ICTV in San Francisco: a Report from the Plenary Session
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Grapevine Virus Diseases: Economic Impact and Current Advances in Viral Prospection and Management1
1/22 ISSN 0100-2945 http://dx.doi.org/10.1590/0100-29452017411 GRAPEVINE VIRUS DISEASES: ECONOMIC IMPACT AND CURRENT ADVANCES IN VIRAL PROSPECTION AND MANAGEMENT1 MARCOS FERNANDO BASSO2, THOR VINÍCIUS MArtins FAJARDO3, PASQUALE SALDARELLI4 ABSTRACT-Grapevine (Vitis spp.) is a major vegetative propagated fruit crop with high socioeconomic importance worldwide. It is susceptible to several graft-transmitted agents that cause several diseases and substantial crop losses, reducing fruit quality and plant vigor, and shorten the longevity of vines. The vegetative propagation and frequent exchanges of propagative material among countries contribute to spread these pathogens, favoring the emergence of complex diseases. Its perennial life cycle further accelerates the mixing and introduction of several viral agents into a single plant. Currently, approximately 65 viruses belonging to different families have been reported infecting grapevines, but not all cause economically relevant diseases. The grapevine leafroll, rugose wood complex, leaf degeneration and fleck diseases are the four main disorders having worldwide economic importance. In addition, new viral species and strains have been identified and associated with economically important constraints to grape production. In Brazilian vineyards, eighteen viruses, three viroids and two virus-like diseases had already their occurrence reported and were molecularly characterized. Here, we review the current knowledge of these viruses, report advances in their diagnosis and prospection of new species, and give indications about the management of the associated grapevine diseases. Index terms: Vegetative propagation, plant viruses, crop losses, berry quality, next-generation sequencing. VIROSES EM VIDEIRAS: IMPACTO ECONÔMICO E RECENTES AVANÇOS NA PROSPECÇÃO DE VÍRUS E MANEJO DAS DOENÇAS DE ORIGEM VIRAL RESUMO-A videira (Vitis spp.) é propagada vegetativamente e considerada uma das principais culturas frutíferas por sua importância socioeconômica mundial. -
MOLECULAR BIOLOGY and EPIDEMIOLOGY of GRAPEVINE LEAFROLL- ASSOCIATED VIRUSES by BHANU PRIYA DONDA a Dissertation Submitted in Pa
MOLECULAR BIOLOGY AND EPIDEMIOLOGY OF GRAPEVINE LEAFROLL- ASSOCIATED VIRUSES By BHANU PRIYA DONDA A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSPHY WASHINGTON STATE UNIVERSITY Department of Plant Pathology MAY 2016 © Copyright by BHANU PRIYA DONDA, 2016 All Rights Reserved THANKS Bioengineering MAY 2014 © Copyright by BHANU PRIYA DONDA, 2016 All Rights Reserved To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of BHANU PRIYA DONDA find it satisfactory and recommend that it be accepted. Naidu A. Rayapati, Ph.D., Chair Dennis A. Johnson, Ph.D. Duroy A. Navarre, Ph.D. George J. Vandemark, Ph.D. Siddarame Gowda, Ph.D. ii ACKNOWLEDGEMENT I would like to express my respect and deepest gratitude towards my advisor and mentor, Dr. Naidu Rayapati. I am truly appreciative of the opportunity to pursue my doctoral degree under his guidance at Washington State University (WSU), a challenging and rewarding experience that I will value the rest of my life. I am thankful to my doctoral committee members: Dr. Dennis Johnson, Dr. George Vandemark, Dr. Roy Navarre and Dr. Siddarame Gowda for helpful advice, encouragement and guidance. I would like to thank Dr. Sandya R Kesoju (USDA-IAREC, Prosser, WA) and Dr. Neil Mc Roberts (University of California, Davis) for their statistical expertise, suggestions and collaborative research on the epidemiology of grapevine leafroll disease. To Dr. Gopinath Kodetham (University of Hyderabad, Hyderabad, India), thank you for believing in me and encouraging me to go the extra mile. I thank Dr. Sridhar Jarugula (Ohio State University Agricultural Research and Development Center, Wooster, University of Ohio, Ohio, USA), Dr. -
Changes to Virus Taxonomy 2004
Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales -
Comparative Analysis, Distribution, and Characterization of Microsatellites in Orf Virus Genome
www.nature.com/scientificreports OPEN Comparative analysis, distribution, and characterization of microsatellites in Orf virus genome Basanta Pravas Sahu1, Prativa Majee 1, Ravi Raj Singh1, Anjan Sahoo2 & Debasis Nayak 1* Genome-wide in-silico identifcation of microsatellites or simple sequence repeats (SSRs) in the Orf virus (ORFV), the causative agent of contagious ecthyma has been carried out to investigate the type, distribution and its potential role in the genome evolution. We have investigated eleven ORFV strains, which resulted in the presence of 1,036–1,181 microsatellites per strain. The further screening revealed the presence of 83–107 compound SSRs (cSSRs) per genome. Our analysis indicates the dinucleotide (76.9%) repeats to be the most abundant, followed by trinucleotide (17.7%), mononucleotide (4.9%), tetranucleotide (0.4%) and hexanucleotide (0.2%) repeats. The Relative Abundance (RA) and Relative Density (RD) of these SSRs varied between 7.6–8.4 and 53.0–59.5 bp/ kb, respectively. While in the case of cSSRs, the RA and RD ranged from 0.6–0.8 and 12.1–17.0 bp/kb, respectively. Regression analysis of all parameters like the incident of SSRs, RA, and RD signifcantly correlated with the GC content. But in a case of genome size, except incident SSRs, all other parameters were non-signifcantly correlated. Nearly all cSSRs were composed of two microsatellites, which showed no biasedness to a particular motif. Motif duplication pattern, such as, (C)-x-(C), (TG)- x-(TG), (AT)-x-(AT), (TC)- x-(TC) and self-complementary motifs, such as (GC)-x-(CG), (TC)-x-(AG), (GT)-x-(CA) and (TC)-x-(AG) were observed in the cSSRs. -
Characterization and Genome Organization of New Luteoviruses and Nanoviruses Infecting Cool Season Food Legumes
Adane Abraham (Autor) Characterization and Genome Organization of New Luteoviruses and Nanoviruses Infecting Cool Season Food Legumes https://cuvillier.de/de/shop/publications/2549 Copyright: Cuvillier Verlag, Inhaberin Annette Jentzsch-Cuvillier, Nonnenstieg 8, 37075 Göttingen, Germany Telefon: +49 (0)551 54724-0, E-Mail: [email protected], Website: https://cuvillier.de CHAPTER 1 General Introduction Viruses and virus diseases of cool season food legumes Legume crops play a major role worldwide as source of human food, feed and also in crop rotation. Faba bean (Vicia faba L.), field pea (Pisum sativum L.), lentil (Lens culinaris Medik.), chickpea (Cicer arietinum L.), and grasspea (Lathyrus sativus L.), collectively re- ferred to as cool season food legumes (Summerfield et al. 1988) are of particular importance in developing countries of Asia, North and Northeast Africa where they provide a cheap source of seed protein for the predominantly poor population. Diseases including those caused by viruses are among the main constraints reducing their yield. Bos et al. (1988) listed some 44 viruses as naturally infecting faba bean, chickpea, field pea and lentil worldwide. Since then, a number of new viruses were described from these crops including Faba bean necrotic yellows virus (FBNYV) (Katul et al. 1993) and Chickpea chlorotic dwarf virus (CpCDV) (Horn et al. 1993), which are widespread and economically important. Most of the viruses of cool season food legumes are known to naturally infect more than one host within this group of crops (Bos et al. 1988, Brunt et al. 1996 and Makkouk et al. 2003a). Virus symptoms in cool season food legumes vary depending on the virus or its strain, host species or cultivar and the prevailing environmental conditions. -
Transforming Properties of Ovine Papillomaviruses E6 and E7 Oncogenes T Gessica Torea, Gian Mario Dorea, Carla Cacciottoa, Rosita Accardib, Antonio G
Veterinary Microbiology 230 (2019) 14–22 Contents lists available at ScienceDirect Veterinary Microbiology journal homepage: www.elsevier.com/locate/vetmic Transforming properties of ovine papillomaviruses E6 and E7 oncogenes T Gessica Torea, Gian Mario Dorea, Carla Cacciottoa, Rosita Accardib, Antonio G. Anfossia, Luisa Boglioloa, Marco Pittaua,c, Salvatore Pirinoa, Tiziana Cubeddua, Massimo Tommasinob, ⁎ Alberto Albertia,c, a Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Italy b Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France c Mediterranean Center for Disease Control, University of Sassari, Italy ARTICLE INFO ABSTRACT Keywords: An increasing number of studies suggest that cutaneous papillomaviruses (PVs) might be involved in skin car- Cancer cinogenesis. However, only a few animal PVs have been investigated regard to their transformation properties. Oncogenic viruses Here, we investigate and compare the oncogenic potential of 2 ovine Delta and Dyokappa PVs, isolated from Sheep ovine skin lesions, in vitro and ex vivo. We demonstrate that both OaPV4 (Delta) and OaPV3 (Dyokappa) E6 and Skin E7 immortalize primary sheep keratinocytes and efficiently deregulate pRb pathway, although they seem unable Cellular immortalisation to alter p53 activity. Moreover, OaPV3 and OaPV4-E6E7 expressing cells show different shape, doubling time, and clonogenic activities, providing evidence for a stronger transforming potential of OaPV3 respect to OaPV4. Also, similarly to high-risk mucosal and cutaneous PVs, the OaPV3-E7 protein, constantly expressed in sheep squamous cell carcinomas, binds pRb with higher affinity compared to the E7 encoded by OaPV4, avirusas- sociated to fibropapilloma. Finally, we found that OaPV3 and OaPV4-E6E7 determine upregulation ofthepro- proliferative proteins cyclin A and cdk1 in both human and ovine primary keratinocytes. -
Viral Diversity in Tree Species
Universidade de Brasília Instituto de Ciências Biológicas Departamento de Fitopatologia Programa de Pós-Graduação em Biologia Microbiana Doctoral Thesis Viral diversity in tree species FLÁVIA MILENE BARROS NERY Brasília - DF, 2020 FLÁVIA MILENE BARROS NERY Viral diversity in tree species Thesis presented to the University of Brasília as a partial requirement for obtaining the title of Doctor in Microbiology by the Post - Graduate Program in Microbiology. Advisor Dra. Rita de Cássia Pereira Carvalho Co-advisor Dr. Fernando Lucas Melo BRASÍLIA, DF - BRAZIL FICHA CATALOGRÁFICA NERY, F.M.B Viral diversity in tree species Flávia Milene Barros Nery Brasília, 2025 Pages number: 126 Doctoral Thesis - Programa de Pós-Graduação em Biologia Microbiana, Universidade de Brasília, DF. I - Virus, tree species, metagenomics, High-throughput sequencing II - Universidade de Brasília, PPBM/ IB III - Viral diversity in tree species A minha mãe Ruth Ao meu noivo Neil Dedico Agradecimentos A Deus, gratidão por tudo e por ter me dado uma família e amigos que me amam e me apoiam em todas as minhas escolhas. Minha mãe Ruth e meu noivo Neil por todo o apoio e cuidado durante os momentos mais difíceis que enfrentei durante minha jornada. Aos meus irmãos André, Diego e meu sobrinho Bruno Kawai, gratidão. Aos meus amigos de longa data Rafaelle, Evanessa, Chênia, Tati, Leo, Suzi, Camilets, Ricardito, Jorgito e Diego, saudade da nossa amizade e dos bons tempos. Amo vocês com todo o meu coração! Minha orientadora e grande amiga Profa Rita de Cássia Pereira Carvalho, a quem escolhi e fui escolhida para amar e fazer parte da família. -
Quito's Virome: Metagenomic Analysis of Viral Diversity in Urban Streams of Ecuador's Capital City
Science of the Total Environment 645 (2018) 1334–1343 Contents lists available at ScienceDirect Science of the Total Environment journal homepage: www.elsevier.com/locate/scitotenv Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city Laura Guerrero-Latorre a,⁎, Brigette Romero a, Edison Bonifaz a, Natalia Timoneda b, Marta Rusiñol b, Rosina Girones b, Blanca Rios-Touma c a Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador b Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain c Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería Ambiental, Universidad de las Américas, Quito, Ecuador HIGHLIGHTS GRAPHICAL ABSTRACT • First viral metagomic study of highly impacted surface waters in Latin America • The study describes human viral patho- gens present in urban rivers of Quito. • Several viral families detected contain- ing emergent species firstly reported in Ecuador. article info abstract Article history: In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to Received 25 May 2018 the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of Received in revised form 16 July 2018 many enteric pathogens through direct consumption, agricultural and recreational use. Among the different Accepted 16 July 2018 pathogens present in urban discharges, viruses play an important role on disease, being causes of gastroenteritis, Available online 23 July 2018 hepatitis, meningitis, respiratory infections, among others. -
Tically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 21 June 2021 doi:10.20944/preprints202106.0526.v1 Review Towards the forest virome: next-generation-sequencing dras- tically expands our understanding on virosphere in temperate forest ecosystems Artemis Rumbou 1,*, Eeva J. Vainio 2 and Carmen Büttner 1 1 Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Ber- lin, Germany; [email protected], [email protected] 2 Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland; [email protected] * Correspondence: [email protected] Abstract: Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont. Symbiotic mi- crobiota and pathogens engage in a permanent interplay, which influences the host. Thanks to the development of NGS technol- ogies, a vast amount of genetic information on the virosphere of temperate forests has been gained the last seven years. To estimate the qualitative/quantitative impact of NGS in forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of NGS methods is ex- tremely significant for forest virology. Reviewed data about viral presence in holobionts, allowed us to address the role of the virome in the holobionts. Genetic variation is a crucial aspect in hologenome, significantly reinforced by horizontal gene transfer among all interacting actors. Through virus-virus interplays synergistic or antagonistic relations may evolve, which may drasti- cally affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protec- tion based on endophytes and mycovirus biocontrol agents. -
Genome Characterization of a Bovine Papillomavirus Type 5 from Cattle in the Amazon Region, Brazil
Virus Genes DOI 10.1007/s11262-016-1406-y Genome characterization of a bovine papillomavirus type 5 from cattle in the Amazon region, Brazil 1,2 1 1 1 Flavio R. C. da Silva • Cı´ntia Daudt • Samuel P. Cibulski • Matheus N. Weber • 3 3 4 1 Ana Paula M. Varela • Fabiana Q. Mayer • Paulo M. Roehe • Cla´udio W. Canal Received: 11 September 2016 / Accepted: 20 October 2016 Ó Springer Science+Business Media New York 2016 Abstract Papillomaviruses are small and complex viruses Keywords Papillomaviridae Á Epsilonpapillomavirus Á with circular DNA genome that belongs to the Papillo- BPV5 Á Complete genome Á Phylogeny mavirus family, which comprises at least 39 genera. The bovine papillomavirus (BPV) causes an infectious disease that is characterized by chronic and proliferative benign Introduction tumors that affect cattle worldwide. In the present work, the full genome sequence of BPV type 5, an Epsilonpa- Viruses from the Papillomaviridae family infect epithelia pillomavirus, is reported. The genome was recovered from in amniotes and are associated with asymptomatic infec- papillomatous lesions excised from cattle raised in the tions, proliferative benign lesions, and different cancers in Amazon region, Northern Brazil. The genome comprises humans and other animals [1]. Papillomaviruses (PVs) 7836 base pairs and exhibits the archetypal organization of have circular, double-stranded DNA genomes of *8kbin the Papillomaviridae. This is of significance for the study length. The organization of PV genomes consists of the of BPV biology, since currently available full BPV genome early and the late regions and the noncoding region sequences are scarce. The availability of genomic infor- between them. -
Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands
viruses Article Novel Ampeloviruses Infecting Cassava in Central Africa and the South-West Indian Ocean Islands Yves Kwibuka 1,2,* , Espoir Bisimwa 2, Arnaud G. Blouin 1, Claude Bragard 3 , Thierry Candresse 4 , Chantal Faure 4, Denis Filloux 5,6, Jean-Michel Lett 7 , François Maclot 1, Armelle Marais 4, Santatra Ravelomanantsoa 8 , Sara Shakir 9 , Hervé Vanderschuren 9,10 and Sébastien Massart 1,* 1 Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium; [email protected] (A.G.B.); [email protected] (F.M.) 2 Faculté des Sciences Agronomiques, Université Catholique de Bukavu, BP 285 Bukavu, Democratic Republic of the Congo; [email protected] 3 Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, 1348 Louvain-la-Neuve, Belgium; [email protected] 4 Université Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, 33882 Villenave d’Ornon, France; [email protected] (T.C.); [email protected] (C.F.); [email protected] (A.M.) 5 CIRAD, UMR PHIM, 34090 Montpellier, France; denis.fi[email protected] 6 PHIM Plant Health Institute, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34000 Montpellier, France 7 CIRAD, UMR PVBMT, Pôle de Protection des Plantes, Saint-Pierre, F-97410 Ile de la Reunion, France; [email protected] 8 FOFIFA-CENRADERU, Laboratoire de Pathologie Végétale, BP 1444 Ambatobe, Madagascar; [email protected] 9 Plant Genetics Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, Citation: Kwibuka, Y.; Bisimwa, E.; 5030 Gembloux, Belgium; [email protected] (S.S.); [email protected] (H.V.) Blouin, A.G.; Bragard, C.; Candresse, 10 Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Biosystems Department, T.; Faure, C.; Filloux, D.; Lett, J.-M.; KU Leuven, 3000 Leuven, Belgium Maclot, F.; Marais, A.; et al. -
Biological and Molecular Characterization of Dahlia Mosaic Caulimovirus Abstract
BIOLOGICAL AND MOLECULAR CHARACTERIZATION OF DAHLIA MOSAIC CAULIMOVIRUS By VIHANGA PAHALAWATTA A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Department of Plant Pathology AUGUST 2007 © Copyright by VIHANGA PAHALAWATTA, 2007 All Rights Reserved i To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of VIHANGA PAHALAWATTA find it satisfactory and recommend that it be accepted. _____________________________ Chair _____________________________ _____________________________ ____________________________ ii ACKNOWLEDGEMENT I would like to express my sincere gratitude to my major advisor, Dr. Hanu Pappu, for the tremendous support, guidance, encouragement and most of all the numerous opportunities that he made available to me during the time I spent working with him. Dr. Pappu has been an exceptional mentor who has been a constant source of inspiration to me. I would also like to thank Dr. Patricia Okubara, Dr. Ken Eastwell and Dr. Gary Chastagner for their advice, guidance and helpful discussions throughout my tenure. I wish to extend my gratitude to Keri Druffel, who taught me numerous techniques in the laboratory and for all the work she did that made my work so much easier. A special thanks to Robert Brueggeman for technical assistance. I am also grateful to the faculty and staff of the Department of Plant Pathology for all the help and support during my graduate studies at Washington State University. A special thank you to Dr. Tim Murray, for arranging departmental financial support and for giving me the opportunity to serve as a teaching assistant.