck virus from Europe.

Zucchini yellow fleck virus (ZYFV), genus Potyvirus, is the causal agent of a disease of cucurbits. The genome sequences of seven ZYFV isolates of different origin were determined, two of which were reconstructed from a squash (Cucurbita sp.) collected in 2017 in Greece, while the others, accessions from the DSMZ Plant Virus Collection, were from samples collected in Italy, Greece, and France in the 1980s and 1990s.

Three new mycoviruses identified in the apple replant disease (ARD)-associated fungus Rugonectria rugulosa.

In this study, three new mycoviruses were identified co-infecting the apple replant disease (ARD)-associated root endophyte Rugonectria rugulosa. After dsRNA extraction, six viral fragments were visualized. Four fragments belong to a quadrivirus, which has a genome size of 17,166 bp.

Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent.

Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent.

The Amino-Proximal Region of the Coat Protein of Cucumber Vein Yellowing Virus (Family ) Affects the Infection Process and Whitefly Transmission.

Most plant viruses rely on vector transmission for their spread and specific interactions between vector and virus have evolved to regulate this relationship. The whitefly - transmitted cucumber vein yellowing virus (CVYV; genus , family ) is endemic in the Mediterranean Basin, where it causes significant losses in cucurbit crops. In this study, the role of the coat protein (CP) of CVYV for transmission and plant infection was investigated using a cloned and infectious CVYV cDNA and a collection of point and deletion mutants derived from this clone.

Differential Tropism in Roots and Shoots of Resistant and Susceptible Cassava ( Crantz) Infected by Cassava Brown Streak Viruses.

Cassava brown streak disease (CBSD) is a destructive disease of cassava in Eastern and Central Africa. Because there was no source of resistance in African varieties to provide complete protection against the viruses causing the disease, we searched in South American germplasm and identified cassava lines that did not become infected with the cassava brown streak viruses. These findings motivated further investigations into the mechanism of virus resistance.

Virus Surveys in Olive Orchards in Greece Identify Olive Virus T, a Novel Member of the Genus .

Field surveys were conducted in Greek olive orchards from 2017 to 2020 to collect information on the sanitary status of the trees. Using a high-throughput sequencing approach, viral sequences were identified in total RNA extracts from several trees and assembled to reconstruct the complete genomes of two isolates of a new viral species of the genus (), for which the name olive virus T (OlVT) is proposed. A reverse transcription-polymerase chain reaction assay was developed which detected OlVT in samples collected in olive growing regions in Central and Northern Greece, showing a virus prevalence of 4.

A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses.

High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization.

Duplex In Situ Hybridization of Virus Nucleic Acids in Plant Tissues Using RNAscope.

RNAscope has been recently introduced by Advanced Cell Diagnostics (Newark, CA, USA) for in situ hybridization (ISH) of target RNAs using a proprietary technology for probe design and hybridization assay. The method has been extensively used as a basis for sensitive diagnostic assays in the medical field, while applications of this technique in plant sciences are still rare. Here, we describe a multiplex ISH protocol for detection of two plant viruses in formalin-fixed paraffin-embedded tissue sections from cassava.

The (TSWV) Genome is Differentially Targeted in TSWV-Infected Tomato () with or without Gene.

Tospoviruses cause significant losses to a wide range of agronomic and horticultural crops worldwide. The type member, (TSWV), causes systemic infection in susceptible tomato cultivars, whereas its infection is localized in cultivars carrying the 5 resistance gene. The response to TSWV infection in tomato cultivars with or without -5 was determined at the virus small RNA level in the locally infected leaf.

Differential gene expression in two grapevine cultivars recovered from "flavescence dorée".

The biological bases of recovery of two grapevine cultivars, Nebbiolo and Barbera, showing different susceptibility and recovery ability to "flavescence dorée" (FD) phytoplasma infection were investigated. The expression over one vegetative season, in FD-recovered and healthy grapevines, of 18 genes involved in defence, hydrogen peroxide and hormone production was verified at two time points. Difference (Δ) between the relative expressions of August and July were calculated for each target gene of both cultivars.

Localization of cassava brown streak virus in Nicotiana rustica and cassava Manihot esculenta (Crantz) using RNAscope® in situ hybridization.

Background: Cassava brown streak disease (CBSD) has a viral aetiology and is caused by viruses belonging to the genus Ipomovirus (family Potyviridae), Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Molecular and serological methods are available for detection, discrimination and quantification of cassava brown streak viruses (CBSVs) in infected plants. However, precise determination of the viral RNA localization in infected host tissues is still not possible pending appropriate methods.

Characterization of the first complete genome sequence of an Impatiens necrotic spot orthotospovirus isolate from the United States and worldwide phylogenetic analyses of INSV isolates.

Objective: Impatiens necrotic spot orthotospovirus (INSV) can impact economically important ornamental plants and vegetables worldwide. Characterization studies on INSV are limited. For most INSV isolates, there are no complete genome sequences available.

Host-specific accumulation and temperature effects on the generation of dimeric viral RNA species derived from the S-RNA of members of the Tospovirus genus.

Polygonum ringspot virus (PolRSV) is a recently characterized Tospovirus reported in Italy. Northern blot analyses of PolRSV infections in Nicotiana benthamiana and tomato plants showed that a viral RNA species with nearly twice the length of the Small genomic RNA (S-RNA) accumulated abundantly in the former host, but was not detected in the latter. Additional assays confirmed that biogenesis of this novel RNA species was common to all PolRSV isolates tested and also to an isolate of Tomato spotted wilt virus (TSWV).

Identification of Ourmiavirus 30K movement protein amino acid residues involved in symptomatology, viral movement, subcellular localization and tubule formation.

Several plant viruses encode movement proteins (MPs) classified in the 30K superfamily. Despite a great functional diversity, alignment analysis of MP sequences belonging to the 30K superfamily revealed the presence of a central core region, including amino acids potentially critical for MP structure and functionality. We performed alanine-scanning mutagenesis of the Ourmia melon virus (OuMV) MP, and studied the effects of amino acid substitutions on MP properties and virus infection.

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection.

Viral small RNAs (vsRNAs) are one of the key elements involved in RNA silencing-based defense against viruses in plants. We analyzed the vsRNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot virus (PolRSV) (Tospovirus, Bunyaviridae). VsRNAs were abundant in both hosts, but a different size profile was observed, with an abundance peak at 21 in N.