A: Picornavirales B: Dicistroviruses
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Using Cell Lines to Study Factors Affecting Transmission of Fish Viruses
Using cell lines to study factors affecting transmission of fish viruses by Phuc Hoang Pham A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Biology Waterloo, Ontario, Canada, 2014 ©Phuc Hoang Pham 2014 AUTHOR'S DECLARATION I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii ABSTRACT Factors that can influence the transmission of aquatic viruses in fish production facilities and natural environment are the immune defense of host species, the ability of viruses to infect host cells, and the environmental persistence of viruses. In this thesis, fish cell lines were used to study different aspects of these factors. Five viruses were used in this study: viral hemorrhagic septicemia virus (VHSV) from the Rhabdoviridae family; chum salmon reovirus (CSV) from the Reoviridae family; infectious pancreatic necrosis virus (IPNV) from the Birnaviridae family; and grouper iridovirus (GIV) and frog virus-3 (FV3) from the Iridoviridae family. The first factor affecting the transmission of fish viruses examined in this thesis is the immune defense of host species. In this work, infections of marine VHSV-IVa and freshwater VHSV-IVb were studied in two rainbow trout cell lines, RTgill-W1 from the gill epithelium, and RTS11 from spleen macrophages. RTgill-W1 produced infectious progeny of both VHSV-IVa and -IVb. However, VHSV-IVa was more infectious than IVb toward RTgill-W1: IVa caused cytopathic effects (CPE) at a lower viral titre, elicited CPE earlier, and yielded higher titres. -
Coordinated Action of RTBV and RTSV Proteins Suppress Host RNA Silencing Machinery
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.19.427099; this version posted January 19, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Coordinated action of RTBV and RTSV proteins suppress host RNA silencing machinery Abhishek Anand1, Malathi Pinninti2, Anita Tripathi1, Satendra Kumar Mangrauthia2 and Neeti Sanan-Mishra1* 1 Plant RNAi Biology Group, International Center for Genetic Engineering and Biotechnology, New Delhi-110067 2 Biotechnology Section, ICAR-Indian Institute of Rice Research, Rajendranangar, Hyderabad- 500030 *Corresponding Author: Neeti Sanan-Mishra E-mail address: [email protected] Author e-mail: Abhishek Anand: [email protected] Malathi Pinninti: [email protected] Anita Tripathi: [email protected] Satendra K. Mangrauthia: [email protected] Abstract RNA silencing is as an adaptive immune response in plants that limits accumulation or spread of invading viruses. Successful virus infection entails countering the RNA silencing for efficient replication and systemic spread in the host. The viruses encode proteins having the ability to suppress or block the host silencing mechanism, resulting in severe pathogenic symptoms and diseases. Tungro virus disease caused by a complex of two viruses provides an excellent system to understand these host and virus interactions during infection. It is known that Rice tungro bacilliform virus (RTBV) is the major determinant of the disease while Rice tungro spherical virus (RTSV) accentuates the symptoms. This study brings to focus the important role of RTBV ORF-IV in Tungro disease manifestation, by acting as both the victim and silencer of the RNA silencing pathway. -
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. -
Detection and Characterization of a Novel Marine Birnavirus Isolated from Asian Seabass in Singapore
Chen et al. Virology Journal (2019) 16:71 https://doi.org/10.1186/s12985-019-1174-0 RESEARCH Open Access Detection and characterization of a novel marine birnavirus isolated from Asian seabass in Singapore Jing Chen1†, Xinyu Toh1†, Jasmine Ong1, Yahui Wang1, Xuan-Hui Teo1, Bernett Lee2, Pui-San Wong3, Denyse Khor1, Shin-Min Chong1, Diana Chee1, Alvin Wee1, Yifan Wang1, Mee-Keun Ng1, Boon-Huan Tan3 and Taoqi Huangfu1* Abstract Background: Lates calcarifer, known as seabass in Asia and barramundi in Australia, is a widely farmed species internationally and in Southeast Asia and any disease outbreak will have a great economic impact on the aquaculture industry. Through disease investigation of Asian seabass from a coastal fish farm in 2015 in Singapore, a novel birnavirus named Lates calcarifer Birnavirus (LCBV) was detected and we sought to isolate and characterize the virus through molecular and biochemical methods. Methods: In order to propagate the novel birnavirus LCBV, the virus was inoculated into the Bluegill Fry (BF-2) cell line and similar clinical signs of disease were reproduced in an experimental fish challenge study using the virus isolate. Virus morphology was visualized using transmission electron microscopy (TEM). Biochemical analysis using chloroform and 5-Bromo-2′-deoxyuridine (BUDR) sensitivity assays were employed to characterize the virus. Next-Generation Sequencing (NGS) was also used to obtain the virus genome for genetic and phylogenetic analyses. Results: The LCBV-infected BF-2 cell line showed cytopathic effects such as rounding and granulation of cells, localized cell death and detachment of cells observed at 3 to 5 days’ post-infection. -
Metagenomic Analysis of the Turkey Gut RNA Virus Community J Michael Day1*, Linda L Ballard2, Mary V Duke2, Brian E Scheffler2, Laszlo Zsak1
Day et al. Virology Journal 2010, 7:313 http://www.virologyj.com/content/7/1/313 RESEARCH Open Access Metagenomic analysis of the turkey gut RNA virus community J Michael Day1*, Linda L Ballard2, Mary V Duke2, Brian E Scheffler2, Laszlo Zsak1 Abstract Viral enteric disease is an ongoing economic burden to poultry producers worldwide, and despite considerable research, no single virus has emerged as a likely causative agent and target for prevention and control efforts. Historically, electron microscopy has been used to identify suspect viruses, with many small, round viruses eluding classification based solely on morphology. National and regional surveys using molecular diagnostics have revealed that suspect viruses continuously circulate in United States poultry, with many viruses appearing concomitantly and in healthy birds. High-throughput nucleic acid pyrosequencing is a powerful diagnostic technology capable of determining the full genomic repertoire present in a complex environmental sample. We utilized the Roche/454 Life Sciences GS-FLX platform to compile an RNA virus metagenome from turkey flocks experiencing enteric dis- ease. This approach yielded numerous sequences homologous to viruses in the BLAST nr protein database, many of which have not been described in turkeys. Our analysis of this turkey gut RNA metagenome focuses in particular on the turkey-origin members of the Picornavirales, the Caliciviridae, and the turkey Picobirnaviruses. Introduction remains elusive, and many enteric viruses can be Enteric disease syndromes such as Poult Enteritis Com- detected in otherwise healthy turkey and chicken flocks plex (PEC) in young turkeys and Runting-Stunting Syn- [3,4]. Regional and national enteric virus surveys have drome (RSS) in chickens are a continual economic revealed the ongoing presence of avian reoviruses, rota- burden for poultry producers. -
Data Mining Cdnas Reveals Three New Single Stranded RNA Viruses in Nasonia (Hymenoptera: Pteromalidae)
Insect Molecular Biology Insect Molecular Biology (2010), 19 (Suppl. 1), 99–107 doi: 10.1111/j.1365-2583.2009.00934.x Data mining cDNAs reveals three new single stranded RNA viruses in Nasonia (Hymenoptera: Pteromalidae) D. C. S. G. Oliveira*, W. B. Hunter†, J. Ng*, Small viruses with a positive-sense single-stranded C. A. Desjardins*, P. M. Dang‡ and J. H. Werren* RNA (ssRNA) genome, and no DNA stage, are known as *Department of Biology, University of Rochester, picornaviruses (infecting vertebrates) or picorna-like Rochester, NY, USA; †United States Department of viruses (infecting non-vertebrates). Recently, the order Agriculture, Agricultural Research Service, US Picornavirales was formally characterized to include most, Horticultural Research Laboratory, Fort Pierce, FL, USA; but not all, ssRNA viruses (Le Gall et al., 2008). Among and ‡United States Department of Agriculture, other typical characteristics – e.g. a small icosahedral Agricultural Research Service, NPRU, Dawson, GA, capsid with a pseudo-T = 3 symmetry and a 7–12 kb USA genome made of one or two RNA segments – the Picor- navirales genome encodes a polyprotein with a replication Abstractimb_934 99..108 module that includes a helicase, a protease, and an RNA- dependent RNA polymerase (RdRp), in this order (see Le We report three novel small RNA viruses uncovered Gall et al., 2008 for details). Pathogenicity of the infections from cDNA libraries from parasitoid wasps in the can vary broadly from devastating epidemics to appar- genus Nasonia. The genome of this kind of virus ently persistent commensal infections. Several human Ј is a positive-sense single-stranded RNA with a 3 diseases, from hepatitis A to the common cold (e.g. -
Structure of Nora Virus at 2.7 Å Resolution and Implications for Receptor Binding, Capsid Stability and Taxonomy
This document is downloaded from the VTT’s Research Information Portal https://cris.vtt.fi VTT Technical Research Centre of Finland Structure of Nora virus at 2.7 Å resolution and implications for receptor binding, capsid stability and taxonomy Laurinmäki, Pasi; Shakeel, Shabih; Ekström, Jens Ola; Mohammadi, Pezhman; Hultmark, Dan; Butcher, Sarah J. Published in: Scientific Reports DOI: 10.1038/s41598-020-76613-1 Published: 01/12/2020 Document Version Publisher's final version License CC BY Link to publication Please cite the original version: Laurinmäki, P., Shakeel, S., Ekström, J. O., Mohammadi, P., Hultmark, D., & Butcher, S. J. (2020). Structure of Nora virus at 2.7 Å resolution and implications for receptor binding, capsid stability and taxonomy. Scientific Reports, 10(1), [19675]. https://doi.org/10.1038/s41598-020-76613-1 VTT By using VTT’s Research Information Portal you are bound by the http://www.vtt.fi following Terms & Conditions. P.O. box 1000FI-02044 VTT I have read and I understand the following statement: Finland This document is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of this document is not permitted, except duplication for research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered for sale. Download date: 03. Oct. 2021 www.nature.com/scientificreports OPEN Structure of Nora virus at 2.7 Å resolution and implications for receptor binding, capsid stability and taxonomy Pasi Laurinmäki 1,2,7, Shabih Shakeel 1,2,5,7, Jens‑Ola Ekström3,4,7, Pezhman Mohammadi 1,6, Dan Hultmark 3,4 & Sarah J. -
Classificação Viral
Classificação Viral Microbiologia As primeiras classificações virais se baseavam na capacidade dos vírus de cau- sar infecções e doenças, baseando-se em suas propriedades patogênicas co- muns, tropismo celular dos vírus e características ecológicas de transmissão. Classificação antiga: • Dermatotrópicos: causam doença de pele • Respiratórios: causam doenças do sistema respiratório • Entéricos: causadores de diarréia • Etc A medida em que se ampliou o conhecimento sobre os vírus, principalmente por meio da microscopia eletrônica, essa classificação tornou-se inadequada. A possibilidade de se visualizar características morfológicas dessas partículas, bem como a identificação de sua composição química por meio de técnicas de biologia molecular, permitiu novos critérios de classificação. A criação do comitê internacional de nomenclatura dos vírus em 1966 padroni- zou a classificação e taxonomia viral, com relatórios periódicos. Os atuais crité- rios mais importantes para a classificação dos vírus são: • Hospedeiro • Morfologia da partícula viral • Tipo de ácido nucléico Outros critérios são: tamanho da partícula viral, características físico-químicas, proteínas virais, sintomas da doença, antigenicidade, entre outros. Na taxonomia viral, as famílias e gêneros são definidos monoteticamente, ou seja, todos os membros dessa classe devem apresentar uma ou mais propriedades que são necessárias e suficientes para ser membro daquela classe. As espécies são poliéticas, ou seja, apresentam algumas características em comum (em ge- ral de uma a cinco), -
A STERILE INSECT TECHNIQUE (S.L.T.) STUDY PROJECT to CONTROL MEDFLY in a SOUTHERN REGION of ITALY
ENTE PER LE NUOVE TECNOLOGIE, ISSN/1120-5571 L’ENERGIA E L’AMBIENTE Dipartimento Innovazione OSTI A STERILE INSECT TECHNIQUE (S.l.T.) STUDY PROJECT TO CONTROL MEDFLY IN A SOUTHERN REGION OF ITALY A. TATA, U. CIRIO, R. BALDUCCI ENEA - Dipartimento Innovazione Centro Ricerche Casaccia, Roma STRIBUTON OF THIS DOCUMENT IS UNUWKE FOREIGN SALES PROHIBITED V>T Work presented at the “First International Symposium on Nuclear and related techniques in Agriculture, Industry, Health and Environment (NURT1997) October, 28-30, 1997 - La Habana, Cuba RT/1NN/97/28 ENTE PER LE NUOVE TECNOLOGIE, L'ENERGIA E L'AMBIENTE Dipartimento Innovazione A STERILE INSECT TECHNIQUE (S.I.T.) STUDY PROJECT TO CONTROL MEDFLY IN A SOUTHERN REGION OF ITALY A. TATA, U. CIRIO, R. BALDUCCI ENEA - Dipartimento Innovazione Centro Ricerche Casaccia, Roma Work presented at the “First International Symposium onNuclear and related techniques in Agriculture, Industry, Health and Environment (NURT1997) October, 28-30, 1997 - La Habana, Cuba RT/INN/97/28 Testo pervenuto net dicembre 1997 I contenuti tecnico-scientifici del rapporti tecnici dell'ENEA rispecchiano I'opinione degli autori e non necessariamente quella dell'Ente. DISCLAIMER Portions of this document may be illegible electronic image products. Images are produced from the best available original document. SUMMARY A Sterile Insect Technique (S.I. T.) Study Project to control Medflyin a Southern region of Italy Since 1967 ENEA, namely the main Italian governmental technological research organization, is carrying out R&D programmes and demonstrative projects aimed to set up S.I.T. (Sterile Insect Technique) processes. In the framework of a world-wide growing interest concerning pest control technology, ENEA developed a very large industrial project aimed to control Medfly (Ceratitis capitata Wied.) with reference to fruit crops situation in Sicily region (southern of Italy), through the production and spreading of over 250 million sterile flies per week. -
Viruses Virus Diseases Poaceae(Gramineae)
Viruses and virus diseases of Poaceae (Gramineae) Viruses The Poaceae are one of the most important plant families in terms of the number of species, worldwide distribution, ecosystems and as ingredients of human and animal food. It is not surprising that they support many parasites including and more than 100 severely pathogenic virus species, of which new ones are being virus diseases regularly described. This book results from the contributions of 150 well-known specialists and presents of for the first time an in-depth look at all the viruses (including the retrotransposons) Poaceae(Gramineae) infesting one plant family. Ta xonomic and agronomic descriptions of the Poaceae are presented, followed by data on molecular and biological characteristics of the viruses and descriptions up to species level. Virus diseases of field grasses (barley, maize, rice, rye, sorghum, sugarcane, triticale and wheats), forage, ornamental, aromatic, wild and lawn Gramineae are largely described and illustrated (32 colour plates). A detailed index Sciences de la vie e) of viruses and taxonomic lists will help readers in their search for information. Foreworded by Marc Van Regenmortel, this book is essential for anyone with an interest in plant pathology especially plant virology, entomology, breeding minea and forecasting. Agronomists will also find this book invaluable. ra The book was coordinated by Hervé Lapierre, previously a researcher at the Institut H. Lapierre, P.-A. Signoret, editors National de la Recherche Agronomique (Versailles-France) and Pierre A. Signoret emeritus eae (G professor and formerly head of the plant pathology department at Ecole Nationale Supérieure ac Agronomique (Montpellier-France). Both have worked from the late 1960’s on virus diseases Po of Poaceae . -
Virus Prospecting in Crickets—Discovery and Strain Divergence of a Novel Iflavirus in Wild and Cultivated Acheta Domesticus
viruses Article Virus Prospecting in Crickets—Discovery and Strain Divergence of a Novel Iflavirus in Wild and Cultivated Acheta domesticus Joachim R. de Miranda 1,* , Fredrik Granberg 2 , Piero Onorati 1, Anna Jansson 3 and Åsa Berggren 1 1 Department of Ecology, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden; [email protected] (P.O.); [email protected] (Å.B.) 2 Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden; [email protected] 3 Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, 756 51 Uppsala, Sweden; [email protected] * Correspondence: [email protected]; Tel.: +46-18-672437 Abstract: Orthopteran insects have high reproductive rates leading to boom-bust population dy- namics with high local densities that are ideal for short, episodic disease epidemics. Viruses are particularly well suited for such host population dynamics, due to their supreme ability to adapt to changing transmission criteria. However, very little is known about the viruses of Orthopteran insects. Since Orthopterans are increasingly reared commercially, for animal feed and human consumption, there is a risk that viruses naturally associated with these insects can adapt to commercial rearing conditions, and cause disease. We therefore explored the virome of the house cricket Acheta domesti- cus, which is both part of the natural Swedish landscape and reared commercially for the pet feed market. Only 1% of the faecal RNA and DNA from wild-caught A. domesticus consisted of viruses. Citation: de Miranda, J.R.; Granberg, These included both known and novel viruses associated with crickets/insects, their bacterial-fungal F.; Onorati, P.; Jansson, A.; Berggren, Å. -
THE USE of IONIZING RADIATION to IMPROVE REGIONAL FRUIT PRODUCTION and EXPORTS THROUGH MEDITERRANEAN FRUIT FLY PEST CONTROL Pedro A
PANEL ON THE SUSTAINABLE USE OF RADIOACTIVE SOURCES FOR AGRICULTURE, FOOD SECURITY AND HEALTH. IAEA THE USE OF IONIZING RADIATION TO IMPROVE REGIONAL FRUIT PRODUCTION AND EXPORTS THROUGH MEDITERRANEAN FRUIT FLY PEST CONTROL Pedro A. Rendón VIENNA, AUGUST, 21st - 2018 INSECT INFESTATIONS – ARTHROPOD INVASIONS INTERNATIONAL TRADE AND GLOBAL WARMING. Are two main phenomena leading increased frequency of introductions of the costliest insect invaders (1). RISING HUMAN POPULATIONS, movement, migration, wealth and international trade, favor Invasions expansions (1). CLIMATE CHANGE PROJECTIONS TO 2050 predict an average increase of 18% in the area of occurrence of current arthropod invaders (1). INVASIVE INSECTS COST A MINIMUM OF US$70.0 BILLION/YEAR globally for goods and services (1). Insect Infestations are a reality and a concern! FRUIT FLY INTRODUCTIONS IN THE AMERICAS Olive Fruit Fly California, 1998 Caribbean Fruit Fly Florida, 1965 Mediterranean fruit Fly DR, 2015 Mediterranean fruit Fly Carambola Fruit Fly Costa Rica, 1955, GT, 1975 Surinam, 1975 Efforts have been made to stop the spread of the pest and avoid Mediterranean Fruit Fly production and market losses of the Brazil, 1901; Peru, 1956 CHILE, countries involved, by forming a tri- 1963. national commission U.S., MEXICO AND GUATEMALA, the REGIONAL PROGRAMA MOSCAMED to stop the northward movement of the pest. The ‘triple burden’ of malnutrition The WHO is promoting fresh fruit / vegetable Overweight consumption; the Under and obesity demand is nutrition growing. 400 – 600 grams of fruit & vegetables/day. Micronutrient deficiencies USE OF IONIZING RADIATION FOR PEST CONTROL *Photo from (2) Ionizing radiation and the Sterile Insect Technique (SIT) have been used since then for pest control and has allowed successful eradication efforts NEW WORLD SCREWWORM (Cochliomyia hominovorax, Coquerel) eradicated from the United States, Mexico, Central America and Libya.