Hepatitis a Virus and Hepatitis E Virus: Emerging and Re-Emerging Enterically Transmitted Hepatitis Viruses
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Multipartite Viruses: Organization, Emergence and Evolution
UNIVERSIDAD AUTÓNOMA DE MADRID FACULTAD DE CIENCIAS DEPARTAMENTO DE BIOLOGÍA MOLECULAR MULTIPARTITE VIRUSES: ORGANIZATION, EMERGENCE AND EVOLUTION TESIS DOCTORAL Adriana Lucía Sanz García Madrid, 2019 MULTIPARTITE VIRUSES Organization, emergence and evolution TESIS DOCTORAL Memoria presentada por Adriana Luc´ıa Sanz Garc´ıa Licenciada en Bioqu´ımica por la Universidad Autonoma´ de Madrid Supervisada por Dra. Susanna Manrubia Cuevas Centro Nacional de Biotecnolog´ıa (CSIC) Memoria presentada para optar al grado de Doctor en Biociencias Moleculares Facultad de Ciencias Departamento de Biolog´ıa Molecular Universidad Autonoma´ de Madrid Madrid, 2019 Tesis doctoral Multipartite viruses: Organization, emergence and evolution, 2019, Madrid, Espana. Memoria presentada por Adriana Luc´ıa-Sanz, licenciada en Bioqumica´ y con un master´ en Biof´ısica en la Universidad Autonoma´ de Madrid para optar al grado de doctor en Biociencias Moleculares del departamento de Biolog´ıa Molecular en la facultad de Ciencias de la Universidad Autonoma´ de Madrid Supervisora de tesis: Dr. Susanna Manrubia Cuevas. Investigadora Cient´ıfica en el Centro Nacional de Biotecnolog´ıa (CSIC), C/ Darwin 3, 28049 Madrid, Espana. to the reader CONTENTS Acknowledgments xi Resumen xiii Abstract xv Introduction xvii I.1 What is a virus? xvii I.2 What is a multipartite virus? xix I.3 The multipartite lifecycle xx I.4 Overview of this thesis xxv PART I OBJECTIVES PART II METHODOLOGY 0.5 Database management for constructing the multipartite and segmented datasets 3 0.6 Analytical -
Molecular Characterization of a Novel Polymycovirus from Penicillium Janthinellum with a Focus on Its Genome-Associated Pasrp
fmicb-11-592789 October 14, 2020 Time: 17:11 # 1 ORIGINAL RESEARCH published: 20 October 2020 doi: 10.3389/fmicb.2020.592789 Molecular Characterization of a Novel Polymycovirus From Penicillium janthinellum With a Focus on Its Genome-Associated PASrp Yukiyo Sato1, Atif Jamal2, Hideki Kondo1 and Nobuhiro Suzuki1* 1 Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan, 2 Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan The genus Polymycovirus of the family Polymycoviridae accommodates fungal RNA viruses with different genomic segment numbers (four, five, or eight). It is suggested that four members form no true capsids and one forms filamentous virus particles Edited by: enclosing double-stranded RNA (dsRNA). In both cases, viral dsRNA is associated Hiromitsu Moriyama, Tokyo University of Agriculture with a viral protein termed “proline-alanine-serine-rich protein” (PASrp). These forms are and Technology, Japan assumed to be the infectious entity. However, the detailed molecular characteristics Reviewed by: of PASrps remain unclear. Here, we identified a novel five-segmented polymycovirus, Ioly Kotta-Loizou, Penicillium janthinellum polymycovirus 1 (PjPmV1), and characterized its purified fraction Imperial College London, United Kingdom form in detail. The PjPmV1 had five dsRNA segments associated with PASrp. Density Wenxing Xu, gradient ultracentrifugation of the PASrp-associated PjPmV1 dsRNA revealed its uneven Huazhong Agricultural University, China structure and a broad fractionation profile distinct from that of typical encapsidated *Correspondence: viruses. Moreover, PjPmV1-PASrp interacted in vitro with various nucleic acids in a Nobuhiro Suzuki sequence-non-specific manner. These PjPmV1 features are discussed in view of the [email protected]; diversification of genomic segment numbers of the genus Polymycovirus. -
Molecular Characterization of a Novel Mycovirus Isolated from Rhizoctonia Solani AG-1 IA 9-11
Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11 Yang Sun Yunnan Agricultural University Yan qiong Li Kunming University Wen han Dong Yunnan Agricultural University Ai li Sun Yunnan Agricultural University Ning wei Chen Yunnan Agricultural University Zi fang Zhao Yunnan Agricultural University Yong qing Li Zhaotong Plant Protection and Quarantine Station Gen hua Yang ( [email protected] ) Yunnan Agricultural University https://orcid.org/0000-0003-3322-1558 Cheng yun Li Yunnan Agricultural University Research Article Keywords: SMC, PRK, RT-like super family, RsRV-HN008, RdRp Posted Date: May 19th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-520549/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/9 Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non- overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but signicant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses. -
50-Plus Years of Fungal Viruses
Virology 479-480 (2015) 356–368 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Review 50-plus years of fungal viruses Said A. Ghabrial a,n, José R. Castón b, Daohong Jiang c, Max L. Nibert d, Nobuhiro Suzuki e a Plant Pathology Department, University of Kentucky, Lexington, KY, USA b Department of Structure of Macromolecules, Centro Nacional Biotecnologıa/CSIC, Campus de Cantoblanco, Madrid, Spain c State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China d Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA e Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan article info abstract Article history: Mycoviruses are widespread in all major taxa of fungi. They are transmitted intracellularly during cell Received 9 January 2015 division, sporogenesis, and/or cell-to-cell fusion (hyphal anastomosis), and thus their life cycles generally Returned to author for revisions lack an extracellular phase. Their natural host ranges are limited to individuals within the same or 31 January 2015 closely related vegetative compatibility groups, although recent advances have established expanded Accepted 19 February 2015 experimental host ranges for some mycoviruses. Most known mycoviruses have dsRNA genomes Available online 13 March 2015 packaged in isometric particles, but an increasing number of positive- or negative-strand ssRNA and Keywords: ssDNA viruses have been isolated and characterized. Although many mycoviruses do not have marked Mycoviruses effects on their hosts, those that reduce the virulence of their phytopathogenic fungal hosts are of Totiviridae considerable interest for development of novel biocontrol strategies. -
University of Oklahoma Graduate College Viral
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE VIRAL METAGENOMICS AND ANTHROPOLOGY IN THE AMERICAS A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By ANDREW T. OZGA Norman, Oklahoma 2015 VIRAL METAGENOMICS AND ANTHROPOLOGY IN THE AMERICAS A DISSERTATION APPROVED FOR THE DEPARTMENT OF ANTHROPOLOGY BY ______________________________ Dr. Cecil M. Lewis, Jr., Chair ______________________________ Dr. Katherine Hirschfeld ______________________________ Dr. Paul Spicer ______________________________ Dr. Kermyt G. Anderson ______________________________ Dr. Tyrrell Conway © Copyright by ANDREW T. OZGA 2015 All Rights Reserved. Acknowledgements This dissertation would not have been possible without the guidance and encouragement of a number of professors, colleagues, friends, and family members. First and foremost I’d like to thank my advisor and chair, Dr. Cecil Lewis. His guidance and critiques throughout the project design, execution, and drafting process were invaluable to my completion of this degree. I’d also like to thank my doctoral committee: Dr. Tassie Hirschfeld, Dr. KG Anderson, Dr. Paul Spicer, and Dr. Tyrrell Conway for their support and insight regarding my project design and manuscript draft. I must thank those that graciously provided fecal samples for this project including the Cheyenne & Arapaho Nation, University of Oklahoma colleagues and students, and those from the coastal and jungle regions of Peru. Additionally, I’d like to thank my LMAMR colleagues including Dr. Christina Warinner and Dr. Jiawu Xu for their encouragement and valuable knowledge. This includes Dr. Alexandra Obregon-Tito and Raul Tito for their relentless support of my pursuit of a Ph.D., their assistance in sample processing, and their assistance in the Peruvian IRB process and sample collection. -
Generación De Una Base De Datos Completa Y No Redundante De Virus Y Su Análisis Composicional
TESINA PARA OPTAR POR EL GRADO DE LICENCIADO EN CIENCIAS BIOLÓGICAS GENERACIÓN DE UNA BASE DE DATOS COMPLETA Y NO REDUNDANTE DE VIRUS Y SU ANÁLISIS COMPOSICIONAL Diego Simón [email protected] Orientador: Dr. Héctor Musto Laboratorio de Organización y Evolución del Genoma Departamento de Ecología y Evolución Instituto de Biología Facultad de Ciencias Universidad de la República Tribunal: Dr. Juan Arbiza Dr. Andrés Iriarte Dr. Héctor Musto Diciembre de 2015 Resumen Las firmas genómicas no dependen de regiones codificantes y son características del genoma en su conjunto. Los mecanismos aún no están entendidos completamente. Los virus están expuestos a sesgos mutacionales propios del hospedero. Aquellos más expuestos a estos sesgos, presentarán efectos más evidentes. El objetivo de esta tesina es explorar la diversidad viral e intentar describir grandes patrones evolutivos. Utilizando un abordaje bioinformático, se trabajó con 4195 genomas completos de Viral Genomes, del NCBI. Se calcularon composiciones de bases y frecuencias de dinucleótidos, por virus y por tipo de genoma, estructura, grupo de Baltimore, orden, familia y hospedero. En muchas de las categorías se observaron empobrecimientos en TpA. El grupo VI y los órdenes Ligamenvirales y Nidovirales no presentaron sesgo para TpA. La única familia con enriquecimiento en TpA fue Globuloviridae, familia de virus de arqueas termófilas. Sesgos en CpG fueron observados en virus de ARN, pero no en el conjunto de todos los virus de ADN, probablemente como consecuencia de la gran cantidad de bacteriófagos. Los grupos IV, V y VI, los tres de ARN de hebra simple, presentaron empobrecimiento en CpG. Virus de animales y de plantas también. -
Identification, Molecular Characterization, and Biology of a Novel Quadrivirus Infecting the Phytopathogenic Fungus Leptosphaeri
viruses Communication Identification, Molecular Characterization, and Biology of a Novel Quadrivirus Infecting the Phytopathogenic Fungus Leptosphaeria biglobosa Unnati A. Shah 1, Ioly Kotta-Loizou 1,2,* , Bruce D. L. Fitt 1 and Robert H. A. Coutts 1 1 Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK; [email protected] (U.A.S.); b.fi[email protected] (B.D.L.F.); [email protected] (R.H.A.C.) 2 Department of Life Sciences, Imperial College London, London SW7 2AZ, UK * Correspondence: [email protected] Received: 2 December 2018; Accepted: 22 December 2018; Published: 25 December 2018 Abstract: Here we report the molecular characterisation of a novel dsRNA virus isolated from the filamentous, plant pathogenic fungus Leptosphaeria biglobosa and known to cause significant alterations to fungal pigmentation and growth and to result in hypervirulence, as illustrated by comparisons between virus-infected and -cured isogenic fungal strains. The virus forms isometric particles approximately 40–45 nm in diameter and has a quadripartite dsRNA genome structure with size ranges of 4.9 to 4 kbp, each possessing a single ORF. Sequence analysis of the putative proteins encoded by dsRNAs 1–4, termed P1–P4, respectively, revealed modest similarities to the amino acid sequences of equivalent proteins predicted from the nucleotide sequences of known and suspected members of the family Quadriviridae and for that reason the virus was nominated Leptosphaeria biglobosa quadrivirus-1 (LbQV-1). Sequence and phylogenetic analysis using the P3 sequence, which encodes an RdRP, revealed that LbQV-1 was most closely related to known and suspected quadriviruses and monopartite totiviruses rather than other quadripartite mycoviruses including chrysoviruses and alternaviruses. -
Characterization of a Botybirnavirus Conferring Hypovirulence in the Phytopathogenic Fungus Botryosphaeria Dothidea
viruses Article Characterization of a Botybirnavirus Conferring Hypovirulence in the Phytopathogenic Fungus Botryosphaeria dothidea Lifeng Zhai 1,2,† , Mengmeng Yang 1,3,†, Meixin Zhang 2, Ni Hong 1,3 and Guoping Wang 1,3,* 1 College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430000, China; [email protected] (L.Z.); [email protected] (M.Y.); [email protected] (N.H.) 2 College of Life Science and Technology, Yangtze Normal University, Chongqing 400000, China; [email protected] 3 National Key Laboratory of Agromicrobiology, Huazhong Agricultural University, Wuhan 430000, China * Correspondence: [email protected]; Tel: +86-027-8728755339; Fax: +86-027-873846 † These authors contributed equally to this study. Received: 2 February 2019; Accepted: 14 March 2019; Published: 17 March 2019 Abstract: A double-stranded RNA (dsRNA) virus was isolated and characterized from strain EW220 of the phytopathogenic fungus Botryosphaeria dothidea. The full-length cDNAs of the dsRNAs were 6434 bp and 5986 bp in size, respectively. The largest dsRNA encodes a cap-pol fusion protein that contains a coat protein gene and an RNA-dependent RNA polymerase (RdRp) domain, and the second dsRNA encodes a hypothetical protein. Genome sequence analysis revealed that the sequences of the dsRNA virus shared 99% identity with Bipolaris maydis botybirnavirus 1(BmBRV1) isolated from the causal agent of corn southern leaf blight, Bipolaris maydis. Hence, the dsRNA virus constitutes a new strain of BmBRV1 and was named Bipolaris maydis botybirnavirus 1 strain BdEW220 (BmBRV1-BdEW220). BmBRV1-BdEW220 contains spherical virions that are 37 nm in diameter and consist of two dsRNA segments. -
Molecular and Biological Characterization of a Novel Botybirnavirus Identified from a Pakistani Isolate of Alternaria Alternata
Virus Research 263 (2019) 119–128 Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres Molecular and biological characterization of a novel botybirnavirus identified from a Pakistani isolate of Alternaria alternata T Wajeeha Shamsia,b,1, Yukiyo Satoa,1, Atif Jamala,c, Sabitree Shahia, Hideki Kondoa, ⁎ ⁎⁎ Nobuhiro Suzukia, , Muhammad Faraz Bhattib, a Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan b Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, Pakistan c Crop Diseases Research Institute (CDRI), National Agricultural Research Centre (NARC), Islamabad, 45500, Pakistan ARTICLE INFO ABSTRACT Keywords: Mycoviruses ubiquitously infect a wide range of fungal hosts in the world. The current study reports a novel Botybirnavirus double stranded RNA (dsRNA) virus, termed Alternaria alternata botybirnavirus 1 (AaBbV1), infecting a DsRNA Pakistani strain, 4a, of a phytopathogenic ascomycetous fungus Alternaria alternata. A combined approach of Alternaria alternata next generation and conventional terminal end sequencing of the viral genome revealed that the virus is a Mycovirus distinct member of the genus Botybirnavirus. This virus comprised of two segments (dsRNA1 and dsRNA2) of sizes 6127 bp and 5860 bp respectively. The dsRNA1-encoded protein carrying the RNA-dependent RNA polymerase domain showed 61% identity to the counterpart of Botrytis porri botybirnavirus 1 and lower levels of amino acid similarity with those of other putative botybirnaviruses and the fungal dsRNA viruses such as members of the families Totiviridae, Chrysoviridae and Megabirnaviridae. The dsRNA2-encoded protein showed resemblance with corresponding proteins of botybirnaviruses. Electron microscopy showed AaBbV1 to form spherical particles of 40 nm in diameter. -
Mimivirus Inaugurated in the 21St Century the Beginning
Available online at www.sciencedirect.com ScienceDirect Mimivirus inaugurated in the 21st century the beginning of a reclassification of viruses 3,4 1,2,4 3 Vikas Sharma , Philippe Colson , Pierre Pontarotti and 1,2 Didier Raoult Mimivirus and other giant viruses are visible by light to microbes [3–5]. Accordingly, these agents were named microscopy and bona fide microbes that differ from other ultraviruses, or inframicrobes, and, eventually, viruses viruses and from cells that have a ribosome. They can be [1 ]. During the 1910–1920s, viruses became increasingly defined by: giant virion and genome sizes; their complexity, established as small entities that need living cells to repli- with the presence of DNA and mRNAs and dozens or hundreds cate; Rickettsia and Chlamydia, also intracellular parasites, of proteins in virions; the presence of translation-associated definitively turned out not being viruses [6,7]. During the components; a mobilome including (pro)virophages (and a 1930–1940s, the first electron micrographs of virions were defence mechanism, named MIMIVIRE, against them) and obtained [8] and the eclipse period of virus replication was transpovirons; their monophyly; the presence of the most discovered [9]. Then, during the 1950s, the virus concept archaic protein motifs they share with cellular organisms but was unravelled by A. Lwoff, based mainly on negative not other viruses; a broader host range than other viruses. criteria [1 ]. Lwoff defined viruses as potentially patho- These features show that giant viruses are specific, genic strictly intracellular entities, which have either DNA autonomous, biological entities that warrant the creation of a or RNA, multiply in the form of their genetic material, are new branch of microbes. -
Viromes in Xylariaceae Fungi Infecting Avocado in Spain
Virology 532 (2019) 11–21 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/virology Viromes in Xylariaceae fungi infecting avocado in Spain T ∗ Leonardo Velascoa, , Isabel Arjona-Gironab, Enrico Cretazzoa, Carlos López-Herrerab a Instituto Andaluz de Investigación y Formación Agraria (IFAPA), 29140, Churriana, Málaga, Spain b Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, C.S.I.C, Córdoba, Spain ARTICLE INFO ABSTRACT Keywords: Four isolates of Entoleuca sp., family Xylariaceae, Ascomycota, recovered from avocado rhizosphere in Spain Mycoviruses were analyzed for mycoviruses presence. For that, the dsRNAs from the mycelia were extracted and subjected to Negative single-stranded RNA virus metagenomics analysis that revealed the presence of eleven viruses putatively belonging to families Partitiviridae, Gammaflexivirus Hypoviridae, Megabirnaviridae, and orders Tymovirales and Bunyavirales, in addition to one ourmia-like virus plus Ourmia-like virus other two unclassified virus species. Moreover, a sequence with 98% nucleotide identity to plant endornavirus Endornavirus Phaseolus vulgaris alphaendornavirus 1 has been identified in the Entoleuca sp. isolates. Concerning the virome Multiple virus infections Entoleuca composition, the four isolates only differed in the presence of the bunyavirus and the ourmia-like virus, whileall Rosellinia necatrix other viruses showed common patterns. Specific primers allowed the detection by RT-PCR of these viruses ina Horizontal virus -
Metatranscriptomic Reconstruction Reveals RNA Viruses with the Potential to Shape Carbon Cycling in Soil
bioRxiv preprint doi: https://doi.org/10.1101/597468; this version posted April 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil Evan P. Starr1, Erin E. Nuccio2, Jennifer Pett-Ridge2, Jillian F. Banfield*3,4,5,6,7✢ and Mary K. Firestone*5 ✢Corresponding author: [email protected] 1Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA 2Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA 3Department of Earth and Planetary Science, University of California, Berkeley, CA, USA 4Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 5Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA 6Chan Zuckerberg Biohub, San Francisco, CA, USA 7Innovative Genomics Institute, Berkeley, CA, USA *These authors share senior authorship 1 bioRxiv preprint doi: https://doi.org/10.1101/597468; this version posted April 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Abstract Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in the most complex microbial system, soil.