Editorial

8 pages, 1092 KiB

Open AccessEditorial

The Fine Legacy of Giovanni P. Martelli (1935–2020), a Preeminent Plant Virologist and the Founder of Modern Grapevine Virology

by Ahmed Hadidi, Marina Barba and Luisa Rubino

Viruses 2023, 15(1), 210; https://doi.org/10.3390/v15010210 - 12 Jan 2023

Cited by 1 | Viewed by 1731

Abstract

Giovanni Paolo Martelli passed away on 8 January 2020 [...] Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

Research

Jump to: Editorial, Review, Other

13 pages, 1441 KiB

Open AccessArticle

Old and New Aphid-Borne Viruses in Coriander in Chile: An Epidemiological Approach

by Alan Zamorano, Paulina Carevic, Camila Gamboa, Weier Cui, Tomislav Curkovic, Pamela Córdova, Gastón Higuera, Luz Ramos-Castillo, Nicolás Quiroga and Nicola Fiore

Viruses 2024, 16(2), 226; https://doi.org/10.3390/v16020226 - 31 Jan 2024

Viewed by 995

Abstract

In Chile, edible herbs are mainly grown by small farmers. This type of horticultural crop typically requires intensive management because it is highly susceptible to insects, some of which transmit viruses that severely affect crop yield and quality. In 2019, in coriander plants [...] Read more.

In Chile, edible herbs are mainly grown by small farmers. This type of horticultural crop typically requires intensive management because it is highly susceptible to insects, some of which transmit viruses that severely affect crop yield and quality. In 2019, in coriander plants tested negative for all previously reported viruses, RNA-Seq analysis of one symptomatic plant revealed a plethora of viruses, including one virus known to infect coriander, five viruses never reported in coriander, and a new cytorhabdovirus with a 14,180 nucleotide RNA genome for which the species name Cytorhabdovirus coriandrum was proposed. Since all the detected viruses were aphid-borne, aphids and weeds commonly growing around the coriander field were screened for viruses. The results showed the occurrence of the same seven viruses and the alfalfa mosaic virus, another aphid-borne virus, in aphids and weeds. Together, our findings document the presence of multiple viruses in coriander and the potential role of weeds as virus reservoirs for aphid acquisition. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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9 pages, 1951 KiB

Open AccessArticle

Identification, Sequencing, and Molecular Analysis of RNA2 of Artichoke Italian Latent Virus Isolates from Known Hosts and a New Host Plant Species

by Toufic Elbeaino, Amani Ben Slimen, Imen Belgacem, Monia Mnari-Hattab, Roberta Spanò, Michele Digiaro and Ahmed Abdelkhalek

Viruses 2023, 15(11), 2170; https://doi.org/10.3390/v15112170 - 28 Oct 2023

Viewed by 1148

Abstract

Despite its first description in 1977 and numerous reports of its presence in various plant species in many countries, the molecular information available in GenBank for artichoke Italian latent virus (AILV) is still limited to a single complete genome sequence (RNA1 and 2) [...] Read more.

Despite its first description in 1977 and numerous reports of its presence in various plant species in many countries, the molecular information available in GenBank for artichoke Italian latent virus (AILV) is still limited to a single complete genome sequence (RNA1 and 2) of a grapevine isolate (AILV-V) and a partial portion of the RNA2 sequence from an isolate of unknown origin and host. Here, we report the results of molecular analyses conducted on the RNA2 of some AILV isolates, sequenced for the first time in this study, together with the first-time identification of AILV in a new host plant species, namely chard (Beta vulgaris subsp. vulgaris), associated with vein clearing and mottling symptoms on leaves. The different AILV isolates sequenced were from artichoke (AILV-C), gladiolus (AILV-G), Sonchus (AILV-S), and chard (AILV-B). At the molecular level, the sequencing results of the RNA2 segments showed that AILV-C, AILV-G, AILV-S, and AILV-B had a length of 4629 nt (excluding the 3′ terminal polyA tail), which is one nt shorter than that of the AILV-V reported in GenBank. A comparison of the RNA2 coding region sequences of all the isolates showed that AILV-V was the most divergent isolate, with the lowest sequence identities of 83.2% at the nucleotide level and 84.7% at the amino acid level. Putative intra-species sequence recombination sites were predicted among the AILV isolates, mainly involving the genomes of AILV-V, AILV-C, and AILV-B. This study adds insights into the variability of AILV and the occurrence of recombination that may condition plant infection. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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16 pages, 3913 KiB

Open AccessArticle

Characterization of a Putative New Member of the Genus Potyvirus from Kudzu (Pueraria montana var. lobata) in Mississippi

by Nina Aboughanem-Sabanadzovic, Ronald Christian Stephenson, Thomas W. Allen, Alan Henn, William F. Moore, Amanda Lawrence and Sead Sabanadzovic

Viruses 2023, 15(11), 2145; https://doi.org/10.3390/v15112145 - 25 Oct 2023

Viewed by 1016

Abstract

Kudzu (Pueraria montana var. lobata), a plant native to Southeastern Asia, has become a major noxious weed covering millions of hectares in the Southern United States. A kudzu patch displaying virus-like symptoms located in Ackerman, northeastern Mississippi (MS), was used as [...] Read more.

Kudzu (Pueraria montana var. lobata), a plant native to Southeastern Asia, has become a major noxious weed covering millions of hectares in the Southern United States. A kudzu patch displaying virus-like symptoms located in Ackerman, northeastern Mississippi (MS), was used as a source for virus isolation and characterization involving mechanical and vector transmission, ultrastructural observation, surveys, Sanger and high-throughput genome sequencing, and sequence analyses. The results revealed the presence of a new potyvirus in infected kudzu, closely related to wisteria vein mosaic virus (WVMV) and provisionally named kudzu chlorotic ring blotch virus (KudCRBV). Genome features and pairwise comparison with six WVMV genomes currently available in GenBank and three additional isolates from MS sequenced in this work suggest that KudCRBV is likely a member of a new species in the genus Potyvirus. Furthermore, under experimental conditions, KudCRBV was successfully transmitted by cotton and potato aphids and mechanically to soybean and beans. A state-wide survey revealed several kudzu patches infected by the virus in northern MS. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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15 pages, 1158 KiB

Open AccessArticle

A NitroPure Nitrocellulose Membrane-Based Grapevine Virus Sampling Kit: Development and Deployment to Survey Japanese Vineyards and Nurseries

by Mizuho Nita, Taylor Jones, Diana McHenry, Elizabeth Bush, Charlotte Oliver, Akira Kawaguchi, Akiko Nita and Miyuki Katori

Viruses 2023, 15(10), 2102; https://doi.org/10.3390/v15102102 - 17 Oct 2023

Viewed by 1112

Abstract

We developed a NitroPure Nitrocellulose (NPN) membrane-based method for sampling and storing grapevine sap for grapevine virus detection. We devised an efficient nucleic acid extraction method for the NPN membrane, resulting in 100% amplification success for grapevine leafroll-associated virus 2 (GLRaV2) and 3 [...] Read more.

We developed a NitroPure Nitrocellulose (NPN) membrane-based method for sampling and storing grapevine sap for grapevine virus detection. We devised an efficient nucleic acid extraction method for the NPN membrane, resulting in 100% amplification success for grapevine leafroll-associated virus 2 (GLRaV2) and 3 (GLRaV3), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine virus A, grapevine virus B, and grapevine red blotch virus (GRBV). This method also allowed the storage of recoverable nucleic acid for 18 months at room temperature. We created a sampling kit to survey GLRaV2, GLRaV3, and GRBV in Japanese vineyards. We tested the kits in the field in 2018 and then conducted mail-in surveys in 2020–2021. The results showed a substantial prevalence of GLRaV3, with 48.5% of 132 sampled vines being positive. On the other hand, only 3% of samples tested positive for GLRaV2 and none for GRBV. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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16 pages, 2534 KiB

Open AccessArticle

Minor Variants of Orf1a, p33, and p23 Genes of VT Strain Citrus Tristeza Virus Isolates Show Symptomless Reactions on Sour Orange and Prevent Superinfection of Severe VT Isolates

by Grazia Licciardello, Giuseppe Scuderi, Marcella Russo, Marina Bazzano, Moshe Bar-Joseph and Antonino F. Catara

Viruses 2023, 15(10), 2037; https://doi.org/10.3390/v15102037 - 30 Sep 2023

Viewed by 1257

Abstract

The control of tristeza quick decline (QD) of citrus is based on the use of rootstocks that are tolerant or resistant to the Citrus tristeza virus (CTV), but some of them show bio-agronomic limits. The application of cross-protection (CP) has been insufficiently explored. [...] Read more.

The control of tristeza quick decline (QD) of citrus is based on the use of rootstocks that are tolerant or resistant to the Citrus tristeza virus (CTV), but some of them show bio-agronomic limits. The application of cross-protection (CP) has been insufficiently explored. The present study examined the possibility of QD control by cross-protection (CP) following reports showing the dependence of the CP strategy on the close genetic relationships between the protective and challenging CTV isolates. Taking advantage of deep sequencing technologies, we located six naturally infected trees harboring no-seedling yellow (no-SY) and no QD decline (mild) VT isolates and used these for challenge inoculation with three QD VT isolates. Symptom monitoring showed that all six Sicilian mild no-SY isolates, based on their genomic relatedness and mild symptoms reactions, provide effective protection against the three severe local VT isolates. The differences between the six mild and three severe isolates were confined to just a few nucleotide variations conserved in eight positions of three CTV genes (p23, p33, and Orf1a). These results confirm that the superinfection exclusion (SIE mechanism) depends on close genetic relatedness between the protective and challenging severe VT strain isolates. Ten years of investigation suggest that CP could turn into an efficient strategy to contain CTV QD infections of sweet orange trees on SO rootstock. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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16 pages, 3271 KiB

Open AccessArticle

Clematis vitalba Is a Natural Host of the Novel Ilarvirus, Prunus Virus I

by Pal Salamon, Zsuzsanna Nagyne-Galbacs, Emese Demian, Adam Achs, Peter Alaxin, Lukáš Predajňa, Evans Duah Agyemang, Francesco Desiderio, Andras Peter Takacs, Wulf Menzel, Dijana Škorić, Miroslav Glasa and Eva Varallyay

Viruses 2023, 15(9), 1964; https://doi.org/10.3390/v15091964 - 20 Sep 2023

Cited by 1 | Viewed by 1241

Abstract

Clematis vitalba L. is a climbing shrub and a pioneer plant in abandoned orchards or vineyards that are widespread in temperate climate zones. In past years, several viruses infecting the Clematis species have been identified, including different ilarviruses. Prunus virus I (PrVI) is [...] Read more.

Clematis vitalba L. is a climbing shrub and a pioneer plant in abandoned orchards or vineyards that are widespread in temperate climate zones. In past years, several viruses infecting the Clematis species have been identified, including different ilarviruses. Prunus virus I (PrVI) is a recently described ilarvirus, which has been shown to infect sweet cherries and peaches in Greece. Moreover, its presence has been detected in ornamental Clematis in Russia. In the present work, we analyzed the virome of wildly growing C. vitalba plants from Hungary, Slovakia and Croatia showing different kinds of symptoms using high-throughput sequencing (HTS) of small RNAs or ribodepleted RNAs. Applying HTS enabled us to identify the presence of PrVI in C. vitalba, and the bioinformatic analyses were further validated with RT-PCR using PrVI-specific primers and Sanger dideoxy sequencing. Nearly full genome sequences of all three viral RNAs of one Hungarian, two Slovak and one Croatian isolate were determined. Their phylogenetic analysis showed high similarity to each other and to other PrVI isolates described from Central Europe. As the sampled plants were co-infected with other viruses, it is not possible to determine a direct correlation between the infection with PrVI and the observed symptoms. Analyses of different Prunus species in stock collection showed infection of several peach and sweet cherry varieties in Hungary. Our results expand the knowledge on the natural host range of PrVI and highlight the necessity to evaluate alternative plant hosts (even non-Prunus) of PrVI and the role of the virus in the etiology of the potential diseases. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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12 pages, 4355 KiB

Open AccessArticle

High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus

by Alfredo Diaz-Lara, Kristian Stevens, Vivian Hayde Aguilar-Molina, José Miguel Fernández-Cortés, Víctor Manuel Chabacano León, Marcos De Donato, Ashutosh Sharma, Teresa M. Erickson and Maher Al Rwahnih

Viruses 2023, 15(7), 1561; https://doi.org/10.3390/v15071561 - 16 Jul 2023

Cited by 2 | Viewed by 1439

Abstract

This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). [...] Read more.

This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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13 pages, 536 KiB

Open AccessArticle

Metaviromic Characterization of Betaflexivirus Populations Associated with a Vitis cultivar Collection in South Africa

by David A. Read, Genevieve D. Thompson, Dirk Z. H. Swanevelder and Gerhard Pietersen

Viruses 2023, 15(7), 1474; https://doi.org/10.3390/v15071474 - 29 Jun 2023

Cited by 1 | Viewed by 1084

Abstract

South Africa is associated with a centuries-old viticultural industry, accompanied by a diverse range of wine and table grape cultivars and an extensive history of pervasive introductions of vine material and associated viruses. The Vitis D2 collection in Stellenbosch represents the most comprehensive [...] Read more.

South Africa is associated with a centuries-old viticultural industry, accompanied by a diverse range of wine and table grape cultivars and an extensive history of pervasive introductions of vine material and associated viruses. The Vitis D2 collection in Stellenbosch represents the most comprehensive collection of Vitis species, hybrids, and cultivars in South Africa. We collected leaf petiole material from 229 accessions from this collection. Our metaviromic analyses revealed a total of 406 complete/near complete genomes of various betaflexiviruses. Among these, we identified the presence of grapevine rupestris stem pitting-associated virus and grapevine viruses A, B, E, F, H (GVH), I (GVI), and M (GVM). Notably, this study marks the first report of GVH, GVI, and GVM in South Africa, which were confirmed via RT-PCR. This research significantly contributes to our understanding of viral diversity and introductions in South African viticulture and emphasizes the need for vigilant monitoring and management of viral infections. Our findings lay the groundwork for strategies that mitigate the impact of viruses on South Africa’s wine industry, which generates an annual revenue of approximately 500 million USD. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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14 pages, 3486 KiB

Open AccessArticle

Genetic Characterization of Raspberry Bushy Dwarf Virus Isolated from Red Raspberry in Kazakhstan

by Mariya Kolchenko, Anastasiya Kapytina, Nazym Kerimbek, Alexandr Pozharskiy, Gulnaz Nizamdinova, Marina Khusnitdinova, Aisha Taskuzhina and Dilyara Gritsenko

Viruses 2023, 15(4), 975; https://doi.org/10.3390/v15040975 - 16 Apr 2023

Cited by 1 | Viewed by 1220

Abstract

Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both [...] Read more.

Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both cultivated and wild raspberry in Kazakhstan and compare them to investigate their genetic diversity and phylogenetic relationships, as well as to predict their protein structure. Phylogenetic and population diversity analyses were performed on all available RBDV RNA2, MP and CP sequences. Nine of the isolates investigated in this study formed a new, well-supported clade, while the wild isolates clustered with the European isolates. Predicted protein structure analysis revealed two regions that differed between α- and β-structures among the isolates. For the first time, the genetic composition of Kazakhstani raspberry viruses has been characterized. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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18 pages, 919 KiB

Open AccessArticle

The Three-Cornered Alfalfa Hopper, Spissistilus festinus, Is a Vector of Grapevine Red Blotch Virus in Vineyards

by Madison T. Flasco, Victoria Hoyle, Elizabeth J. Cieniewicz, Greg Loeb, Heather McLane, Keith Perry and Marc F. Fuchs

Viruses 2023, 15(4), 927; https://doi.org/10.3390/v15040927 - 07 Apr 2023

Cited by 7 | Viewed by 2359

Abstract

Spissistilus festinus (Hemiptera: Membracidae) transmit grapevine red blotch virus (GRBV, Grablovirus, Geminiviridae) in greenhouse settings; however, their role as a vector of GRBV in vineyards is unknown. Following controlled exposures of aviruliferous S. festinus for two weeks on infected, asymptomatic vines [...] Read more.

Spissistilus festinus (Hemiptera: Membracidae) transmit grapevine red blotch virus (GRBV, Grablovirus, Geminiviridae) in greenhouse settings; however, their role as a vector of GRBV in vineyards is unknown. Following controlled exposures of aviruliferous S. festinus for two weeks on infected, asymptomatic vines in a California vineyard in June and a 48 h gut clearing on alfalfa, a nonhost of GRBV, approximately half of the released insects tested positive for GRBV (45%, 46 of 102), including in the salivary glands of dissected individuals (11%, 3 of 27), indicating acquisition. Following controlled exposures of viruliferous S. festinus for two to six weeks on GRBV-negative vines in vineyards in California and New York in June, transmission of GRBV was detected when two S. festinus were restricted to a single leaf (3%, 2 of 62 in California; 10%, 5 of 50 in New York) but not with cohorts of 10–20 specimens on entire or half shoots. This work was consistent with greenhouse assays in which transmission was most successful with S. festinus exposed to a single leaf (42%, 5 of 12), but rarely occurred on half shoots (8%, 1 of 13), and never on entire shoots (0%, 0 of 18), documenting that the transmission of GRBV is facilitated through the feeding of fewer S. festinus on a restricted area of grapevine tissue. This work demonstrates S. festinus is a GRBV vector of epidemiological importance in vineyards. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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18 pages, 2290 KiB

Open AccessArticle

Phylogenetic and Evolutionary Studies of Grapevine Pinot Gris Virus Isolates from Canada

by Minh Vu, Bhadra Murthy Vemulapati, Wendy McFadden-Smith, Mamadou L. Fall, José Ramón Úrbez-Torres, Debra L. Moreau and Sudarsana Poojari

Viruses 2023, 15(3), 735; https://doi.org/10.3390/v15030735 - 12 Mar 2023

Cited by 5 | Viewed by 1779

Abstract

This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced [...] Read more.

This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced and compared to genomes of 43 GPGV isolates representing eight countries and three continents. Phylogenetic analysis based on full genome sequences revealed an unambiguous separation of North American GPGV isolates with isolates from Europe and Asia. Within the North American clade, GPGV isolates from the USA segregated into a distinct subclade, whereas the relationships amongst GPGV isolates from different regions of Canada were not clearly defined. The phylogenetic analysis of the overlapping regions of MP and CP genes involving 169 isolates from 14 countries resulted in two distinctive clades, which were seemingly independent of their country of origin. Clade 1 included the majority of asymptomatic isolates (81% asymptomatic), whereas clade 2 was predominantly formed of symptomatic isolates (78% symptomatic). This research is the first study focused on the genetic variability and origin of GPGV in Canada. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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15 pages, 1193 KiB

Open AccessArticle

Identification of Interactions between Proteins Encoded by Grapevine Leafroll-Associated Virus 3

by Ilani Mostert, Rachelle Bester, Johan T. Burger and Hans J. Maree

Viruses 2023, 15(1), 208; https://doi.org/10.3390/v15010208 - 11 Jan 2023

Cited by 2 | Viewed by 1723

Abstract

The roles of proteins encoded by members of the genus Ampelovirus, family Closteroviridae are largely inferred by sequence homology or analogy to similarly located ORFs in related viruses. This study employed yeast two-hybrid and bimolecular fluorescence complementation assays to investigate interactions between [...] Read more.

The roles of proteins encoded by members of the genus Ampelovirus, family Closteroviridae are largely inferred by sequence homology or analogy to similarly located ORFs in related viruses. This study employed yeast two-hybrid and bimolecular fluorescence complementation assays to investigate interactions between proteins of grapevine leafroll-associated virus 3 (GLRaV-3). The p5 movement protein, HSP70 homolog, coat protein, and p20B of GLRaV-3 were all found to self-interact, however, the mechanism by which p5 interacts remains unknown due to the absence of a cysteine residue crucial for the dimerisation of the closterovirus homolog of this protein. Although HSP70h forms part of the virion head of closteroviruses, in GLRaV-3, it interacts with the coat protein that makes up the body of the virion. Silencing suppressor p20B has been shown to interact with HSP70h, as well as the major coat protein and the minor coat protein. The results of this study suggest that the virion assembly of a member of the genus Ampelovirus occurs in a similar but not identical manner to those of other genera in the family Closteroviridae. Identification of interactions of p20B with virus structural proteins provides an avenue for future research to explore the mechanisms behind the suppression of host silencing and suggests possible involvement in other aspects of the viral replication cycle. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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14 pages, 1734 KiB

Open AccessArticle

Fast and Sensitive Detection of Soil-Borne Cereal Mosaic Virus in Leaf Crude Extract of Durum Wheat

by Monica Marra, Chiara D’Errico, Cinzia Montemurro, Claudio Ratti, Elena Baldoni, Slavica Matic and Gian Paolo Accotto

Viruses 2023, 15(1), 140; https://doi.org/10.3390/v15010140 - 31 Dec 2022

Cited by 2 | Viewed by 1695

Abstract

Soil-borne cereal mosaic virus (SBCMV) is a furovirus with rigid rod-shaped particles containing an ssRNA genome, transmitted by Polymyxa graminis Led., a plasmodiophorid that can persist in soil for up to 20 years. SBCMV was reported on common and durum wheat and it [...] Read more.

Soil-borne cereal mosaic virus (SBCMV) is a furovirus with rigid rod-shaped particles containing an ssRNA genome, transmitted by Polymyxa graminis Led., a plasmodiophorid that can persist in soil for up to 20 years. SBCMV was reported on common and durum wheat and it can cause yield losses of up to 70%. Detection protocols currently available are costly and time-consuming (real-time PCR) or have limited sensitivity (ELISA). To facilitate an efficient investigation of the real dispersal of SBCMV, it is necessary to develop a new detection tool with the following characteristics: no extraction steps, very fast results, and high sensitivity to allow pooling of a large number of samples. In the present work, we have developed a reverse transcription loop-mediated isothermal amplification (RT-LAMP) protocol with such characteristics, and we have compared it with real-time PCR. Our results show that the sensitivity of LAMP and real-time PCR on cDNA and RT-LAMP on crude extracts are comparable, with the obvious advantage that RT-LAMP produces results in minutes rather than hours. This paves the way for extensive field surveys, leading to a better knowledge of the impact of this virus on wheat health and yield. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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17 pages, 2729 KiB

Open AccessArticle

Identification of Seven Additional Genome Segments of Grapevine-Associated Jivivirus 1

by Thierry Candresse, Laurence Svanella-Dumas, Armelle Marais, Flora Depasse, Chantal Faure and Marie Lefebvre

Viruses 2023, 15(1), 39; https://doi.org/10.3390/v15010039 - 22 Dec 2022

Cited by 1 | Viewed by 1537

Abstract

Jiviruses are a group of recently described viruses characterized with a tripartite genome and having affinities with Virgaviridae (RNA1 and 2) and Flaviviridae (RNA3). Using a combination of high-throughput sequencing, datamining and RT-PCR approaches, we demonstrate here that in grapevine samples infected by [...] Read more.

Jiviruses are a group of recently described viruses characterized with a tripartite genome and having affinities with Virgaviridae (RNA1 and 2) and Flaviviridae (RNA3). Using a combination of high-throughput sequencing, datamining and RT-PCR approaches, we demonstrate here that in grapevine samples infected by grapevine-associated jivivirus 1 (GaJV-1) up to 7 additional molecules can be consistently detected with conserved 5′ and 3′ non-coding regions in common with the three previously identified GaJV-1 genomic RNAs. RNA4, RNA5, RNA6, RNA7, RNA8 and RNA10, together with a recombinant RNArec7-8, are all members of a family sharing a previously non recognized conserved protein domain, while RNA9 is part of a distinct family characterized by another conserved motif. Datamining of pecan (Carya illinoinensis) public transcriptomic data allowed the identification of two further jiviviruses and the identification of supplementary genomic RNAs with homologies to those of GaJV-1. Taken together, these results reshape our vision of the divided genome of jiviviruses and raise novel questions about the function(s) of the proteins encoded by jiviviruses supplementary RNAs. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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15 pages, 4593 KiB

Open AccessArticle

Biology and Ultrastructural Characterization of Grapevine Badnavirus 1 and Grapevine Virus G

by Martin Jagunić, Angelo De Stradis, Darko Preiner, Pierfederico La Notte, Maher Al Rwahnih, Rodrigo P. P. Almeida and Darko Vončina

Viruses 2022, 14(12), 2695; https://doi.org/10.3390/v14122695 - 30 Nov 2022

Cited by 5 | Viewed by 1643

Abstract

The biological characteristics of grapevine viruses, such as their transmission and host range, are important for the adoption of successful prophylaxis strategies. The aim of this study was to investigate the traits of two newly described grapevine viruses widely distributed in Croatia, grapevine [...] Read more.

The biological characteristics of grapevine viruses, such as their transmission and host range, are important for the adoption of successful prophylaxis strategies. The aim of this study was to investigate the traits of two newly described grapevine viruses widely distributed in Croatia, grapevine badnavirus 1 (GBV-1) and grapevine virus G (GVG). The vine mealybug (Planoccocus ficus) proved to be a vector of GBV-1 and GVG capable of vine-to-vine transmission with overall experimental transmission rates of 61% and 14.6%, respectively. Transmission was also demonstrated by grafting, with an overall transmission rate of 53.8% for GBV-1 and 100% for GVG, as well as by green grafting using the T-budding technique. Symptoms of GBV-1 and GVG were not observed on the woody cylinders of the indicators LN 33, Kober 5BB, 110 Richter and cvs. Chardonnay and Cabernet Sauvignon. Seed transmission and mechanical transmission were not confirmed. Electron microscopy revealed accumulation of GBV-1 particles and viroplasms in the cytoplasm, but no alternations of the cell structure. Infection with GVG revealed the proliferation of tonoplast-associated vesicles inside phloem cells and cell wall thickening. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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13 pages, 641 KiB

Open AccessArticle

Transmission of Grapevine Leafroll-Associated Viruses and Grapevine Virus A by Vineyard-Sampled Soft Scales (Parthenolecanium corni, Hemiptera: Coccidae)

by Gérard Hommay, Monique Beuve and Etienne Herrbach

Viruses 2022, 14(12), 2679; https://doi.org/10.3390/v14122679 - 29 Nov 2022

Cited by 1 | Viewed by 1233

Abstract

Grapevine-infecting ampelo- and vitiviruses are transmitted by scale insects belonging to several species, among which is the European fruit lecanium, Parthenolecanium corni (Bouché) (Hemiptera Coccidae). Our objective was to characterize the transmission biology of grapevine leafroll-associated viruses (GLRaV) and grapevine virus A (GVA) [...] Read more.

Grapevine-infecting ampelo- and vitiviruses are transmitted by scale insects belonging to several species, among which is the European fruit lecanium, Parthenolecanium corni (Bouché) (Hemiptera Coccidae). Our objective was to characterize the transmission biology of grapevine leafroll-associated viruses (GLRaV) and grapevine virus A (GVA) by this soft scale species in order to evaluate its ability to spread these viruses. In transmission experiments with nymphs sampled from different vineyards infected with GLRaV 1, 2, 3 and GVA, P. corni transmitted only GLRaV 1 and GVA to healthy vines. GVA was predominantly transmitted along with GLRaV 1, whereas the latter could be transmitted alone from single or co-infected vines. Vineyard-sampled second instar nymphs were more efficient than first instars at transmitting GLRaV 1, whereas both instars displayed similar transmission rates for GVA. Short virus inoculation access periods and the absence of virus in eggs of females living on infected grapevines fulfilled the criteria of non-circulative semi-persistent transmission mode. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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26 pages, 3389 KiB

Open AccessArticle

Metagenomic Analysis of Ampelographic Collections of Dagestan Revealed the Presence of Two Novel Grapevine Viruses

by Darya Shvets, Kirill Sandomirsky, Elena Porotikova and Svetlana Vinogradova

Viruses 2022, 14(12), 2623; https://doi.org/10.3390/v14122623 - 24 Nov 2022

Cited by 5 | Viewed by 2039

Abstract

In this study, we analyzed the virome of 73 grape samples from two Dagestan ampelographic collections in Russia using high-throughput sequencing of total RNAs. Fourteen viruses and four viroids were identified, with one to eleven of them detected in each plant. For the [...] Read more.

In this study, we analyzed the virome of 73 grape samples from two Dagestan ampelographic collections in Russia using high-throughput sequencing of total RNAs. Fourteen viruses and four viroids were identified, with one to eleven of them detected in each plant. For the first time in Russia, we identified grapevine leafroll-associated virus 7 and grapevine Kizil Sapak virus. A total of 206 genomes of viruses and viroids were obtained, and their phylogenetic analysis was carried out. The de novo assembly and tblastx analysis allowed us to obtain contigs of a novel (+) ssRNA genome of a plant virus from the genus Umbravirus, which was tentatively named grapevine umbra-like virus (GULV), as well as contigs of a novel dsDNA pararetrovirus from the genus Caulimovirus, which was tentatively named grapevine pararetrovirus (GPRV). Complete genomes of these viruses were obtained and used for Sequence Demarcation Tool (SDT) analysis and phylogeny studies. GULV and GPRV were detected in 16 and 33 germplasm samples from the Dagestan collections, respectively. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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10 pages, 4054 KiB

Open AccessArticle

Mixed Infection of Blackcurrant with a Novel Cytorhabdovirus and Black Currant-Associated Nucleorhabdovirus

by Karel Petrzik, Jaroslava Přibylová, Josef Špak, Tatiana Sarkisova, Jana Fránová, Jan Holub, Jan Skalík and Igor Koloniuk

Viruses 2022, 14(11), 2456; https://doi.org/10.3390/v14112456 - 06 Nov 2022

Cited by 4 | Viewed by 1460

Abstract

A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined [...] Read more.

A virome screen was performed on a new breeding line, KB1, of blackcurrant. Rhabdovirus-like particles were observed by electron microscopy in ultrathin sections of flower stalks, and the complete genome sequence of a novel virus, provisionally named blackcurrant rhabdovirus 2 (BCRV2), was determined and verified using high-throughput sequencing. The genomic organization of BCRV2 was characteristic of cytorhabdoviruses (family Rhabdoviridae) and included seven genes: 3′-N-P′-P-P3-M-G-L-5′. BLASTP analysis revealed that the putative L protein had the highest amino acid sequence identity (75%) with strawberry virus 2. BCRV2 was detected in Cryptomyzus galeopsidis, but efficient transmission by this aphid was not confirmed. Of note, we observed coinfection of the KB1 line with blackcurrant-associated rhabdovirus (BCaRV) by RT-PCR. This is likely the first evidence of the presence of a cyto- and a nucleorhabdovirus in a single host. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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21 pages, 2349 KiB

Open AccessArticle

Characterization of Grapevine Fanleaf Virus Isolates in ‘Chardonnay’ Vines Exhibiting Severe and Mild Symptoms in Two Vineyards

by Julie Kubina, Jean-Michel Hily, Pierre Mustin, Véronique Komar, Shahinez Garcia, Isabelle Rachel Martin, Nils Poulicard, Amandine Velt, Véronique Bonnet, Laurence Mercier, Olivier Lemaire and Emmanuelle Vigne

Viruses 2022, 14(10), 2303; https://doi.org/10.3390/v14102303 - 20 Oct 2022

Cited by 3 | Viewed by 2224

Abstract

Fanleaf degeneration is a complex viral disease of Vitis spp. that detrimentally impacts fruit yield and reduces the productive lifespan of most vineyards worldwide. In France, its main causal agent is grapevine fanleaf virus (GFLV). In the past, field experiments were conducted to [...] Read more.

Fanleaf degeneration is a complex viral disease of Vitis spp. that detrimentally impacts fruit yield and reduces the productive lifespan of most vineyards worldwide. In France, its main causal agent is grapevine fanleaf virus (GFLV). In the past, field experiments were conducted to explore cross-protection as a management strategy of fanleaf degeneration, but results were unsatisfactory because the mild virus strain negatively impacted fruit yield. In order to select new mild GFLV isolates, we examined two old ‘Chardonnay’ parcels harbouring vines with distinct phenotypes. Symptoms and agronomic performances were monitored over the four-year study on 21 individual vines that were classified into three categories: asymptomatic GFLV-free vines, GFLV-infected vines severely diseased and GFLV-infected vines displaying mild symptoms. The complete coding genomic sequences of GFLV isolates in infected vines was determined by high-throughput sequencing. Most grapevines were infected with multiple genetically divergent variants. While no specific molecular features were apparent for GFLV isolates from vines displaying mild symptoms, a genetic differentiation of GFLV populations depending on the vineyard parcel was observed. The mild symptomatic grapevines identified during this study were established in a greenhouse to recover GFLV variants of potential interest for cross-protection studies. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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14 pages, 2813 KiB

Open AccessArticle

A Novel Self-Cleaving Viroid-Like RNA Identified in RNA Preparations from a Citrus Tree Is Not Directly Associated with the Plant

by Beatriz Navarro, Shuai Li, Andreas Gisel, Michela Chiumenti, Maria Minutolo, Daniela Alioto and Francesco Di Serio

Viruses 2022, 14(10), 2265; https://doi.org/10.3390/v14102265 - 15 Oct 2022

Cited by 2 | Viewed by 1600

Abstract

Viroid and viroid-like satellite RNAs are infectious, circular, non-protein coding RNAs reported in plants only so far. Some viroids (family Avsunviroidae) and viroid-like satellite RNAs share self-cleaving activity mediated by hammerhead ribozymes (HHRzs) endowed in both RNA polarity strands. Using a homology-independent [...] Read more.

Viroid and viroid-like satellite RNAs are infectious, circular, non-protein coding RNAs reported in plants only so far. Some viroids (family Avsunviroidae) and viroid-like satellite RNAs share self-cleaving activity mediated by hammerhead ribozymes (HHRzs) endowed in both RNA polarity strands. Using a homology-independent method based on the search for conserved structural motifs of HHRzs in reads and contigs from high-throughput sequenced RNAseq libraries, we identified a novel small (550 nt) viroid-like RNA in a library from a Citrus reticulata tree. Such a viroid-like RNA contains a HHRz in both polarity strands. Northern blot hybridization assays showed that circular forms of both polarity strands of this RNA (tentatively named citrus transiently-associated hammerhead viroid-like RNA1 (CtaHVd-LR1)) exist, supporting its replication through a symmetric pathway of the rolling circle mechanism. CtaHVd-LR1 adopts a rod-like conformation and has the typical features of quasispecies. Its HHRzs were shown to be active during transcription and in the absence of any protein. CtaHVd-LR1 was not graft-transmissible, and after its first identification, it was not found again in the original citrus source when repeatedly searched in the following years, suggesting that it was actually not directly associated with the plant. Therefore, the possibility that this novel self-cleaving viroid-like RNA is actually associated with another organism (e.g., a fungus), in turn, transiently associated with citrus plants, is proposed. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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22 pages, 1977 KiB

Open AccessArticle

Transcriptomic Analyses of Grapevine Leafroll-Associated Virus 3 Infection in Leaves and Berries of ‘Cabernet Franc’

by Yashu Song, Robert H. Hanner and Baozhong Meng

Viruses 2022, 14(8), 1831; https://doi.org/10.3390/v14081831 - 21 Aug 2022

Cited by 4 | Viewed by 1954

Abstract

Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses affecting global grape and wine production. GLRaV-3 is the chief agent associated with grapevine leafroll disease (GLRD), the most prevalent and economically destructive grapevine viral disease complex. Response of grapevine to [...] Read more.

Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses affecting global grape and wine production. GLRaV-3 is the chief agent associated with grapevine leafroll disease (GLRD), the most prevalent and economically destructive grapevine viral disease complex. Response of grapevine to GLRaV-3 infection at the gene expression level is poorly characterized, limiting the understanding of GLRaV-3 pathogenesis and viral-associated symptom development. In this research, we used RNA-Seq to profile the changes in global gene expression of Cabernet franc, a premium red wine grape, analyzing leaf and berry tissues at three key different developmental stages. We have identified 1457 differentially expressed genes (DEGs) in leaves and 1181 DEGs in berries. The expression profiles of a subset of DEGs were validated through RT-qPCR, including those involved in photosynthesis (VvPSBP1), carbohydrate partitioning (VvSUT2, VvHT5, VvGBSS1, and VvSUS), flavonoid biosynthesis (VvUFGT, VvLAR1, and VvFLS), defense response (VvPR-10.3, and VvPR-10.7), and mitochondrial activities (ETFB, TIM13, and NDUFA1). GLRaV-3 infection altered source–sink relationship between leaves and berries. Photosynthesis and photosynthate assimilation were inhibited in mature leaves while increased in young berries. The expression of genes involved in anthocyanin biosynthesis increased in GLRaV-3-infected leaves, correlating with interveinal tissue reddening, a hallmark of GLRD symptoms. Notably, we identified changes in gene expression that suggest a compromised sugar export and increased sugar retrieval in GLRaV-3-infected leaves. Genes associated with mitochondria were down-regulated in both leaves and berries of Cabernet franc infected with GLRaV-3. Results of the present study suggest that GLRaV-3 infection may disrupt mitochondrial function in grapevine leaves, leading to repressed sugar export and accumulation of sugar in mature leaf tissues. The excessive sugar accumulation in GLRaV-3-infected leaves may trigger downstream GLRD symptom development and negatively impact berry quality. We propose a working model to account for the molecular events underlying the pathogenesis of GLRaV-3 and symptom development. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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16 pages, 1688 KiB

Open AccessArticle

A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley

by Jennifer Dahan, Yuri I. Wolf, Gardenia E. Orellana, Erik J. Wenninger, Eugene V. Koonin and Alexander V. Karasev

Viruses 2022, 14(6), 1320; https://doi.org/10.3390/v14061320 - 16 Jun 2022

Cited by 7 | Viewed by 3015

Abstract

Alfalfa is an important perennial forage crop in Idaho supporting dairy and cattle industries that is typically grown in the same field for as many as 4 years. Alfalfa stands of different ages were subjected to screening for viruses using high-throughput sequencing and [...] Read more.

Alfalfa is an important perennial forage crop in Idaho supporting dairy and cattle industries that is typically grown in the same field for as many as 4 years. Alfalfa stands of different ages were subjected to screening for viruses using high-throughput sequencing and RT-PCR. The two most common viruses found were alfalfa mosaic virus and bean leafroll virus, along with Medicago sativa amalgavirus, two alphapartitiviruses, and one deltapartitivirus. Additionally, a new flavi-like virus with an unusual genome organization was discovered, dubbed Snake River alfalfa virus (SRAV). The 11,745 nt, positive-sense (+) RNA genome of SRAV encodes a single 3835 aa polyprotein with only two identifiable conserved domains, an RNA-dependent RNA polymerase (RdRP) and a predicted serine protease. Notably, unlike all +RNA virus genomes in the similar size range, the SRAV polyprotein contained no predicted helicase domain. In the RdRP phylogeny, SRAV was placed inside the flavi-like lineage as a sister clade to a branch consisting of hepaci-, and pegiviruses. To the best of our knowledge, SRAV is the first flavi-like virus identified in a plant host. Although commonly detected in alfalfa crops in southern Idaho, SRAV sequences were also amplified from thrips feeding in alfalfa stands in the area, suggesting a possible role of Frankliniella occidentalis in virus transmission. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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Review

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15 pages, 774 KiB

Open AccessReview

Traditional Approaches and Emerging Biotechnologies in Grapevine Virology

by Giulia Tarquini, Mattia Dall’Ara, Paolo Ermacora and Claudio Ratti

Viruses 2023, 15(4), 826; https://doi.org/10.3390/v15040826 - 24 Mar 2023

Cited by 4 | Viewed by 2114

Abstract

Environmental changes and global warming may promote the emergence of unknown viruses, whose spread is favored by the trade in plant products. Viruses represent a major threat to viticulture and the wine industry. Their management is challenging and mostly relies on prophylactic measures [...] Read more.

Environmental changes and global warming may promote the emergence of unknown viruses, whose spread is favored by the trade in plant products. Viruses represent a major threat to viticulture and the wine industry. Their management is challenging and mostly relies on prophylactic measures that are intended to prevent the introduction of viruses into vineyards. Besides the use of virus-free planting material, the employment of agrochemicals is a major strategy to prevent the spread of insect vectors in vineyards. According to the goal of the European Green Deal, a 50% decrease in the use of agrochemicals is expected before 2030. Thus, the development of alternative strategies that allow the sustainable control of viral diseases in vineyards is strongly needed. Here, we present a set of innovative biotechnological tools that have been developed to induce virus resistance in plants. From transgenesis to the still-debated genome editing technologies and RNAi-based strategies, this review discusses numerous illustrative studies that highlight the effectiveness of these promising tools for the management of viral infections in grapevine. Finally, the development of viral vectors from grapevine viruses is described, revealing their positive and unconventional roles, from targets to tools, in emerging biotechnologies. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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Other

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7 pages, 992 KiB

Open AccessBrief Report

Occurrence of Nine Grapevine Viruses in Commercial Vineyards of Mendoza, Argentina

by Sebastian Gomez Talquenca, Rodrigo Alonso, Facundo Luna, Melisa Lanza Volpe and Fernando Buscema

Viruses 2023, 15(1), 177; https://doi.org/10.3390/v15010177 - 07 Jan 2023

Cited by 1 | Viewed by 1520

Abstract

Grapevine is a widely grown fruit crop that is seriously affected by different viruses, reducing grape yield and quality, as well as threatening profitability. Vineyard disease management requires accurate identification of viral infections. This study aimed to survey the presence of ten grapevine [...] Read more.

Grapevine is a widely grown fruit crop that is seriously affected by different viruses, reducing grape yield and quality, as well as threatening profitability. Vineyard disease management requires accurate identification of viral infections. This study aimed to survey the presence of ten grapevine viruses in four geographic sites in the Mendoza province of Argentina. Two hundred twenty-three composite cane samples from 1060 plants of six cultivars were collected from 26 blocks distributed across 11 vineyards. The cane samples were screened by RT-PCR for the following viruses: grapevine leafroll-associated viruses 1–4 (GLRaV 1, 2, 3, and 4), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine virus A (GVA) and B (GVB), grapevine rupestris stem pitting associated virus (GRSPaV), and arabis mosaic virus (ArMV). The results showed an uneven occurrence of viruses through the sampled regions, with GRSPaV being prevalent (71.1%), followed by GFLV (28.9%), GFkV (20.6%), and GLRaV-2 (14.7%). GVB was not detected. This study revealed a moderate prevalence of viruses associated with economically impactful diseases in the vineyards surveyed. Full article

(This article belongs to the Special Issue A Tribute to Giovanni P. Martelli)

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