Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA)
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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. -
Heartland and Bourbon Virus Testing Guideance for Healthcare Providers
Heartland and Bourbon Virus Testing Guidance for Healthcare Providers Heartland virus is an RNA virus believed to be transmitted by the Lone Star tick (Amblyomma americanum). Most patients reported tick exposure in the two weeks prior to illness onset. While no cases have been reported in Louisiana, this tick is found in Louisiana. First discovered as a cause of human illness in 2009 in Missouri, more than 40 cases have been reported from states in Midwestern and southern U.S. to date. Initial symptoms of Heartland virus disease are very similar to those of ehrlichiosis or anaplasmosis, which include fever, fatigue, anorexia, nausea and diarrhea. Cases have also had leukopenia, thrombocytopenia, and mild to moderate elevation of liver transaminases. Heartland virus disease should be considered in patients being treated for ehrlichiosis who do not respond to treatment with doxycycline. For several years, CDC has been working under IRB-approved protocols to identify additional cases and validate diagnostic test for several novel pathogens. Now the CDC Arboviral Diseases Branch offers routine diagnostic testing for Heartland and Bourbon viruses (RT-PCR, IgM and IgG MIA, PRNT). There is no commercial testing available. Treatment of Heartland virus disease is supportive only. Many patients diagnosed with the disease have required hospitalization. With supportive care, most people have fully recovered; however, a few older individuals with medical comorbidities have died. The best way to prevent Heartland virus infection is to avoid exposure -
Genome Sequencing by Random Priming Methods for Viral Identification
Genome sequencing by random priming methods for viral identification Rosseel Toon Dissertation submitted in fulfillment of the requirements for the degree of Doctor of Philosophy (PhD) in Veterinary Sciences, Faculty of Veterinary Medicine, Ghent University, 2015 Promotors: Dr. Steven Van Borm Prof. Dr. Hans Nauwynck “The real voyage of discovery consist not in seeking new landscapes, but in having new eyes” Marcel Proust, French writer, 1923 Table of contents Table of contents ....................................................................................................................... 1 List of abbreviations ................................................................................................................. 3 Chapter 1 General introduction ................................................................................................ 5 1. Viral diagnostics and genomics ....................................................................................... 7 2. The DNA sequencing revolution ................................................................................... 12 2.1. Classical Sanger sequencing .................................................................................. 12 2.2. Next-generation sequencing ................................................................................... 16 3. The viral metagenomic workflow ................................................................................. 24 3.1. Sample preparation ............................................................................................... -
Generic Amplification and Next Generation Sequencing Reveal
Dinçer et al. Parasites & Vectors (2017) 10:335 DOI 10.1186/s13071-017-2279-1 RESEARCH Open Access Generic amplification and next generation sequencing reveal Crimean-Congo hemorrhagic fever virus AP92-like strain and distinct tick phleboviruses in Anatolia, Turkey Ender Dinçer1†, Annika Brinkmann2†, Olcay Hekimoğlu3, Sabri Hacıoğlu4, Katalin Földes4, Zeynep Karapınar5, Pelin Fatoş Polat6, Bekir Oğuz5, Özlem Orunç Kılınç7, Peter Hagedorn2, Nurdan Özer3, Aykut Özkul4, Andreas Nitsche2 and Koray Ergünay2,8* Abstract Background: Ticks are involved with the transmission of several viruses with significant health impact. As incidences of tick-borne viral infections are rising, several novel and divergent tick- associated viruses have recently been documented to exist and circulate worldwide. This study was performed as a cross-sectional screening for all major tick-borne viruses in several regions in Turkey. Next generation sequencing (NGS) was employed for virus genome characterization. Ticks were collected at 43 locations in 14 provinces across the Aegean, Thrace, Mediterranean, Black Sea, central, southern and eastern regions of Anatolia during 2014–2016. Following morphological identification, ticks were pooled and analysed via generic nucleic acid amplification of the viruses belonging to the genera Flavivirus, Nairovirus and Phlebovirus of the families Flaviviridae and Bunyaviridae, followed by sequencing and NGS in selected specimens. Results: A total of 814 specimens, comprising 13 tick species, were collected and evaluated in 187 pools. Nairovirus and phlebovirus assays were positive in 6 (3.2%) and 48 (25.6%) pools. All nairovirus sequences were closely-related to the Crimean-Congo hemorrhagic fever virus (CCHFV) strain AP92 and formed a phylogenetically distinct cluster among related strains. -
2020 Taxonomic Update for Phylum Negarnaviricota (Riboviria: Orthornavirae), Including the Large Orders Bunyavirales and Mononegavirales
Archives of Virology https://doi.org/10.1007/s00705-020-04731-2 VIROLOGY DIVISION NEWS 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales Jens H. Kuhn1 · Scott Adkins2 · Daniela Alioto3 · Sergey V. Alkhovsky4 · Gaya K. Amarasinghe5 · Simon J. Anthony6,7 · Tatjana Avšič‑Županc8 · María A. Ayllón9,10 · Justin Bahl11 · Anne Balkema‑Buschmann12 · Matthew J. Ballinger13 · Tomáš Bartonička14 · Christopher Basler15 · Sina Bavari16 · Martin Beer17 · Dennis A. Bente18 · Éric Bergeron19 · Brian H. Bird20 · Carol Blair21 · Kim R. Blasdell22 · Steven B. Bradfute23 · Rachel Breyta24 · Thomas Briese25 · Paul A. Brown26 · Ursula J. Buchholz27 · Michael J. Buchmeier28 · Alexander Bukreyev18,29 · Felicity Burt30 · Nihal Buzkan31 · Charles H. Calisher32 · Mengji Cao33,34 · Inmaculada Casas35 · John Chamberlain36 · Kartik Chandran37 · Rémi N. Charrel38 · Biao Chen39 · Michela Chiumenti40 · Il‑Ryong Choi41 · J. Christopher S. Clegg42 · Ian Crozier43 · John V. da Graça44 · Elena Dal Bó45 · Alberto M. R. Dávila46 · Juan Carlos de la Torre47 · Xavier de Lamballerie38 · Rik L. de Swart48 · Patrick L. Di Bello49 · Nicholas Di Paola50 · Francesco Di Serio40 · Ralf G. Dietzgen51 · Michele Digiaro52 · Valerian V. Dolja53 · Olga Dolnik54 · Michael A. Drebot55 · Jan Felix Drexler56 · Ralf Dürrwald57 · Lucie Dufkova58 · William G. Dundon59 · W. Paul Duprex60 · John M. Dye50 · Andrew J. Easton61 · Hideki Ebihara62 · Toufc Elbeaino63 · Koray Ergünay64 · Jorlan Fernandes195 · Anthony R. Fooks65 · Pierre B. H. Formenty66 · Leonie F. Forth17 · Ron A. M. Fouchier48 · Juliana Freitas‑Astúa67 · Selma Gago‑Zachert68,69 · George Fú Gāo70 · María Laura García71 · Adolfo García‑Sastre72 · Aura R. Garrison50 · Aiah Gbakima73 · Tracey Goldstein74 · Jean‑Paul J. Gonzalez75,76 · Anthony Grifths77 · Martin H. Groschup12 · Stephan Günther78 · Alexandro Guterres195 · Roy A. -
Rapid Identification of Known and New RNA Viruses from Animal Tissues
Rapid Identification of Known and New RNA Viruses from Animal Tissues Joseph G. Victoria1,2*, Amit Kapoor1,2, Kent Dupuis3, David P. Schnurr3, Eric L. Delwart1,2 1 Department of Molecular Virology, Blood Systems Research Institute, San Francisco, California, United States of America, 2 Department of Laboratory Medicine, University of California, San Francisco, California, United States of America, 3 Viral and Rickettsial Disease Laboratory, Division of Communicable Disease Control, California State Department of Public Health, Richmond, California, United States of America Abstract Viral surveillance programs or diagnostic labs occasionally obtain infectious samples that fail to be typed by available cell culture, serological, or nucleic acid tests. Five such samples, originating from insect pools, skunk brain, human feces and sewer effluent, collected between 1955 and 1980, resulted in pathology when inoculated into suckling mice. In this study, sequence-independent amplification of partially purified viral nucleic acids and small scale shotgun sequencing was used on mouse brain and muscle tissues. A single viral agent was identified in each sample. For each virus, between 16% to 57% of the viral genome was acquired by sequencing only 42–108 plasmid inserts. Viruses derived from human feces or sewer effluent belonged to the Picornaviridae family and showed between 80% to 91% amino acid identities to known picornaviruses. The complete polyprotein sequence of one virus showed strong similarity to a simian picornavirus sequence in the provisional Sapelovirus genus. Insects and skunk derived viral sequences exhibited amino acid identities ranging from 25% to 98% to the segmented genomes of viruses within the Reoviridae family. Two isolates were highly divergent: one is potentially a new species within the orthoreovirus genus, and the other is a new species within the orbivirus genus. -
Investigating the Role of Host TTR-Rbps During SFV4 and MHV-68 Infection
Investigating the role of host TTR-RBPs during SFV4 and MHV-68 infection Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Jamie Casswell October 2019 Contents Figure Contents Page……………………………………………………………………………………7 Table Contents Page…………………………………………………………………………………….9 Acknowledgements……………………………………………………………………………………10 Abbreviations…………………………………………………………………………………………….11 Abstract……………………………………………………………………………………………………..17 1. Chapter 1 Introduction……………………………………………………………………………19 1.1 DNA and RNA viruses ............................................................................. 20 1.2 Taxonomy of eukaryotic viruses ............................................................. 21 1.3 Arboviruses ............................................................................................ 22 1.4 Togaviridae ............................................................................................ 22 1.4.1 Alphaviruses ............................................................................................................................. 23 1.4.1.1 Semliki Forest Virus ........................................................................................................... 25 1.4.1.2 Alphavirus virion structure and structural proteins ......................................................... 26 1.4.1.3 Alphavirus non-structural proteins ................................................................................... 29 1.4.1.4 Alphavirus genome organisation -
Construção E Aplicação De Hmms De Perfil Para a Detecção E Classificação De Vírus
UNIVERSIDADE DE SÃO PAULO PROGRAMA INTERUNIDADES DE PÓS-GRADUAÇÃO EM BIOINFORMÁTICA Construção e Aplicação de HMMs de Perfil para a Detecção e Classificação de Vírus Miriã Nunes Guimarães SÃO PAULO 2019 Construção e Aplicação de HMMs de Perfil para a Detecção e Classificação de Vírus Miriã Nunes Guimarães Dissertação apresentada à Universidade de São Paulo, como parte das exigências do Programa de Pós-Graduação Interunidades em Bioinformática, para obtenção do título de Mestre em Ciências. Área de Concentração: Bioinformática Orientador: Prof. Dr. Arthur Gruber SÃO PAULO 2019 “Na vida, não existe nada a temer, mas a entender.” Marie Curie Agradecimentos Ao Professor Arthur Gruber pela oportunidade desde o início como estagiária no laboratório, pela orientação neste período de aprendizado no mestrado e por fornecer um ambiente de trabalho favorável. À aluna de doutorado Liliane Santana Oliveira que aguentou todas as minhas amolações diárias no laboratório pelo Hangouts, por dúvidas que eram erros meus em comandos de execução, pela paciência, pela amizade, pela companhia nos bandejões da faculdade com cardápio glutenfree que nem sempre eram tão bons assim. À aluna de mestrado Irina Yuri Kawashima que estava comigo no laboratório diariamente, pelas várias discussões sobre o mundo dos vírus e de conhecimentos da bioinformática, pelas ferramentas para facilitar o andamento do projeto, por todas guloseimas glutenfree que seria impossível eu não agradecer pois tenho ciência que não vou encontrar outra amiga masterchef assim. À Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) pelo financiamento durante estes 24 meses de mestrado. Aos meus pais pelo carinho e preocupação comigo durante estes 24 anos, pelo incentivo aos estudos e pelo apoio para eu me manter a uma distância de quase 400km de pura saudade. -
Tick-Borne Disease Working Group 2020 Report to Congress
2nd Report Supported by the U.S. Department of Health and Human Services • Office of the Assistant Secretary for Health Tick-Borne Disease Working Group 2020 Report to Congress Information and opinions in this report do not necessarily reflect the opinions of each member of the Working Group, the U.S. Department of Health and Human Services, or any other component of the Federal government. Table of Contents Executive Summary . .1 Chapter 4: Clinical Manifestations, Appendices . 114 Diagnosis, and Diagnostics . 28 Chapter 1: Background . 4 Appendix A. Tick-Borne Disease Congressional Action ................. 8 Chapter 5: Causes, Pathogenesis, Working Group .....................114 and Pathophysiology . 44 The Tick-Borne Disease Working Group . 8 Appendix B. Tick-Borne Disease Working Chapter 6: Treatment . 51 Group Subcommittees ...............117 Second Report: Focus and Structure . 8 Chapter 7: Clinician and Public Appendix C. Acronyms and Abbreviations 126 Chapter 2: Methods of the Education, Patient Access Working Group . .10 to Care . 59 Appendix D. 21st Century Cures Act ...128 Topic Development Briefs ............ 10 Chapter 8: Epidemiology and Appendix E. Working Group Charter. .131 Surveillance . 84 Subcommittees ..................... 10 Chapter 9: Federal Inventory . 93 Appendix F. Federal Inventory Survey . 136 Federal Inventory ....................11 Chapter 10: Public Input . 98 Appendix G. References .............149 Minority Responses ................. 13 Chapter 11: Looking Forward . .103 Chapter 3: Tick Biology, Conclusion . 112 Ecology, and Control . .14 Contributions U.S. Department of Health and Human Services James J. Berger, MS, MT(ASCP), SBB B. Kaye Hayes, MPA Working Group Members David Hughes Walker, MD (Co-Chair) Adalbeto Pérez de León, DVM, MS, PhD Leigh Ann Soltysiak, MS (Co-Chair) Kevin R. -
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. -
Genetic Characterization, Molecular Epidemiology, and Phylogenetic MARK Relationships of Insect-Specific Viruses in the Taxon Negevirus
Virology 504 (2017) 152–167 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Genetic characterization, molecular epidemiology, and phylogenetic MARK relationships of insect-specific viruses in the taxon Negevirus Marcio R.T. Nunesa, María Angélica Contreras-Gutierrezb,c, Hilda Guzmand,e,f, Livia C. Martinsf, Mayla Feitoza Barbiratog, Chelsea Savith, Victoria Baltai, Sandra Uribec, Rafael Viverob,c, Juan David Suazab,c, Hamilton Oliveiraf, Joaquin P. Nunes Netof, Valeria L. Carvalhog, Sandro Patroca da Silvaa, Jedson F. Cardosoa, Rodrigo Santo de Oliveiraa, Poliana da Silva Lemosf, Thomas G. Woodj, Steven G. Widenj, Pedro F.C. Vasconcelosf, Durland Fishk, ⁎ ⁎ Nikos Vasilakisd,e,f, , Robert B. Teshd,e,f, a Center for Technological Innovation, Evandro Chagas Institute, Ministry of Health, Ananindeua, Para, Brazil b Programa de Estudio y Control de Enfermedades Tropicales – PECET - SIU-Sede de Investigación Universitaria – Universidad de Antioquia, Medellín, Colombia c Grupo de Investigación en Sistemática Molecular-GSM, Facultad de Ciencias,Ciencias, Universidad Nacional de Colombia, sede Medellín, Medellín, Colombia d Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States e Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, United States f Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ministry of Health, Ananindeua, -
Possible Insights Into the Use of Silver Nanoparticles in Targeting SARS-Cov-2 (COVID-19)
Review Article Possible Insights into the Use of Silver Nanoparticles in Targeting SARS-CoV-2 (COVID-19) Abhinav Raj Ghosh, Bhooshitha AN, Chandan HM, KL Krishna* Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, Karnataka, INDIA. ABSTRACT Aim: The aims of this review are to assess the anti-viral and targeting strategies using nano materials and the possibility of using Silver nanoparticles for combating the SARS-CoV-2. Background: The novel Coronavirus (SARS-CoV-2) has become a global pandemic and has spread rapidly worldwide. Researchers have successfully identified the molecular structure of the novel coronavirus however significant success has not yet been observed with the therapies currently in clinical trials and exhaustive studies are yet to be carried out in the long road to discovery of a vaccine or a possible cure. Another hurdle associated with the discovery of a cure is the mutation of this virus which may occur at any point in time. Hypothesis: Previous studies have identified a wide number of strains of Coronaviruses with differences in virulent properties. Silver nanoparticles have been used extensively in anti-viral research with promising results in-vitro. However, it has not yet been tested for the same in clinical subjects. It has also been tested on two variants of coronavirus in-vitro with significant data to understand the pathogenesis and which may be implemented in further research possibly in other variants of coronavirus. Another interesting targeting approach would be to test the effect of Silver Nanoparticles on TNF-α as well as Interleukins in SARS-CoV-2 patients.