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Toufic Elbeaino - One of the best experts on this subject based on the ideXlab platform.

  • Production of a polyclonal antiserum against recombinant nucleocapsid protein and its application for the detection of fig mosaic virus.
    Journal of virological methods, 2018
    Co-Authors: Morteza Shahmirzaie, Mohammad Reza Safarnejad, F. Rakhshandehroo, Hossein Safarpour, Hodjattallah Rabbani, Hamid Reza Zamanizadeh, Toufic Elbeaino
    Abstract:

    Abstract Mosaic disease (MD), caused by Fig mosaic Emaravirus (FMV), is the most important and devastating virus disease of fig trees worldwide. The detection of FMV in infected plants is possible only through the use of molecular techniques, i.e. RT-PCR and LAMP, which both offer high sensitivity of detection, but are also considered laborious when dealing with a large number of samples. To cope with this restriction, a polyclonal antiserum through the immunization of a rabbit by injecting the recombinant nucleocapsid protein (NP) of FMV was raised and evaluated for its efficacy in Western Blot, Dot immuno-binding and DAS-ELISA. The results obtained showed that the raised antiserum was able to identify the nucleocapsid protein of FMV (p3) which was found to have an estimated molecular weight of ca. 35 KDa. In addition, the antiserum, when used in the three serological assays, was able to detect the p3 of FMV in protein extracts of infected plants with different levels of efficacy. Dot immuno-binding, using denatured plant protein extract, proved to be the most efficient serological assay for detecting FMV in samples collected from different fig orchards. This is the first report on an antiserum raised against FMV that could be used for immunological detection of the virus.

  • ICTV Virus Taxonomy Profile: Fimoviridae.
    The Journal of general virology, 2018
    Co-Authors: Toufic Elbeaino, Nicole Mielke-ehret, Michele Digiaro, Hans-peter Muehlbach, Giovanni P. Martelli
    Abstract:

    Members of the family Fimoviridae, order Bunyavirales are plant viruses with segmented, linear, single-stranded, negative-sense RNA genomes. They are distantly related to orthotospoviruses and orthobunyaviruses of the families Tospoviridae and Peribunyaviridae, respectively. The family Fimoviridae includes the genus Emaravirus, which comprises several species with European mountain ash ringspot-associated Emaravirus as the type species. Fimoviruses are transmitted to plants by eriophyid mite vectors and induce similar characteristic cytopathologies in their host plants, including the presence of double membrane-bound bodies in the cytoplasm of the virus-infected cells. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Fimoviridae, which is available at www.ictv.global/report/fimoviridae.

  • High-Throughput Sequencing Reveals Cyclamen persicum Mill. as a Natural Host for Fig Mosaic Virus.
    Viruses, 2018
    Co-Authors: Toufic Elbeaino, Thierry Candresse, Armelle Marais, Chantal Faure, Elisa Trioano, Giuseppe Parrella
    Abstract:

    In a search for viral infections, double-stranded RNA (dsRNA) were recovered from a diseased cyclamen (Cyclamen persicum Mill.) accession (Cic) and analyzed by high-throughput sequencing (HTS) technology. Analysis of the HTS data showed the presence of Fig mosaic Emaravirus (FMV) in this accession. The complete sequences of six FMV-Cic RNA genomic segments were determined from the HTS data and using Sanger sequencing. All FMV-Cic RNA segments are similar in size to those of FMV from fig (FMV-Gr10), with the exception of RNA-6 that is one nucleotide longer. The occurrence of FMV in cyclamen was investigated through a small-scale survey, from which four plants (out of 18 tested) were found RT-PCR positive. To study sequence variations of cyclamen isolates of FMV, RT-PCR products generated through the amplification of the partially RNA-dependent RNA polymerase (RdRp, RNA-1), glycoprotein (GP, RNA-2), and nucleocapsid (NCP, RNA-3) genes were explored. The nucleotide sequence identities for cyclamen isolates ranged between 86% and 99% in RNA-1, 93% and 99% in RNA-2, and 98% and 99% in RNA-3, while lower identity levels were observed with the sequences of fig isolates. Based on the phylogenetic tree obtained with a 304-nt fragment of RNA3, all FMV isolates from cyclamens were assigned to a single cluster close to fig isolates from the Mediterranean. FMV was graft-transmitted to healthy cyclamens eliciting symptoms similar to those observed in the Cic accession, thus suggesting a causal role of FMV in the symptoms that prompted the investigation. This is the first report of FMV in a non-fig host, Cyclamen persicum, a finding that may help in the control of the mosaic and mosaic-like diseases of fig and cyclamen, respectively.

  • Detection and phylogenetic analyses of fig-infecting viruses in Bosnia and Herzegovina and Montenegro
    Phytopathologia Mediterranea, 2017
    Co-Authors: D. Delić, Tatjana Perović, Snježana Hrnčić, B. Lolić, Gordana Đurić, Toufic Elbeaino
    Abstract:

    During spring 2016, a survey was carried out in Bosnian-Herzegovinian (BiH) and Montenegrin (MNE) fig orchards, germplasm collection plots and outdoor gardens, to investigate the presence of unreported fig viruses possibly present in both countries, i.e. Fig leaf mottle-associated virus 2 (FLMaV-2), Fig latent virus 1 (FLV-1), Fig cryptic virus 1 (FCV-1), Fig fleck-associated virus (FFkaV) and Fig badnavirus 1 (FBV-1); as well as those previously reported, i.e. Fig leaf mottle-associated virus 1 (FLMaV-1), Fig mild mottle-associated virus (FMMaV) and Fig mosaic Emaravirus (FMV). A total of 84 fig samples (49 from BIH and 35 from MNE) were collected and tested by PCR/RT-PCR using sets of virus-specific primers. Results showed that FBV-1 was the prevailing virus with all samples (100%) infected, followed by FLMaV-1 (54% ) , FMV (35%), FMMaV (7%), FFkaV (6%) and FLMaV-2 (1%); whereas FLV-1 and FCV-1 were not detected. Excluding the FBV-1 detection, 35% of tested trees were infected with at least one other virus. Sequence analyses of PCR/RT-PCR fragments obtained from different viruses showed that FBV-1 was the least variable (0.9% of nucleotides divergent) compared with FLMaV-1 (15.7% sequence variation), FLMaV-2 (17.4%), FMMaV (14.9%), FMV (16.9%) and FFkaV (14.3%). Phylogenetic trees constructed with obtained sequences, together with their homologues retrieved from the Genbank database, showed distinct separation of the BiH and MNE isolates from those of different origins, in particular for FFkaV and FMV; whereas for closteroviruses (FLMaV-1, FLMaV-2 and FMMaV), there was no distinction between the isolates. This is the first report on sequence analyses of fig viruses in this geographical region, and of the presence of FBV-1 in BiH and MNE, and of FLMaV-2 and FFkaV.

  • Deep sequencing of dsRNAs recovered from mosaic-diseased pigeonpea reveals the presence of a novel Emaravirus: pigeonpea sterility mosaic virus 2
    Archives of Virology, 2015
    Co-Authors: Toufic Elbeaino, Michele Digiaro, Mangala Uppala, Harikishan Sudini
    Abstract:

    Deep-sequencing analysis of double-stranded RNA extracted from a mosaic-diseased pigeonpea plant ( Cajanus cajan L., family Fabaceae) revealed the complete sequence of six Emaravirus-like negative-sense RNA segments of 7009, 2229, 1335, 1491, 1833 and 1194 nucleotides in size. In the order from RNA1 to RNA6, these genomic RNAs contained ORFs coding for the RNA-dependent RNA polymerase (RdRp, p1 of 266 kDa), the glycoprotein precursor (GP, p2 of 74.5 kDa), the nucleocapsid (NC, p3 of 34.9 kDa), and the putative movement protein (MP, p4 of 40.7 kDa), while p5 (55 kDa) and p6 (27 kDa) had unknown functions. All RNA segments showed distant relationships to viruses of the genus Emaravirus , and in particular to pigeonpea sterility mosaic virus (PPSMV), with which they shared nucleotide sequence identity ranging from 48.5 % (RNA3) to 62.5 % (RNA1). In phylogenetic trees constructed from the sequences of the proteins encoded by RNA1, RNA2 and RNA3 (p1, p2 and p3), this new viral entity showed a consistent grouping with fig mosaic virus (FMV) and rose rosette virus (RRV), which formed a cluster of their own, clearly distinct from PPSMV-1. In experimental greenhouse trials, this novel virus was successfully transmitted to pigeonpea and French bean seedlings by the eriophyid mite Aceria cajani . Preliminary surveys conducted in the Hyderabad region (India) showed that the virus in question is widespread in pigeonpea plants affected by sterility mosaic disease (86.4 %) but is absent in symptomless plants. Based on molecular, biological and epidemiological features, this novel virus is the second Emaravirus infecting pigeonpea, for which the provisional name pigeonpea sterility mosaic virus 2 (PPSMV-2) is proposed.

Ioannis E. Tzanetakis - One of the best experts on this subject based on the ideXlab platform.

  • The population structure of Rose rosette virus in the USA.
    The Journal of general virology, 2020
    Co-Authors: Asimina Katsiani, Daisy Stainton, Kurt Lamour, Ioannis E. Tzanetakis
    Abstract:

    Rose rosette virus (RRV) (genus Emaravirus) is the causal agent of the homonymous disease, the most destructive malady of roses in the USA. Although the importance of the disease is recognized, little sequence information and no full genomes are available for RRV, a multi-segmented RNA virus. To better understand the population structure of the virus we implemented a Hi-Plex PCR amplicon high-throughput sequencing approach to sequence all 7 segments and to quantify polymorphisms in 91 RRV isolates collected from 16 states in the USA. Analysis revealed insertion/deletion (indel) polymorphisms primarily in the 5' and 3' non-coding, but also within coding regions, including some resulting in changes of protein length. Phylogenetic analysis showed little geographical structuring, suggesting that topography does not have a strong influence on virus evolution. Overall, the virus populations were homogeneous, possibly because of regular movement of plants, the recent emergence of RRV and/or because the virus is under strong purification selection to preserve its integrity and biological functions.

  • A new, widespread Emaravirus discovered in blackberry.
    Virus research, 2017
    Co-Authors: Mohamed K. Hassan, Karen E. Keller, Robert R Martin, Patrick L. Di Bello, Sead Sabanadzovic, Ioannis E. Tzanetakis
    Abstract:

    A new virus was identified in blackberry plants exhibiting leaf mottling, chlorotic ringspots and curved midribs, symptoms associated with blackberry yellow vein disease (BYVD). The genome of the new virus, provisionally named blackberry leaf mottle-associated virus (BLMaV), was characterized and phylogenetic analysis revealed its close relationship to recognized members of the genus Emaravirus. BLMaV was transmitted by a yet to be described eriophyid mite species, further reinforcing its placement in the genus. Detection protocols were developed and used to determine the presence of the virus in plants collected from several areas in the U.S.A. The incidence of BLMaV was greater than 40% in BYVD-affected material.

  • A novel Emaravirus is associated with redbud yellow ringspot disease.
    Virus research, 2016
    Co-Authors: Patrick L. Di Bello, Alma G. Laney, Karen E. Keller, Robert R Martin, Tobiasz Druciarek, Rose C. Gergerich, Ioannis E. Tzanetakis
    Abstract:

    Yellow ringspot is the only virus-like disease reported in redbud (Cercis spp.) with symptoms including vein clearing, chlorotic ringspots and oak-leaf pattern. A putative new Emaravirus was present in all trees displaying typical yellow ringspot symptoms and the name redbud yellow ringspot associated virus is proposed. The virus genome is composed of at least five RNA segments. Two coding regions were studied to determine isolate diversity with results pointing to a homogeneous virus population. Host range was evaluated using graft transmission and by testing species found in close proximity to infected trees. Mite transmission with Aculops cercidis, the predominant species found in redbud trees in the epicenter of the disease, was evaluated but was not found to be a vector of the virus. Based on this study and the accumulated knowledge on Emaravirus evolution we propose that speciation is allopatric, with vectors being a major component of the process.

  • The evolution of Emaraviruses is becoming more complex: seven segments identified in the causal agent of Rose rosette disease
    Virus research, 2015
    Co-Authors: Patrick L. Di Bello, Ioannis E. Tzanetakis
    Abstract:

    There are few examples of a plant disease as devastating as rose rosette, a disorder that could lead to total loss for the nursery industry and rosarians alike. Although described over 75 years ago, the causal agent of rose rosette remains elusive. Utilizing the bottleneck created during vector transmission and large scale sequencing it was determined that the causal agent of the disease is rose rosette virus (RRV), a member of the genus Emaravirus. The genome structure of Emaraviruses displays significant fluidity and for this reason the genome composition of RRV was revisited, leading to the discovery of three additional segments, one of which is predicted to be bicistronic.

  • a discovery 70 years in the making characterization of the rose rosette virus
    Journal of General Virology, 2011
    Co-Authors: Alma G. Laney, Karen E. Keller, Robert R Martin, Ioannis E. Tzanetakis
    Abstract:

    Rose rosette was first described in the early 1940s and it has emerged as one of the most devastating diseases of roses. Although it has been 70 years since the disease description, the rosette agent is yet to be characterized. In this communication, we identify and characterize the putative causal agent of the disease, a negative-sense RNA virus and new member of the genus Emaravirus. The virus was detected in 84/84 rose rosette-affected plants collected from the eastern half of the USA, but not in any of 30 symptomless plants tested. The strong correlation between virus and disease is a good indication that the virus, provisionally named Rose rosette virus, is the causal agent of the disease. Diversity studies using two virus proteins, p3 and p4, demonstrated that the virus has low diversity between isolates as they share nucleotide identities ranging from 97 to 99%.

Satyanarayana Tatineni - One of the best experts on this subject based on the ideXlab platform.

  • P7 and P8 proteins of High Plains wheat mosaic virus, a negative-strand RNA virus, employ distinct mechanisms of RNA silencing suppression.
    Virology, 2019
    Co-Authors: Adarsh K. Gupta, Gary L Hein, Satyanarayana Tatineni
    Abstract:

    High Plains wheat mosaic virus (genus Emaravirus), an octapartite negative-sense RNA virus, encodes two RNA silencing suppressors, P7 and P8. In this study, we found that P7 and P8 efficiently delayed the onset of dsRNA-induced transitive pathway of RNA silencing. Electrophoretic mobility shift assays (EMSA) revealed that only P7 protected long dsRNAs from dicing in vitro and bound weakly to 21- and 24-nt PTGS-like ds-siRNAs. In contrast, P8 bound strongly and relatively weakly to 21- and 24-nt ds-siRNAs, respectively, suggesting size-specific binding. In EMSA, neither protein bound to 180-nt and 21-nt ssRNAs at detectable levels. Sequence analysis revealed that P7 contains a conserved GW motif. Mutational disruption of this motif resulted in loss of suppression of RNA silencing and pathogenicity enhancement, and failure to complement the silencing suppression-deficient wheat streak mosaic virus. Collectively, these data suggest that P7 and P8 proteins utilize distinct mechanisms to overcome host RNA silencing for successful establishment of systemic infection in planta.

  • Octapartite negative-sense RNA genome of High Plains wheat mosaic virus encodes two suppressors of RNA silencing.
    Virology, 2018
    Co-Authors: Adarsh K. Gupta, Gary L Hein, Robert A Graybosch, Satyanarayana Tatineni
    Abstract:

    Abstract High Plains wheat mosaic virus (HPWMoV, genus Emaravirus; family Fimoviridae), transmitted by the wheat curl mite (Aceria tosichella Keifer), harbors a monocistronic octapartite single-stranded negative-sense RNA genome. In this study, putative proteins encoded by HPWMoV genomic RNAs 2–8 were screened for potential RNA silencing suppression activity by using a green fluorescent protein-based reporter agroinfiltration assay. We found that proteins encoded by RNAs 7 (P7) and 8 (P8) suppressed silencing induced by single- or double-stranded RNAs and efficiently suppressed the transitive pathway of RNA silencing. Additionally, a Wheat streak mosaic virus (WSMV, genus Tritimovirus; family Potyviridae) mutant lacking the suppressor of RNA silencing (ΔP1) but having either P7 or P8 from HPWMoV restored cell-to-cell and long-distance movement in wheat, thus indicating that P7 or P8 rescued silencing suppressor-deficient WSMV. Furthermore, HPWMoV P7 and P8 substantially enhanced the pathogenicity of Potato virus X in Nicotiana benthamiana. Collectively, these data demonstrate that the octapartite genome of HPWMoV encodes two suppressors of RNA silencing.

  • New Zealand Stresses that It Is High Plains Virus Free, and the Virus Struggles with an Identity Crisis
    Journal of virology, 2015
    Co-Authors: Satyanarayana Tatineni, Anthony J Mcmechan, Everlyne N Wosula, Stephen N Wegulo, Robert A Graybosch, Roy French, Gary L Hein
    Abstract:

    High Plains virus (HPV), a tentative member of the genus Emaravirus, causes a potentially serious economic disease in cereals. Recently, in this journal, Tatineni et al. (1) mistakenly reported HPV as being present in New Zealand, citing the paper by Lebas et al. from 2005 (2). The 2005 report clearly states that New Zealand is HPV free in both the abstract and the introduction (2). To date, HPV is not known to occur in New Zealand. The Ministry for Primary Industries of New Zealand has very strict regulations in place to prevent the importation of unwanted organisms such as HPV. For example, the importation of Zea mays seeds must follow the requirements stated in Import Health Standard 155.02.05 (for seed for sowing) (3), which includes testing of HPV by enzyme-linked immunosorbent assay (ELISA) or PCR. The Tatineni et al. statement (1) will mislead regulatory officials of New Zealand’s trading partners who regularly monitor world microbe dynamics in the scientific literature. In fact, there are plant biosecurity actions in place (4) that directly affect New Zealand’s international trade when a regulated plant virus like HPV is reported as present. The situation above is aggravated by the lack of a definitive virus name yet to be ruled on by the Emaravirus Study Group, Plant Viruses Subcommittee, International Committee on Taxonomy of Viruses (ICTV). Historically, many names have been used to refer to this virus. The name Wheat spot mosaic virus (WSpM virus) was given to a virus associated with High Plains disease studied in the 1950s (5). WSpM virus-diseased samples were not preserved, and therefore it is not possible to do comparative studies (6, 7). The name High Plains virus, which causes red striping symptoms on maize, was first coined by Jensen et al. in 1996 (8). Subsequently, a virus associated with High Plains disease also eliciting red striping symptoms was partially characterized and sequenced and the name maize red stripe virus (MRStV) was introduced as a replacement for HPV (9). A note added in proof for this paper suggested the name of Wheat mosaic virus (WMoV) based on the fact that the virus is more prevalent in wheat than in maize (9). WMoV was subsequently referred to into recent publications (10, 11). All proposed names reflect diverse symptoms observed among infected wheat and sweet corn varieties and the fact that the virus is commonly detected in mixed infections. HPV is reported to coinfect with Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), Barley yellow dwarf virus PAV (BYDVPAV), and Cereal yellow dwarf virus RPV (CYDV-RPV) in the Great Plains region of the United States (10, 12). In general, all proposed names do not conflict with ICTV definitions of species, construction of names, and/or rules for orthography. The fact that the HPV name does not refer to a specific host name, but to a geographical location, and its elusiveness for years may have sparked this populated name list. However, other plant viruses have been named based only on geographical origin; examples are the tombusviruses Havel River virus, Lato River virus, and Neckar River virus, which are all ICTV-approved names (13). MacDiarmid et al. in 2013 (4) had proposed and justified new recommendations for plant virus characterization and classification in the context of new virus discovery. Both the ICTV and MacDiarmid et al. (4) are seeking (i) fluent communication among scientists, (ii) stability, (iii) to not use names that might cause error or confusion, and (iv) to avoid the unnecessary creation of names as stated by the ICTV principles of nomenclature. Certainly, HPV is not known to be present in New Zealand, and acknowledgment of the HPV-free status of New Zealand is urgently required. This also implies the requirement of a more meticulous review of manuscripts by referees and editors of the journal. Regarding HPV naming, less confusion in the long term will be expected if HPV is kept as a name, which is justified by the existence of precedent plant virus naming using geographical location markers and HPV’s broader usage in literature and sequence repositories.

  • an eriophyid mite transmitted plant virus contains eight genomic rna segments with unusual heterogeneity in the nucleocapsid protein
    Journal of Virology, 2014
    Co-Authors: Satyanarayana Tatineni, Anthony J Mcmechan, Everlyne N Wosula, Stephen N Wegulo, Robert A Graybosch, Roy French, Gary L Hein
    Abstract:

    Eriophyid mite-transmitted, multipartite, negative-sense RNA plant viruses with membrane-bound spherical virions are classified in the genus Emaravirus. We report here that the eriophyid mite-transmitted Wheat mosaic virus (WMoV), an Emaravirus, contains eight genomic RNA segments, the most in a known negative-sense RNA plant virus. Remarkably, two RNA 3 consensus sequences, encoding the nucleocapsid protein, were found with 12.5% sequence divergence, while no heterogeneity was observed in the consensus sequences of additional genomic RNA segments. The RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid, and P4 proteins of WMoV exhibited limited sequence homology with the orthologous proteins of other Emaraviruses, while proteins encoded by additional genomic RNA segments displayed no significant homology with proteins reported in GenBank, suggesting that the genus Emaravirus evolved further with a divergent octapartite genome. Phylogenetic analyses revealed that WMoV formed an evolutionary link between members of the Emaravirus genus and the family Bunyaviridae. Furthermore, genomic-length virus- and virus-complementary (vc)-sense strands of all WMoV genomic RNAs accumulated asymmetrically in infected wheat, with 10- to 20-fold more virus-sense genomic RNAs than vc-sense RNAs. These data further confirm the octapartite negative-sense polarity of the WMoV genome. In WMoV-infected wheat, subgenomic-length mRNAs of vc sense were detected for genomic RNAs 3, 4, 7, and 8 but not for other RNA species, suggesting that the open reading frames present in the complementary sense of genomic RNAs are expressed through subgenomic- or near-genomic-length vc-sense mRNAs. IMPORTANCE Wheat mosaic virus (WMoV), an Emaravirus, is the causal agent of High Plains disease of wheat and maize. In this study, we demonstrated that the genome of WMoV comprises eight negative-sense RNA segments with an unusual sequence polymorphism in an RNA encoding the nucleocapsid protein but not in the additional genomic RNA segments. WMoV proteins displayed weak or no homology with reported Emaraviruses, suggesting that the genus Emaravirus further evolved with a divergent octapartite genome. The current study also examined the profile of WMoV RNA accumulation in wheat and provided evidence for the synthesis of subgenomic-length mRNAs of virus complementary sense. This is the first report to demonstrate that Emaraviruses produce subgenomic-length mRNAs that are most likely utilized for genome expression. Importantly, this study facilitates the examination of gene functions and virus diversity and the development of effective diagnostic methods and management strategies for an economically important but poorly understood virus.

Ni Hong - One of the best experts on this subject based on the ideXlab platform.

  • Molecular Characteristics of Jujube Yellow Mottle-Associated Virus Infecting Jujube (Ziziphus jujuba Mill.) Grown at Aksu in Xinjiang of China.
    Viruses, 2020
    Co-Authors: Jiashu Guo, Yanxiang Wang, Zuokun Yang, Guoping Wang, Jian Hong, Jianyu Bai, Ni Hong
    Abstract:

    Chinese jujube (Ziziphus jujuba Mill.) is a native fruit crop in China. Leaf mottle and dapple fruit disease is prevalent in cultivated jujube plants grown at Aksu in Xinjiang Uygur Autonomous Region of China. Jujube yellow mottle-associated virus (JYMaV), a tentative member in the genus Emaravirus, was recently identified from mottle-diseased jujube plants grown in Liaoning Province in China, but its incidence and genetic diversity in China is unknown. In this study, the genome sequences of three JYMaV isolates from two jujube cultivars and one jujube variant were determined by high-throughput sequencing (HTS) for small RNA and rRNA-depleted RNA coupled with RT-PCR assays. Comparison of these sequences together with sequences of the viral RNA segments derived by primer set 3C/5H-based RT-PCR revealed that genetic diversity was present in the virus populations and high sequence variation occurred at the non-translational regions of each of the viral genomic segments. Field investigation confirmed the close association of the virus with leaf mottle symptoms of jujube plants. Furthermore, this study revealed that P5 encoded in the viral RNA5 displayed a nuclear localization feature differing from the plasmodesma (PD) subcellular localization of the virus movement protein (P4), and the two proteins could interact with each other in the BiFC assays. Our study provides a snapshot of JYMaV genetic diversity in its natural hosts.

  • Identification and Characterization of a Pear Chlorotic Leaf Spot-Associated Virus, a Novel Emaravirus Associated with a Severe Disease of Pear Trees in China.
    Plant disease, 2020
    Co-Authors: Huazhen Liu, Yanxiang Wang, Zuokun Yang, Guoping Wang, Ni Hong, Zhe Zhang, Muhammad Waqas, Jian Hong, Jinguo Zhang
    Abstract:

    Pear chlorotic leaf spot (PCLS) is a recently emerged disease of commercially cultivated sandy pear (Pyrus pyrifolia) trees in central and southern China. By integrating high-throughput sequencing and conventional Sanger sequencing of reverse-transcription (RT)-PCR products, a novel Emaravirus infecting pear trees was identified and molecularly characterized. The virus was provisionally named pear chlorotic leaf spot-associated virus (PCLSaV). PCLSaV shows the typical molecular features of members of the genus Emaravirus in the family Fimoviridae. It has a genome composed of at least five negative-sense RNA segments, with each containing a single open reading frame and two complementary 13-nucleotide stretches at the 5' and 3' termini. PCLSaV shows a close phylogenetic relationship with recognized Emaraviruses but forms a separate clade. Moreover, double-membrane-bound bodies were observed in PCLSaV-infected tissues and in extracts of PCLSaV-infected leaves. For the first time, our study revealed the profile distribution of viral RNA reads from the RNA-seq libraries of three samples along the RNA1 to RNA5 of an Emaravirus. Field surveys combined with specific RT-PCR assays revealed the presence of PCLSaV in almost all PCLS-diseased pear samples, strongly supporting the association of the virus with the PCLS disease. This study revealed the first Emaravirus infecting pear trees and its association with a severe pear chlorotic leaf disease.

  • Molecular characterization of a novel emaravrius infecting Actinidia spp. in China.
    Virus research, 2019
    Co-Authors: Yanxiang Wang, Lifeng Zhai, Shaohua Wen, Zuokun Yang, Guoping Wang, Ni Hong
    Abstract:

    Abstract Viruses in the genus Emaravirus contain 5–8 negative genomic RNAs and cause severe diseases of plants. In this study, a novel Emaravirus, provisionally named Actinidia Emaravirus 2 (AcEV-2), was identified from a kiwifruit tree showing leaf mottle and chlorosis symptoms. The genome of AcEV-2 consisted of at least six RNAs (RNAs 1–6) with sizes of 7079, 2252, 1387, 1514, 1744 and 1233 nucleotides (nts), respectively. Proteins encoded by RNAs1–4 of AcEV-2 shared the highest amino acid (aa) sequence identities of 62.2%–77.3% with the corresponding proteins of fig mosaic emaravirues (FMV) and pigeonpea sterility mosaic Emaravirus 2 (PPSMV-2). Whilst, the P5 and P6 encoded by AcEV-2 exhibited the highest identities of 44.2% and 39.2% with the corresponding proteins of PPSMV-2. It was the second Emaravirus infecting Actinidia trees in China. Preliminary virus detection disclosed the presence of AcEV-2 in three Actinidia species grown in three provinces in the central and southern China.

  • actinidia chlorotic ringspot associated virus a novel Emaravirus infecting kiwifruit plants
    Molecular Plant Pathology, 2017
    Co-Authors: Yazhou Zheng, Yanxiang Wang, Zuokun Yang, Guoping Wang, Beatriz Navarro, Chenxi Zhu, Liping Wang, Francesco Di Serio, Ni Hong
    Abstract:

    By integrating next-generation sequencing (NGS), bioinformatics, electron microscopy and conventional molecular biology tools, a new virus infecting kiwifruit vines has been identified and characterized. Being associated with double-membrane-bound bodies in infected tissues and having a genome composed of RNA segments, each one containing a single open reading frame in negative polarity, this virus shows the typical features of members of the genus Emaravirus. Five genomic RNA segments were identified. Additional molecular signatures in the viral RNAs and in the proteins they encode, together with data from phylogenetic analyses, support the proposal of creating a new species in the genus Emaravirus to classify the novel virus, which is tentatively named Actinidia chlorotic ringspot-associated virus (AcCRaV). Bioassays showed that AcCRaV is mechanically transmissible to Nicotiana benthamiana plants which, in turn, may develop chlorotic spots and ringspots. Field surveys disclosed the presence of AcCRaV in four different species of kiwifruit vines in five different provinces of central and western China, and support the association of the novel virus with symptoms of leaf chlorotic ringspots in Actinidia. Data on the molecular features of small RNAs of 21-24 nucleotides, derived from AcCRaV RNAs targeted by host RNA silencing mechanisms, are also reported, and possible molecular pathways involved in their biogenesis are discussed.

  • Actinidia chlorotic ringspot‐associated virus: a novel Emaravirus infecting kiwifruit plants
    Molecular plant pathology, 2016
    Co-Authors: Yazhou Zheng, Yanxiang Wang, Zuokun Yang, Guoping Wang, Beatriz Navarro, Chenxi Zhu, Liping Wang, Francesco Di Serio, Ni Hong
    Abstract:

    By integrating next-generation sequencing (NGS), bioinformatics, electron microscopy and conventional molecular biology tools, a new virus infecting kiwifruit vines has been identified and characterized. Being associated with double-membrane-bound bodies in infected tissues and having a genome composed of RNA segments, each one containing a single open reading frame in negative polarity, this virus shows the typical features of members of the genus Emaravirus. Five genomic RNA segments were identified. Additional molecular signatures in the viral RNAs and in the proteins they encode, together with data from phylogenetic analyses, support the proposal of creating a new species in the genus Emaravirus to classify the novel virus, which is tentatively named Actinidia chlorotic ringspot-associated virus (AcCRaV). Bioassays showed that AcCRaV is mechanically transmissible to Nicotiana benthamiana plants which, in turn, may develop chlorotic spots and ringspots. Field surveys disclosed the presence of AcCRaV in four different species of kiwifruit vines in five different provinces of central and western China, and support the association of the novel virus with symptoms of leaf chlorotic ringspots in Actinidia. Data on the molecular features of small RNAs of 21-24 nucleotides, derived from AcCRaV RNAs targeted by host RNA silencing mechanisms, are also reported, and possible molecular pathways involved in their biogenesis are discussed.

Jari P. T. Valkonen - One of the best experts on this subject based on the ideXlab platform.

  • Occurrence and genetic diversity of Raspberry leaf blotch virus (RLBV) infecting cultivated and wild Rubus species in Finland
    Annals of Applied Biology, 2015
    Co-Authors: L. Dong, Anne Lemmetty, Satu Latvala, Olga Samuilova, Jari P. T. Valkonen
    Abstract:

    Raspberry leaf blotch virus (RLBV) is a recently described (−)ssRNA virus (genus Emaravirus) associated with the long-known, severe raspberry leaf blotch disorder (RLBD). The virus is presumably transmitted by the raspberry leaf and bud mite (Phyllocoptes gracilis; Eriophyidae). Cultivated and wild raspberries (Rubus idaeus) displaying RLBD or yellowing symptoms were sampled in 14 districts in Finland and tested for RNA3 and RNA5 of RLBV by reverse transcription PCR (RT-PCR) and dot blot hybridization. A total of 59 samples were tested for RLBV, including 36 plants of cultivated raspberry, 20 wild raspberry plants, one ornamental purple flowering raspberry plant (Rubus odoratus), and two samples of P. gracilis (20 mites pooled per sample) collected from RLBD-affected Glen Ample. Fifty-three (93%) of the 57 plants tested were RLBV-positive, including seven raspberry cultivars (Balder, Glen Ample, Jenkka, Malling Minerva, Maurin Makea, Muskoka, Ottawa) and purple flowering raspberry, which is a new host for RLBV. RLBV was also detected by RT-PCR in mites (P. gracilis) collected from buds of RLBV-positive raspberry plants. The partial nucleotide (nt) sequence of the RLBV NP gene (nt 835–1284 of RNA3) was determined for 21 isolates obtained from 10 districts in Finland. Identical isolates were detected in distant districts, and distinctly different isolates were found in the same raspberry cultivation. Furthermore, eight different NP sequence variants were detected in the nine plants of a single raspberry cultivar (Glen Ample) tested from two districts. The nt and deduced amino acid sequences of the 21 isolates were 92.0–100% and 89.3–100% identical, respectively. Phylogenetic analysis revealed two main clusters. One cluster included three isolates, of which two isolates were from one farm in Finland and one isolate was previously characterised in Scotland. The other cluster contained the remaining 19 isolates characterised in this study. The results indicate that RLBV is widely distributed in cultivated and wild raspberries in Finland and shows considerable genetic variability.

  • Small-RNA Deep Sequencing Reveals Arctium tomentosum as a Natural Host of Alstroemeria virus X and a New Putative Emaravirus
    PloS one, 2012
    Co-Authors: Arthur K. Tugume, Jari P. T. Valkonen
    Abstract:

    Background Arctium species (Asteraceae) are distributed worldwide and are used as food and rich sources of secondary metabolites for the pharmaceutical industry, e.g., against avian influenza virus. RNA silencing is an antiviral defense mechanism that detects and destroys virus-derived double-stranded RNA, resulting in accumulation of virus-derived small RNAs (21–24 nucleotides) that can be used for generic detection of viruses by small-RNA deep sequencing (SRDS). Methodology/Principal Findings SRDS was used to detect viruses in the biennial wild plant species Arctium tomentosum (woolly burdock; family Asteraceae) displaying virus-like symptoms of vein yellowing and leaf mosaic in southern Finland. Assembly of the small-RNA reads resulted in contigs homologous to Alstroemeria virus X (AlsVX), a positive/single-stranded RNA virus of genus Potexvirus (family Alphaflexiviridae), or related to negative/single-stranded RNA viruses of the genus Emaravirus. The coat protein gene of AlsVX was 81% and 89% identical to the two AlsVX isolates from Japan and Norway, respectively. The deduced, partial nucleocapsid protein amino acid sequence of the emara-like virus was only 78% or less identical to reported Emaraviruses and showed no variability among the virus isolates characterized. This virus—tentatively named as Woolly burdock yellow vein virus—was exclusively associated with yellow vein and leaf mosaic symptoms in woolly burdock, whereas AlsVX was detected in only one of the 52 plants tested. Conclusions/Significance These results provide novel information about natural virus infections in Acrtium species and reveal woolly burdock as the first natural host of AlsVX besides Alstroemeria (family Alstroemeriaceae). Results also revealed a new virus related to the recently emerged Emaravirus genus and demonstrated applicability of SRDS to detect negative-strand RNA viruses. SRDS potentiates virus surveys of wild plants, a research area underrepresented in plant virology, and helps reveal natural reservoirs of viruses that cause yield losses in cultivated plants.

  • First Report of Raspberry leaf blotch virus in Raspberries in Finland
    Plant Disease, 2012
    Co-Authors: Y. Bi, K. Artola, Takeshi Kurokura, Timo Hytönen, Jari P. T. Valkonen
    Abstract:

    Raspberry (Rubus idaeus L.) is a valuable and widely grown softfruit that is a host for 40 viruses and virus-like agents, of which many are not characterized at the molecular level. Recently, Raspberry leaf blotch virus (RLBV, putative Emaravirus species) was described from raspberries (cv. Glen Ample) in the United Kingdom and Serbia. Plants displayed conspicuous yellow blotches on leaves and abnormal development of leaf hairs in the corresponding areas of the abaxial side (3). Similar symptoms were observed in ‘Glen Ample’ grown in protective plastic tunnels and open fields in the main berry growing area in eastern Finland in June 2011. In three farms, leaves were sampled from symptomatic and symptomless plants of ‘Glen Ample’ and also cv. Polka displaying no symptoms. Total RNA was extracted using CTAB reagent. Equal amounts of RNA were pooled from 13 samples and subjected to small-RNA (sRNA) deep sequencing (Fasteris SA, Plan-les-Ouates, Switzerland) to detect viruses without advance information (2). ...

  • First Report of Raspberry leaf blotch virus in Raspberries in Finland.
    Plant disease, 2012
    Co-Authors: K. Artola, Takeshi Kurokura, Timo Hytönen, Jari P. T. Valkonen
    Abstract:

    Raspberry (Rubus idaeus L.) is a valuable and widely grown softfruit that is a host for 40 viruses and virus-like agents, of which many are not characterized at the molecular level. Recently, Raspberry leaf blotch virus (RLBV, putative Emaravirus species) was described from raspberries (cv. Glen Ample) in the United Kingdom and Serbia. Plants displayed conspicuous yellow blotches on leaves and abnormal development of leaf hairs in the corresponding areas of the abaxial side (3). Similar symptoms were observed in 'Glen Ample' grown in protective plastic tunnels and open fields in the main berry growing area in eastern Finland in June 2011. In three farms, leaves were sampled from symptomatic and symptomless plants of 'Glen Ample' and also cv. Polka displaying no symptoms. Total RNA was extracted using CTAB reagent. Equal amounts of RNA were pooled from 13 samples and subjected to small-RNA (sRNA) deep sequencing (Fasteris SA, Plan-les-Ouates, Switzerland) to detect viruses without advance information (2). Contigs were built on 21- to 24-nt sRNA reads using Velvet. Contigs larger than 50 nt were used to search homologous sequences in GenBank by BLAST and significant similarity (up to 99%) was observed with RLBV RNA3 and RNA4. Mapping sRNA reads to the genome of RLBV (1) by MAQ resulted in significant coverage of RNA1 (16%), RNA2 (37%), RNA3 (46%), RNA4 (65%), and RNA5 (27%). cDNA was synthesized on RNA of one symptom-expressing plant using random hexamer primers and the cDNA tested by PCR with a forward primer (RLBV-F 5'-TCAAATCCACTTGCATAGAACC-3', nt 723 to 744) and reverse primer (RLBV-R1 5'-CCTCAAACCTTGCAAACACA-3', nt 1,318 to 1,337) designed according to the nucleocapsid (NP) gene of the Scottish RLBV isolate (3). The sequence of the amplified partial NP gene (576 nt; GenBank Accession No. JQ684678) was 92.8% and 94.8% identical to the Scottish isolate at nt and amino acid levels, respectively. The forward primer RLBV-F and a new reverse primer (RLBV-R2 5'-GCCGAAAGTCAAACCTGGTG-3', nt 943 to 962) were used to test additional plants for RBLV and to make a probe (198 nt) to detect RLBV using digoxigen-labeled sense and antisense RNA probes, as described for European mountain ash ringspot associated virus (1). RLBV was detected in all tested plants of 'Glen Ample' with yellow leaf blotch symptoms in the three farms, but not in any symptomless plants of 'Glen Ample' and 'Polka.' The sense probes gave strong signals, in contrast to the antisense probes, which gave only weak or no detectable signals in the virus-positive plants, consistent with the negative RNA strand of RLBV being encapsidated in virus particles. The results show RLBV is associated with severe, distinct, and characteristic symptoms in raspberries of cv. Glen Ample grown in plastic tunnels and open fields in Finland and has an apparent negative impact on plant growth and yield. Our observations in 2011 also suggest that the incidence of diseased plants is much higher in plastic tunnels than in open fields, perhaps because the conditions for the vector of RLBV (raspberry leaf and bud mite, Phyllocoptes gracilis Nalepa) (1) are more favorable in plastic tunnels. These results clarify the etiology of raspberry leaf blotch disease in Finland and emphasize the need to inspect raspberry planting materials for RLBV for better control of the disease. References: (1) A. K. Kallinen et al. Phytopathology 99:344, 2009. (2) J. F. Kreuze et al. Virology 388:1, 2009. (3) W. J. McGavin et al. J. Gen. Virol. 93:430, 2012.

  • first report of european mountain ash ringspot associated virus in sorbus aucuparia from eastern karelia russia
    Plant Disease, 2010
    Co-Authors: Jari P. T. Valkonen, M Rannali
    Abstract:

    Mountain ash (Sorbus aucuparia L.) is a tree that is native to northern Europe. It was recently found to be infected with European mountain ash ringspot-associated virus (EMARaV) in Germany and Finland (2,3). EMARaV is not transmitted mechanically and no vector is known, but it is related to negative-sense RNA viruses transmitted by eriophyid mites (3) and represents a new viral species of the genus Emaravirus, which is not assigned to any family. In Finland, EMARaV is common, widely distributed, and detected in all tested ringspot disease-affected and symptomless mountain ash trees (2). Ringspot symptoms occur in mountain ash also in Sweden (west from Finland). In this study, ringspot-affected mountain ash trees were found in Ustreka, which marks the eastern edge of the geologically defined Baltic Shield and the eastern geobotanical borderline of Fennoscandia in eastern Karelia, Russia (1). This border zone can be recognized by changes in vegetation, including occurrence of Siberian larch (Larix sibirica...