Induction of Necrosis Via Mitochondrial Targeting of Melon Necrotic Spot Virus Replication Protein P29 by Its Second Transmembrane Domain
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Vector Capability of Xiphinema Americanum Sensu Lato in California 1
Journal of Nematology 21(4):517-523. 1989. © The Society of Nematologists 1989. Vector Capability of Xiphinema americanum sensu lato in California 1 JOHN A. GRIESBACH 2 AND ARMAND R. MAGGENTI s Abstract: Seven field populations of Xiphineraa americanum sensu lato from California's major agronomic areas were tested for their ability to transmit two nepoviruses, including the prune brownline, peach yellow bud, and grapevine yellow vein strains of" tomato ringspot virus and the bud blight strain of tobacco ringspot virus. Two field populations transmitted all isolates, one population transmitted all tomato ringspot virus isolates but failed to transmit bud blight strain of tobacco ringspot virus, and the remaining four populations failed to transmit any virus. Only one population, which transmitted all isolates, bad been associated with field spread of a nepovirus. As two California populations of Xiphinema americanum sensu lato were shown to have the ability to vector two different nepoviruses, a nematode taxonomy based on a parsimony of virus-vector re- lationship is not practical for these populations. Because two California populations ofX. americanum were able to vector tobacco ringspot virus, commonly vectored by X. americanum in the eastern United States, these western populations cannot be differentiated from eastern populations by vector capability tests using tobacco ringspot virus. Key words: dagger nematode, tobacco ringspot virus, tomato ringspot virus, nepovirus, Xiphinema americanum, Xiphinema californicum. Populations of Xiphinema americanum brownline (PBL), prunus stem pitting (PSP) Cobb, 1913 shown through rigorous test- and cherry leaf mottle (CLM) (8). Both PBL ing (23) to be nepovirus vectors include X. and PSP were transmitted with a high de- americanum sensu lato (s.1.) for tobacco gree of efficiency, whereas CLM was trans- ringspot virus (TobRSV) (5), tomato ring- mitted rarely. -
2014.008Ap Officers) Short Title: One New Sequence-Only Species, Trailing Lespedeza Virus 1, in the Family Tombusviridae (E.G
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2014.008aP officers) Short title: One new sequence-only species, Trailing lespedeza virus 1, in the family Tombusviridae (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Kay Scheets ([email protected]) and Ulrich Melcher ([email protected]) List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . If in doubt, contact the appropriate subcommittee Tombusviridae and Umbravirus Study Group chair (fungal, invertebrate, plant, prokaryote or vertebrate viruses) ICTV-EC or Study Group comments and response of the proposer: SG comment: The decision to accept this proposal was unanimous. EC comment: This proposal, which is related to the proposal suggesting the creation of the genus Pelarspovirus, was coded “Ud” because of concerns associated with the creation of the genus (see comments on the related proposal). However, the proposal for creation of the species could be approved this year if the proposal was modified to propose that the species remains unassigned in the family Tombusviridae or possibly be assigned to the current genus Carmovirus. -
Journal of Virological Methods 153 (2008) 16–21
Journal of Virological Methods 153 (2008) 16–21 Contents lists available at ScienceDirect Journal of Virological Methods journal homepage: www.elsevier.com/locate/jviromet Use of primers with 5 non-complementary sequences in RT-PCR for the detection of nepovirus subgroups A and B Ting Wei, Gerard Clover ∗ Plant Health and Environment Laboratory, Investigation and Diagnostic Centre, MAF Biosecurity New Zealand, P.O. Box 2095, Auckland 1140, New Zealand abstract Article history: Two generic PCR protocols were developed to detect nepoviruses in subgroups A and B using degenerate Received 21 April 2008 primers designed to amplify part of the RNA-dependent RNA polymerase (RdRp) gene. It was observed that Received in revised form 17 June 2008 detection sensitivity and specificity could be improved by adding a 12-bp non-complementary sequence Accepted 19 June 2008 to the 5 termini of the forward, but not the reverse, primers. The optimized PCR protocols amplified a specific product (∼340 bp and ∼250 bp with subgroups A and B, respectively) from all 17 isolates of the 5 Keywords: virus species in subgroup A and 3 species in subgroup B tested. The primers detect conserved protein motifs Nepoviruses in the RdRp gene and it is anticipated that they have the potential to detect unreported or uncharacterised Primer flap Universal primers nepoviruses in subgroups A and B. RT-PCR © 2008 Elsevier B.V. All rights reserved. 1. Introduction together with nematode transmission make these viruses partic- ularly hard to eradicate or control (Harrison and Murant, 1977; The genus Nepovirus is classified in the family Comoviridae, Fauquet et al., 2005). -
Nucleotide Sequence of Hungarian Grapevine Chrome Mosaic Nepovirus RNA1 Olivier Le Gall, Thierry Candresse, Veronique Brault, Jean Dunez
Nucleotide sequence of Hungarian Grapevine Chrome Mosaic Nepovirus RNA1 Olivier Le Gall, Thierry Candresse, Veronique Brault, Jean Dunez To cite this version: Olivier Le Gall, Thierry Candresse, Veronique Brault, Jean Dunez. Nucleotide sequence of Hungarian Grapevine Chrome Mosaic Nepovirus RNA1. Nucleic Acids Research, Oxford University Press, 1989, 17 (19), pp.7795-7807. hal-02726835 HAL Id: hal-02726835 https://hal.inrae.fr/hal-02726835 Submitted on 2 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Nucleic Research Volume 17 Number 19 1989 Nucleic Acids Research Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1 O.Le Gall, T.Candresse, V.Brault and J.Dunez Station de Pathologie Vegetale, INRA, BP 131, 33140 Pont de la Maye, France Received May 24, 1989; Revised and Accepted August 25, 1989 EMBL accesssion no. X15346 ABSTRACT The nucleotide sequence of the RNAl of hungarian grapevine chrome mosaic virus, a nepovirus very closely related to tomato black ring virus, has been determined from cDNA clones. It is 7212 nucleotides in length excluding the 3' terminal poly(A) tail and contains a large open reading frame extending from nucleotides 216 to 6971. -
Icosahedral Viruses Defined by Their Positively Charged Domains: a Signature for Viral Identity and Capsid Assembly Strategy
Support Information for: Icosahedral viruses defined by their positively charged domains: a signature for viral identity and capsid assembly strategy Rodrigo D. Requião1, Rodolfo L. Carneiro 1, Mariana Hoyer Moreira1, Marcelo Ribeiro- Alves2, Silvana Rossetto3, Fernando L. Palhano*1 and Tatiana Domitrovic*4 1 Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil. 2 Laboratório de Pesquisa Clínica em DST/Aids, Instituto Nacional de Infectologia Evandro Chagas, FIOCRUZ, Rio de Janeiro, RJ, 21040-900, Brazil 3 Programa de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil. 4 Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil. *Corresponding author: [email protected] or [email protected] MATERIALS AND METHODS Software and Source Identifier Algorithms Calculation of net charge (1) Calculation of R/K ratio This paper https://github.com/mhoyerm/Total_ratio Identify proteins of This paper https://github.com/mhoyerm/Modulate_RK determined net charge and R/K ratio Identify proteins of This paper https://github.com/mhoyerm/Modulate_KR determined net charge and K/R ratio Data sources For all viral proteins, we used UniRef with the advanced search options (uniprot:(proteome:(taxonomy:"Viruses [10239]") reviewed:yes) AND identity:1.0). For viral capsid proteins, we used the advanced search options (proteome:(taxonomy:"Viruses [10239]") goa:("viral capsid [19028]") AND reviewed:yes) followed by a manual selection of major capsid proteins. Advanced search options for H. -
(Zanthoxylum Armatum) by Virome Analysis
viruses Article Discovery of Four Novel Viruses Associated with Flower Yellowing Disease of Green Sichuan Pepper (Zanthoxylum armatum) by Virome Analysis 1,2, , 1,2, 1,2 1,2 3 3 Mengji Cao * y , Song Zhang y, Min Li , Yingjie Liu , Peng Dong , Shanrong Li , Mi Kuang 3, Ruhui Li 4 and Yan Zhou 1,2,* 1 National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China 2 Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China 3 Chongqing Agricultural Technology Extension Station, Chongqing 401121, China 4 USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD 20705, USA * Correspondences: [email protected] (M.C.); [email protected] (Y.Z.) These authors contributed equally to this work. y Received: 17 June 2019; Accepted: 28 July 2019; Published: 31 July 2019 Abstract: An emerging virus-like flower yellowing disease (FYD) of green Sichuan pepper (Zanthoxylum armatum v. novemfolius) has been recently reported. Four new RNA viruses were discovered in the FYD-affected plant by the virome analysis using high-throughput sequencing of transcriptome and small RNAs. The complete genomes were determined, and based on the sequence and phylogenetic analysis, they are considered to be new members of the genera Nepovirus (Secoviridae), Idaeovirus (unassigned), Enamovirus (Luteoviridae), and Nucleorhabdovirus (Rhabdoviridae), respectively. Therefore, the tentative names corresponding to these viruses are green Sichuan pepper-nepovirus (GSPNeV), -idaeovirus (GSPIV), -enamovirus (GSPEV), and -nucleorhabdovirus (GSPNuV). The viral population analysis showed that GSPNeV and GSPIV were dominant in the virome. The small RNA profiles of these viruses are in accordance with the typical virus-plant interaction model for Arabidopsis thaliana. -
Virus Diseases of Trees and Shrubs
VirusDiseases of Treesand Shrubs Instituteof TerrestrialEcology NaturalEnvironment Research Council á Natural Environment Research Council Institute of Terrestrial Ecology Virus Diseases of Trees and Shrubs J.1. Cooper Institute of Terrestrial Ecology cfo Unit of Invertebrate Virology OXFORD Printed in Great Britain by Cambrian News Aberystwyth C Copyright 1979 Published in 1979 by Institute of Terrestrial Ecology 68 Hills Road Cambridge CB2 ILA ISBN 0-904282-28-7 The Institute of Terrestrial Ecology (ITE) was established in 1973, from the former Nature Conservancy's research stations and staff, joined later by the Institute of Tree Biology and the Culture Centre of Algae and Protozoa. ITE contributes to and draws upon the collective knowledge of the fourteen sister institutes \Which make up the Natural Environment Research Council, spanning all the environmental sciences. The Institute studies the factors determining the structure, composition and processes of land and freshwater systems, and of individual plant and animal species. It is developing a sounder scientific basis for predicting and modelling environmental trends arising from natural or man- made change. The results of this research are available to those responsible for the protection, management and wise use of our natural resources. Nearly half of ITE's work is research commissioned by customers, such as the Nature Con- servancy Council who require information for wildlife conservation, the Forestry Commission and the Department of the Environment. The remainder is fundamental research supported by NERC. ITE's expertise is widely used by international organisations in overseas projects and programmes of research. The photograph on the front cover is of Red Flowering Horse Chestnut (Aesculus carnea Hayne). -
Genomic Characterization of the Cacao Swollen Shoot Virus Complex and Other Theobroma Cacao-Infecting Badnaviruses
Genomic Characterization of the Cacao Swollen Shoot Virus Complex and other Theobroma Cacao-Infecting Badnaviruses Item Type text; Electronic Dissertation Authors Chingandu, Nomatter Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 29/09/2021 07:25:04 Link to Item http://hdl.handle.net/10150/621859 GENOMIC CHARACTERIZATION OF THE CACAO SWOLLEN SHOOT VIRUS COMPLEX AND OTHER THEOBROMA CACAO-INFECTING BADNAVIRUSES by Nomatter Chingandu __________________________ A Dissertation Submitted to the Faculty of the SCHOOL OF PLANT SCIENCES In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY WITH A MAJOR IN PLANT PATHOLOGY In the Graduate College THE UNIVERSITY OF ARIZONA 2016 1 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Nomatter Chingandu, entitled “Genomic characterization of the Cacao swollen shoot virus complex and other Theobroma cacao-infecting badnaviruses” and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy. _______________________________________________________ Date: 7.27.2016 Dr. Judith K. Brown _______________________________________________________ Date: 7.27.2016 Dr. Zhongguo Xiong _______________________________________________________ Date: 7.27.2016 Dr. Peter J. Cotty _______________________________________________________ Date: 7.27.2016 Dr. Barry M. Pryor _______________________________________________________ Date: 7.27.2016 Dr. Marc J. Orbach Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertation to the Graduate College. -
Peach Rosette Mosaic Nepovirus
EPPO quarantine pest Prepared by CABI and EPPO for the EU under Contract 90/399003 Data Sheets on Quarantine Pests Peach rosette mosaic nepovirus IDENTITY Name: Peach rosette mosaic nepovirus Taxonomic position: Viruses: Comoviridae: Nepovirus Common names: PRMV (acronym) Notes on taxonomy and nomenclature: Apart from that caused by PRMV, there are a number of diseases of peach that include the name "peach rosette". In Europe, the disease "peach rosette" is caused by strawberry latent ringspot nepovirus; in Australia, "peach rosette and decline" is due to a combined infection with prune dwarf and prunus necrotic ringspot ilarviruses; in parts of the USA, peach rosette phytoplasma causes the "peach rosette" symptom. EPPO computer code: PCRMXX EPPO A1 list: No. 219 EU Annex designation: IA/1 HOSTS The principal host is the American grape species Vitis labrusca. Some cultivars of V. vinifera, and French-American Vitis spp. hybrids are also susceptible. Peach rosette mosaic nepovirus (PRMV) is also an important pathogen of peaches (Prunus persica) and has experimentally caused disease in Vaccinium corymbosum. In addition, several weed species have been shown to be hosts for the virus: Rumex crispus, Solanum carolinense and Taraxacum officinale. The experimental herbaceous host range is rather narrow. Some species of Chenopodiaceae, Cucurbitaceae, Fabaceae and Solanaceae are infected by mechanical inoculation with sap from infected grapes or peaches. GEOGRAPHICAL DISTRIBUTION PRMV is one of the North American nepoviruses of fruit trees, and has not extended its range to any other continent. No basis has been found for the possible presence of the virus in India or Italy, as mentioned by Németh (1986). -
Virological Sampling of Inaccessible Wildlife with Drones
viruses Communication Virological Sampling of Inaccessible Wildlife with Drones Jemma L. Geoghegan 1,*,† ID , Vanessa Pirotta 1,† ID , Erin Harvey 2,†, Alastair Smith 3, Jan P. Buchmann 2, Martin Ostrowski 4, John-Sebastian Eden 2,5 ID , Robert Harcourt 1 and Edward C. Holmes 2 ID 1 Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; [email protected] (V.P.); [email protected] (R.H.) 2 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] (E.H.); [email protected] (J.P.B.); [email protected] (J.-S.E.); [email protected] (E.C.H.) 3 Heliguy Scientific Pty Ltd., Sydney, NSW 2204, Australia; [email protected] 4 Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; [email protected] 5 Westmead Institute for Medical Research, Centre for Virus Research, Westmead, NSW 2145, Australia * Correspondence: [email protected]; Tel.: +61-2-9850-8204 † The authors contributed equally to this paper. Received: 12 May 2018; Accepted: 31 May 2018; Published: 2 June 2018 Abstract: There is growing interest in characterizing the viromes of diverse mammalian species, particularly in the context of disease emergence. However, little is known about virome diversity in aquatic mammals, in part due to difficulties in sampling. We characterized the virome of the exhaled breath (or blow) of the Eastern Australian humpback whale (Megaptera novaeangliae). -
Duck Gut Viral Metagenome Analysis Captures Snapshot of Viral Diversity Mohammed Fawaz1†, Periyasamy Vijayakumar1†, Anamika Mishra1†, Pradeep N
Fawaz et al. Gut Pathog (2016) 8:30 DOI 10.1186/s13099-016-0113-5 Gut Pathogens RESEARCH Open Access Duck gut viral metagenome analysis captures snapshot of viral diversity Mohammed Fawaz1†, Periyasamy Vijayakumar1†, Anamika Mishra1†, Pradeep N. Gandhale1, Rupam Dutta1, Nitin M. Kamble1, Shashi B. Sudhakar1, Parimal Roychoudhary2, Himanshu Kumar3, Diwakar D. Kulkarni1 and Ashwin Ashok Raut1* Abstract Background: Ducks (Anas platyrhynchos) an economically important waterfowl for meat, eggs and feathers; is also a natural reservoir for influenza A viruses. The emergence of novel viruses is attributed to the status of co-existence of multiple types and subtypes of viruses in the reservoir hosts. For effective prediction of future viral epidemic or pan- demic an in-depth understanding of the virome status in the key reservoir species is highly essential. Methods: To obtain an unbiased measure of viral diversity in the enteric tract of ducks by viral metagenomic approach, we deep sequenced the viral nucleic acid extracted from cloacal swabs collected from the flock of 23 ducks which shared the water bodies with wild migratory birds. Result: In total 7,455,180 reads with average length of 146 bases were generated of which 7,354,300 reads were de novo assembled into 24,945 contigs with an average length of 220 bases and the remaining 100,880 reads were singletons. The duck virome were identified by sequence similarity comparisons of contigs and singletons (BLASTx 3 E score, <10− ) against viral reference database. Numerous duck virome sequences were homologous to the animal virus of the Papillomaviridae family; and phages of the Caudovirales, Inoviridae, Tectiviridae, Microviridae families and unclassified phages. -
Culex Virome V34
Page 1 of 31 Virome of >12 thousand Culex mosquitoes from throughout California Mohammadreza Sadeghi1,2,3; Eda Altan1,2; Xutao Deng12; Christopher M. Barker4, Ying Fang4, Lark L Coffey4; Eric Delwart1,2 1Blood Systems Research Institute, San Francisco, CA, USA. 2Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA. 3Department of Virology, University of Turku, Turku, Finland. 4Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA. §Reprints or correspondence: Eric Delwart 270 Masonic Ave. San Francisco, CA 94118 Phone: (415) 923-5763 Fax: (415) 276-2311 Email: [email protected] Page 2 of 31 Abstract Metagenomic analysis of mosquitoes allows the genetic characterization of all associated viruses, including arboviruses and insect-specific viruses, plus those in their diet or infecting their parasites. We describe here the virome in mosquitoes, primarily Culex pipiens complex, Cx. tarsalis and Cx. erythrothorax, collected in 2016 from 23 counties in California, USA. The nearly complete genomes of 54 different virus species, including 28 novel species and some from potentially novel RNA and DNA viral families and genera, were assembled and phylogenetically analyzed, significantly expanding the known Culex-associated virome. The majority of detected viral sequences originated from single-stranded RNA viral families with members known to infect insects, plants, or unknown hosts. These reference viral genomes will facilitate the identification of related viruses in other insect species and to monitor changes in the virome of Culex mosquito populations to define factors influencing their transmission and possible impact on their insect hosts. Page 3 of 31 Introduction Mosquitoes transmit numerous arboviruses, many of which result in significant morbidity and/or mortality in humans and animals (Ansari and Shope, 1994; Driggers et al., 2016; Gan and Leo, 2014; Reimann et al., 2008; Weaver and Vasilakis, 2009).