Varsani, Arvind Devshi
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Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses from Bacterial and Archaeal Plasmids
ARTICLE https://doi.org/10.1038/s41467-019-11433-0 OPEN Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids Darius Kazlauskas 1, Arvind Varsani 2,3, Eugene V. Koonin 4 & Mart Krupovic 5 Single-stranded (ss) DNA viruses are a major component of the earth virome. In particular, the circular, Rep-encoding ssDNA (CRESS-DNA) viruses show high diversity and abundance 1234567890():,; in various habitats. By combining sequence similarity network and phylogenetic analyses of the replication proteins (Rep) belonging to the HUH endonuclease superfamily, we show that the replication machinery of the CRESS-DNA viruses evolved, on three independent occa- sions, from the Reps of bacterial rolling circle-replicating plasmids. The CRESS-DNA viruses emerged via recombination between such plasmids and cDNA copies of capsid genes of eukaryotic positive-sense RNA viruses. Similarly, the rep genes of prokaryotic DNA viruses appear to have evolved from HUH endonuclease genes of various bacterial and archaeal plasmids. Our findings also suggest that eukaryotic polyomaviruses and papillomaviruses with dsDNA genomes have evolved via parvoviruses from CRESS-DNA viruses. Collectively, our results shed light on the complex evolutionary history of a major class of viruses revealing its polyphyletic origins. 1 Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius 10257, Lithuania. 2 The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA. 3 Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, 7700 Cape Town, South Africa. -
Small Circular DNA Viruses: the Muddy Viral “Playground” of Recombinant, Reassortant, and Highly Diverse Viruses
Small Circular DNA Viruses: The muddy viral “playground” of recombinant, reassortant, and highly diverse viruses @Varsani_lab Arizona State University, USA University of Canterbury, New Zealand University of Cape Town, South Africa Arvind Varsani Nucleotide substitutions Recombination Reassortment Viral evolution Viral Nucleotide substitutions Recombination Reassortment Viral evolution Viral Nucleotide substitutions Recombination Reassortment Viral evolution Viral I II III IV V dsDNA ssDNA VI VII dsRNA ssRNA(+) ssRNA(-) ssRNA(RT) dsDNA(RT) viruses Archaea Bacteria Diatoms Fungi Invertebrates Plants Vertebrates Unknown Anelloviridae – circular (~2.1 - 3.8kb) Bacillidnaviridae - circular (~4.5 - 6kb) Circoviridae – circular (~1.6 - 2.3kb) Geminiviridae – circular (~2.7kb; monopartite, bipartite, associated with α/β satellites) Genomovirdae – circular (1.8 -2.3 kb) ssDNA Inoviridae – circular (~5.8 - 8.7kb) Microviridae – circular (~4.5 - 6kb) Nanoviridae – circular (~1.2kb; multicomponent viruses; associated with satellites) Parvoviridae – linear (~3.7 - 6kb) Pleolipoviridae* – circular ssDNA; circular dsDNA or liner dsDNA (7-16kb) Smacoviridae* - circular (2.3 - 2.9kb) ssDNA viruses Chimerism in Rep Geminiviruses MSV: ~2 x 10-4 subs/site/year SSRV: ~3 x 10-4 subs/site/year EACMV: ~1 x 10-3 subs/site/year TYLCV: ~3 x 10-4 subs/site/year Nanoviruses FBNYV: ~1 x 10-3 subs/site/year BBTV: ~3 x 10-4 subs/site/year Circoviruses BFDV: ~2 x 10-3 subs/site/year PCV-2: ~1 x 10-3 subs/site/year Parvoviruses CPV: ~2 x 10-4 - 8 x 10-5 subs/site/year -
And Giant Guitarfish (Rhynchobatus Djiddensis)
VIRAL DISCOVERY IN BLUEGILL SUNFISH (LEPOMIS MACROCHIRUS) AND GIANT GUITARFISH (RHYNCHOBATUS DJIDDENSIS) BY HISTOPATHOLOGY EVALUATION, METAGENOMIC ANALYSIS AND NEXT GENERATION SEQUENCING by JENNIFER ANNE DILL (Under the Direction of Alvin Camus) ABSTRACT The rapid growth of aquaculture production and international trade in live fish has led to the emergence of many new diseases. The introduction of novel disease agents can result in significant economic losses, as well as threats to vulnerable wild fish populations. Losses are often exacerbated by a lack of agent identification, delay in the development of diagnostic tools and poor knowledge of host range and susceptibility. Examples in bluegill sunfish (Lepomis macrochirus) and the giant guitarfish (Rhynchobatus djiddensis) will be discussed here. Bluegill are popular freshwater game fish, native to eastern North America, living in shallow lakes, ponds, and slow moving waterways. Bluegill experiencing epizootics of proliferative lip and skin lesions, characterized by epidermal hyperplasia, papillomas, and rarely squamous cell carcinoma, were investigated in two isolated poopulations. Next generation genomic sequencing revealed partial DNA sequences of an endogenous retrovirus and the entire circular genome of a novel hepadnavirus. Giant Guitarfish, a rajiform elasmobranch listed as ‘vulnerable’ on the IUCN Red List, are found in the tropical Western Indian Ocean. Proliferative skin lesions were observed on the ventrum and caudal fin of a juvenile male quarantined at a public aquarium following international shipment. Histologically, lesions consisted of papillomatous epidermal hyperplasia with myriad large, amphophilic, intranuclear inclusions. Deep sequencing and metagenomic analysis produced the complete genomes of two novel DNA viruses, a typical polyomavirus and a second unclassified virus with a 20 kb genome tentatively named Colossomavirus. -
Heparan Sulfate Proteoglycan Is an Important Attachment Factor for Cell Entry of Akabane and Schmallenberg Viruses
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Enlighten Murakami, S., Takenaka-Uema, A., Kobayashi, T., Kato, K., Shimojima, M., Palmarini, M. and Horimoto, T. (2017) Heparan sulfate proteoglycan is an important attachment factor for cell entry of Akabane and Schmallenberg viruses. Journal of Virology, 91(15), e00503-17. (doi:10.1128/JVI.00503-17) This is the author’s final accepted version. There may be differences between this version and the published version. You are advised to consult the publisher’s version if you wish to cite from it. http://eprints.gla.ac.uk/141940/ Deposited on: 03 July 2017 Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk 1 Heparan sulfate proteoglycan is an important attachment factor for cell 2 entry of Akabane and Schmallenberg viruses 3 4 5 Shin Murakamia,#, Akiko Takenaka-Uemab, Tomoya Kobayashia, Kentaro Katoa,c, 6 Masayuki Shimojimaa,d, Massimo Palmarinie, and Taisuke Horimotoa,# 7 8 Department of Veterinary Microbiology, Graduate School of Agricultural and Life 9 Sciences, The University of Tokyo, Tokyo, Japana; 10 Department of Infection Control and Disease Prevention, Graduate School of 11 Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japanb; 12 National Research Center for Protozoan Diseases, Obihiro University of 13 Agriculture and Veterinary Medicine, Obihiro, Japanc; 14 Department of Virology I, Special Pathogens Laboratory, National Institute of 15 Infectious Diseases, Tokyo, Japand; -
Beet Curly Top Virus Strains Associated with Sugar Beet in Idaho, Oregon, and a Western U.S
Plant Disease • 2017 • 101:1373-1382 • http://dx.doi.org/10.1094/PDIS-03-17-0381-RE Beet curly top virus Strains Associated with Sugar Beet in Idaho, Oregon, and a Western U.S. Collection Carl A. Strausbaugh and Imad A. Eujayl, United States Department of Agriculture–Agricultural Research Service (USDA-ARS) Northwest Irrigation and Soils Research Laboratory, Kimberly, ID 83341; and William M. Wintermantel, USDA-ARS, Salinas, CA 93905 Abstract Curly top of sugar beet is a serious, yield-limiting disease in semiarid pro- Logan) strains and primers that amplified a group of Worland (Wor)- duction areas caused by Beet curly top virus (BCTV) and transmitted like strains. The BCTV strain distribution averaged 2% Svr, 30% CA/ by the beet leafhopper. One of the primary means of control for BCTV Logan, and 87% Wor-like (16% had mixed infections), which differed in sugar beet is host resistance but effectiveness of resistance can vary from the previously published 2006-to-2007 collection (87% Svr, 7% among BCTV strains. Strain prevalence among BCTV populations CA/Logan, and 60% Wor-like; 59% mixed infections) based on a contin- was last investigated in Idaho and Oregon during a 2006-to-2007 collec- gency test (P < 0.0001). Whole-genome sequencing (GenBank acces- tion but changes in disease severity suggested a need for reevaluation. sions KT276895 to KT276920 and KX867015 to KX867057) with Therefore, 406 leaf samples symptomatic for curly top were collected overlapping primers found that the Wor-like strains included Wor, Colo- from sugar beet plants in commercial sugar beet fields in Idaho and rado and a previously undescribed strain designated Kimberly1. -
Geminiviruses Encode Additional Small Proteins with Specific
ARTICLE https://doi.org/10.1038/s41467-021-24617-4 OPEN Geminiviruses encode additional small proteins with specific subcellular localizations and virulence function Pan Gong 1,6, Huang Tan 2,3,6, Siwen Zhao1, Hao Li1, Hui Liu4,YuMa2,3, Xi Zhang2,3, Junjie Rong2,3, Xing Fu2, ✉ ✉ ✉ Rosa Lozano-Durán 2,5 , Fangfang Li1 & Xueping Zhou 1,4 1234567890():,; Geminiviruses are plant viruses with limited coding capacity. Geminivirus-encoded proteins are traditionally identified by applying a 10-kDa arbitrary threshold; however, it is increasingly clear that small proteins play relevant roles in biological systems, which calls for the reconsideration of this criterion. Here, we show that geminiviral genomes contain additional ORFs. Using tomato yellow leaf curl virus, we demonstrate that some of these small ORFs are expressed during the infection, and that the encoded proteins display specific subcellular localizations. We prove that the largest of these additional ORFs, which we name V3, is required for full viral infection, and that the V3 protein localizes in the Golgi apparatus and functions as an RNA silencing suppressor. These results imply that the repertoire of gemi- niviral proteins can be expanded, and that getting a comprehensive overview of the molecular plant-geminivirus interactions will require the detailed study of small ORFs so far neglected. 1 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China. 2 Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China. 3 University of the Chinese Academy of Sciences, Beijing, China. -
Ocorrência Natural De Espécies Virais E Avaliação De Potenciais Hospedeiras Experimentais De Begomovírus, Potyvírus E Tospovírus Em Plantas Arbóreas E Berinjela
UNIVERSIDADE DE BRASÍLIA INSTITUTO DE CIÊNCIAS BIOLÓGICAS DEPARTAMENTO DE FITOPATOLOGIA PROGRAMA DE PÓS-GRADUAÇÃO EM FITOPATOLOGIA Ocorrência natural de espécies virais e avaliação de potenciais hospedeiras experimentais de begomovírus, potyvírus e tospovírus em plantas arbóreas e berinjela (Solanum melongena) JOSIANE GOULART BATISTA Brasília - DF 2014 JOSIANE GOULART BATISTA Ocorrência natural de espécies virais e avaliação de potenciais hospedeiras experimentais de begomovírus, potyvírus e tospovírus em plantas arbóreas e berinjela (Solanum melongena) Dissertação apresentada à Universidade de Brasília como requisito parcial para a obtenção do título de Mestre em Fitopatologia pelo Programa de Pós Graduação em Fitopatologia. Orientadora Dra. Rita de Cássia Pereira Carvalho BRASÍLIA DISTRITO FEDERAL – BRASIL 2014 FICHA CATALOGRÁFICA Batista, G.J. Ocorrência natural de espécies virais e avaliação de potenciais hospedeiras experimentais de begomovírus, potyvírus e tospovírus em plantas arbóreas e berinjela (Solanum melongena). Josiane Goulart Batista. Brasília, 2014 Número de páginas p.: 183 Dissertação de mestrado - Programa de Pós-Graduação em Fitopatologia, Universidade de Brasília, Brasília. Árvores, berinjela, vírus, resistência. I. Universidade de Brasília. PPG/FIT. II. Título. Ocorrência natural de espécies virais e avaliação de potenciais hospedeiras experimentais de begomovírus, potyvírus e tospovírus em plantas arbóreas e berinjela (Solanum melongena). Dedico a minha pequena linda filha Giovanna, ao meu pai Josvaldo, a minha mãe Nelma, ao meu namorado Airton, a minha irmã Josefa e minha sobrinha Júlia. Agradecimentos A Deus. Aos meus pais Josvaldo e Nelma. A minha filha Giovanna, minha irmã Josefa e minha sobrinha Júlia. A minha orientadora Professora Rita de Cássia. Aos colegas do mestrado e doutorado Rafaela, Marcella, Juliana, Ícaro, Cléia, Monica, Elenice, William, Rayane e Nédio. -
Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics
viruses Article Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics Ashleigh F. Porter 1, Mang Shi 1, John-Sebastian Eden 1,2 , Yong-Zhen Zhang 3,4 and Edward C. Holmes 1,3,* 1 Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life & Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; [email protected] (A.F.P.); [email protected] (M.S.); [email protected] (J.-S.E.) 2 Centre for Virus Research, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia 3 Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 201500, China; [email protected] 4 Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China * Correspondence: [email protected]; Tel.: +61-2-9351-5591 Received: 17 October 2019; Accepted: 23 November 2019; Published: 25 November 2019 Abstract: DNA viruses comprise a wide array of genome structures and infect diverse host species. To date, most studies of DNA viruses have focused on those with the strongest disease associations. Accordingly, there has been a marked lack of sampling of DNA viruses from invertebrates. Bulk RNA sequencing has resulted in the discovery of a myriad of novel RNA viruses, and herein we used this methodology to identify actively transcribing DNA viruses in meta-transcriptomic libraries of diverse invertebrate species. Our analysis revealed high levels of phylogenetic diversity in DNA viruses, including 13 species from the Parvoviridae, Circoviridae, and Genomoviridae families of single-stranded DNA virus families, and six double-stranded DNA virus species from the Nudiviridae, Polyomaviridae, and Herpesviridae, for which few invertebrate viruses have been identified to date. -
Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses
viruses Article Soybean Thrips (Thysanoptera: Thripidae) Harbor Highly Diverse Populations of Arthropod, Fungal and Plant Viruses Thanuja Thekke-Veetil 1, Doris Lagos-Kutz 2 , Nancy K. McCoppin 2, Glen L. Hartman 2 , Hye-Kyoung Ju 3, Hyoun-Sub Lim 3 and Leslie. L. Domier 2,* 1 Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA; [email protected] 2 Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Urbana, IL 61801, USA; [email protected] (D.L.-K.); [email protected] (N.K.M.); [email protected] (G.L.H.) 3 Department of Applied Biology, College of Agriculture and Life Sciences, Chungnam National University, Daejeon 300-010, Korea; [email protected] (H.-K.J.); [email protected] (H.-S.L.) * Correspondence: [email protected]; Tel.: +1-217-333-0510 Academic Editor: Eugene V. Ryabov and Robert L. Harrison Received: 5 November 2020; Accepted: 29 November 2020; Published: 1 December 2020 Abstract: Soybean thrips (Neohydatothrips variabilis) are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, the metatranscriptome of soybean thrips, collected by the Midwest Suction Trap Network during 2018, was analyzed. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. -
The Ins and Outs of Nondestructive Cell-To-Cell and Systemic Movement of Plant Viruses
Critical Reviews in Plant Sciences, 23(3):195–250 (2004) Copyright C Taylor and Francis Inc. ISSN: 0735-2689 print / 1549-7836 online DOI: 10.1080/07352680490452807 The Ins and Outs of Nondestructive Cell-to-Cell and Systemic Movement of Plant Viruses Elisabeth Waigmann Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Institute of Medical Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9 A-1030, Vienna, Austria Shoko Ueki Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215 Kateryna Trutnyeva Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Institute of Medical Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9 A-1030, Vienna, Austria Vitaly Citovsky∗ Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY 11794-5215 Referee: Dr. Ernest Hiebert, Professor, Department of Plant Pathology, University of Florida/IFAS, P.O. Box 110680, 1541 Fifield Hall, Gainesville, FL 32611-0680, USA. Table of Contents 1. Introduction ..........................................................................................................................................................196 2. Structure and Composition of Plasmodesmata, the Intercellular Conduits for Viral Movement ..............................198 3. Cell-to-Cell Transport of Plant Viruses: Have Movement Protein, Will Travel ........................................................200 3.1. MP Structure: Are Common Functions Supported by -
The Intestinal Virome of Malabsorption Syndrome-Affected and Unaffected
Virus Research 261 (2019) 9–20 Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres The intestinal virome of malabsorption syndrome-affected and unaffected broilers through shotgun metagenomics T ⁎ Diane A. Limaa, , Samuel P. Cibulskib, Caroline Tochettoa, Ana Paula M. Varelaa, Fabrine Finklera, Thais F. Teixeiraa, Márcia R. Loikoa, Cristine Cervac, Dennis M. Junqueirad, Fabiana Q. Mayerc, Paulo M. Roehea a Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde (ICBS), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil b Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil c Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil d Centro Universitário Ritter dos Reis - UniRitter, Health Science Department, Porto Alegre, RS, Brazil ARTICLE INFO ABSTRACT Keywords: Malabsorption syndrome (MAS) is an economically important disease of young, commercially reared broilers, Enteric disorders characterized by growth retardation, defective feather development and diarrheic faeces. Several viruses have Virome been tentatively associated to such syndrome. Here, in order to examine potential associations between enteric Broiler chickens viruses and MAS, the faecal viromes of 70 stool samples collected from diseased (n = 35) and healthy (n = 35) High-throughput sequencing chickens from seven flocks were characterized and compared. Following high-throughput sequencing, a total of 8,347,319 paired end reads, with an average of 231 nt, were generated. Through analysis of de novo assembled contigs, 144 contigs > 1000 nt were identified with hits to eukaryotic viral sequences, as determined by GenBank database. -
ICTV Code Assigned: 2011.001Ag Officers)
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: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (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: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [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 .