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Entwicklung Einer Software Zur Identifizierung Neuartiger Und
Entwicklung einer Software zur Identifizierung neuartiger und bekannter Infektionserreger in klinischen Proben Dissertation zur Erlangung des Doktorgrades an der Fakult¨at fur¨ Mathematik, Informatik und Naturwissenschaften Fachbereich Biologie der Universit¨at Hamburg vorgelegt von Malik Alawi Hamburg, 2020 Vorsitzender der Prufungskommission¨ Dr. PD Andreas Pommerening-R¨oser Gutachter Professor Dr. Adam Grundhoff Professor Dr. Stefan Kurtz Datum der Disputation 30. April 2021 Abstract Sequencing of diagnostic samples is widely considered a key technology that may fun- damentally improve infectious disease diagnostics. The approach can not only identify pathogens already known to cause a specific disease, but may also detect pathogens that have not been previously attributed to this disease, as well as completely new, previously unknown pathogens. Therefore, it may significantly increase the level of preparedness for future outbreaks of emerging pathogens. This study describes the development and application of methods for the identification of pathogenic agents in diagnostic samples. The methods have been successfully applied multiple times under clinical conditions. The corresponding results have been published within the scope of this thesis. Finally, the methods were made available to the scientific community as an open source bioinformatics tool. The novel software was validated by conventional diagnostic methods and it was compared to established analysis pipelines using authentic clinical samples. It is able to identify pathogens from different diagnostic entities and often classifies viral agents down to strain level. Furthermore, the method is capable of assembling complete viral genomes, even from samples containing multiple closely related viral strains of the same viral family. In addition to an improved method for taxonomic classification, the software offers functionality which is not present in established analysis pipelines. -
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. -
A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies
www.nature.com/scientificreports OPEN Kanyawara Virus: A Novel Rhabdovirus Infecting Newly Discovered Nycteribiid Bat Flies Received: 19 April 2017 Accepted: 25 May 2017 Infesting Previously Unknown Published: xx xx xxxx Pteropodid Bats in Uganda Tony L. Goldberg 1,2,3, Andrew J. Bennett1, Robert Kityo3, Jens H. Kuhn4 & Colin A. Chapman3,5 Bats are natural reservoir hosts of highly virulent pathogens such as Marburg virus, Nipah virus, and SARS coronavirus. However, little is known about the role of bat ectoparasites in transmitting and maintaining such viruses. The intricate relationship between bats and their ectoparasites suggests that ectoparasites might serve as viral vectors, but evidence to date is scant. Bat flies, in particular, are highly specialized obligate hematophagous ectoparasites that incidentally bite humans. Using next- generation sequencing, we discovered a novel ledantevirus (mononegaviral family Rhabdoviridae, genus Ledantevirus) in nycteribiid bat flies infesting pteropodid bats in western Uganda. Mitochondrial DNA analyses revealed that both the bat flies and their bat hosts belong to putative new species. The coding-complete genome of the new virus, named Kanyawara virus (KYAV), is only distantly related to that of its closest known relative, Mount Elgon bat virus, and was found at high titers in bat flies but not in blood or on mucosal surfaces of host bats. Viral genome analysis indicates unusually low CpG dinucleotide depletion in KYAV compared to other ledanteviruses and rhabdovirus groups, with KYAV displaying values similar to rhabdoviruses of arthropods. Our findings highlight the possibility of a yet- to-be-discovered diversity of potentially pathogenic viruses in bat ectoparasites. Bats (order Chiroptera) represent the second largest order of mammals after rodents (order Rodentia). -
Viruses 2015, 7, 456-479; Doi:10.3390/V7020456 OPEN ACCESS
Viruses 2015, 7, 456-479; doi:10.3390/v7020456 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Article In Search of Pathogens: Transcriptome-Based Identification of Viral Sequences from the Pine Processionary Moth (Thaumetopoea pityocampa) Agata K. Jakubowska 1, Remziye Nalcacioglu 2, Anabel Millán-Leiva 3, Alejandro Sanz-Carbonell 1, Hacer Muratoglu 4, Salvador Herrero 1,* and Zihni Demirbag 2,* 1 Department of Genetics, Universitat de València, Dr Moliner 50, 46100 Burjassot, Spain; E-Mails: [email protected] (A.K.J.); [email protected] (A.S.-C.) 2 Department of Biology, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey; E-Mail: [email protected] 3 Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental “La Mayora”, Algarrobo-Costa, 29750 Málaga, Spain; E-Mail: [email protected] 4 Department of Molecular Biology and Genetics, Faculty of Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey; E-Mail: [email protected] * Authors to whom correspondence should be addressed; E-Mails: [email protected] (S.H.); [email protected] (Z.D.); Tel.: +34-96-354-3006 (S.H.); +90-462-377-3320 (Z.D.); Fax: +34-96-354-3029 (S.H.); +90-462-325-3195 (Z.D.). Academic Editors: John Burand and Madoka Nakai Received: 29 November 2014 / Accepted: 13 January 2015 / Published: 23 January 2015 Abstract: Thaumetopoea pityocampa (pine processionary moth) is one of the most important pine pests in the forests of Mediterranean countries, Central Europe, the Middle East and North Africa. Apart from causing significant damage to pinewoods, T. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID-19 Pandemic: a Repo
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. November 2020 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Paul Allison, Faculty of Dentistry, McGill University Raphael Freitas de Souza, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University November 30th, 2020 1 Contents Page Introduction 3 Project goal and specific objectives 3 Methods used to identify and include relevant literature 4 Report structure 5 Summary of update report 5 Report results a) Which patients are at greater risk of the consequences of COVID-19 and so 7 consideration should be given to delaying elective in-person oral health care? b) What are the signs and symptoms of COVID-19 that oral health professionals 9 should screen for prior to providing in-person health care? c) What evidence exists to support patient scheduling, waiting and other non- treatment management measures for in-person oral health care? 10 d) What evidence exists to support the use of various forms of personal protective equipment (PPE) while providing in-person oral health care? 13 e) What evidence exists to support the decontamination and re-use of PPE? 15 f) What evidence exists concerning the provision of aerosol-generating 16 procedures (AGP) as part of in-person -
Biosafety in Microbiological and Biomedical Laboratories—6Th Edition
Section VIII—Agent Summary Statements The agent summary statements contained in Section VIII of the sixth edition of Biosafety in Microbiological and Biomedical Laboratories (BMBL) are designed to assist the reader with the risk assessment for their work, as directed in Section II. The statements are assembled by subject matter experts and represent a summary of key information regarding pathogens with significance to the biomedical community. Although the statements provide recommendations regarding containment for specific activities, they should serve only as the starting point for a laboratory’s risk assessment and should not serve as a substitute for an assessment. The statements cannot fully factor in the change in risk due to the size of a sample, concentration of agent present, change in virulence or pathogenicity, nor any change in ability to provide medical countermeasures due to antibiotic or antiviral resistance. The following list of agents is also not comprehensive, and the reader is directed to other information to assist in the risk assessment, including the Public Health Agency of Canada’s Pathogen Safety Data Sheets (PSDS),1 the American Public Health Association’s Control of Communicable Diseases Manual,2 American Society for Microbiology Manual of Clinical Microbiology,3 and the ABSA Interna- tional Risk Group Database.4 References 1. Government of Canada [Internet]. Canada: Public Health Agency of Canada; c2018 [cited 2018 Dec 20]. Pathogen Safety Data Sheets. Available from: https://www.canada.ca/en/public-health/services/laboratory- biosafety-biosecurity/pathogen-safety-data-sheets-risk-assessment.html 2. Heymann DL, editor. Control of Communicable Diseases Manual. 20th ed. -
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Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Stremlau, M. H., K. G. Andersen, O. A. Folarin, J. N. Grove, I. Odia, P. E. Ehiane, O. Omoniwa, et al. 2015. “Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa.” PLoS Neglected Tropical Diseases 9 (3): e0003631. doi:10.1371/journal.pntd.0003631. http://dx.doi.org/10.1371/ journal.pntd.0003631. Published Version doi:10.1371/journal.pntd.0003631 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:14351060 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA RESEARCH ARTICLE Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa Matthew H. Stremlau1,2☯*, Kristian G. Andersen1,2☯*, Onikepe A. Folarin3,4, Jessica N. Grove5, Ikponmwonsa Odia3, Philomena E. Ehiane3, Omowunmi Omoniwa3, Omigie Omoregie3, Pan-Pan Jiang1,2, Nathan L. Yozwiak1,2, Christian B. Matranga2, Xiao Yang2, Stephen K. Gire1,2, Sarah Winnicki1,2, Ridhi Tariyal2, Stephen F. Schaffner2, Peter O. Okokhere3, Sylvanus Okogbenin3, George O. Akpede3, Danny A. Asogun3, Dennis E. Agbonlahor6, Peter J. Walker7, Robert B. Tesh8, Joshua Z. Levin2, Robert F. Garry5, Pardis C. Sabeti1,2,9‡*, Christian -
Biosafety in Microbiological and Biomedical Laboratories—6Th Edition
Section VIII-A: Bacterial Agents Bacillus anthracis Bacillus anthracis, a Gram-positive, non-hemolytic, and non-motile bacillus, is the etiologic agent of anthrax, an acute bacterial disease among wild and domestic mammals, including humans. Like all members of the genus Bacillus, under adverse conditions, B. anthracis has the ability to produce spores that allow the organism to persist for long periods (i.e., years), withstanding heat and drying, until the return of more favorable conditions for vegetative growth.1 It is because of this ability to produce spores coupled with significant pathogenic potential in humans that this organism is considered one of the most serious and threatening biowarfare or bioterrorism agents.2 Most mammals are susceptible to anthrax; it mostly affects herbivores that ingest spores from contaminated soil and, to a lesser extent, carnivores that scavenge on the carcasses of diseased animals. In the United States, it occurs sporadically in animals in parts of the West, Midwest, and Southwest. Human case rates for anthrax are highest in Africa and central and southern Asia.3 The infectious dose varies greatly from species to species and is route-dependent. The inhalation anthrax infectious dose (ID) for humans has been primarily extrapolated from inhalation challenges of non-human primates (NHPs) or studies done in contaminated wool mills. Estimates vary greatly but the median lethal dose (LD50) is likely within the range of 2,500–55,000 spores.4 It is believed that very few spores (ten or fewer) are required for cutaneous anthrax infection.5 Anthrax cases have been rare in the United States since the first half of the 20th century. -
Evidence to Support Safe Return to Clinical Practice by Oral Health Professionals in Canada During the COVID- 19 Pandemic: A
Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID- 19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. March 2021 update This evidence synthesis was prepared for the Office of the Chief Dental Officer, based on a comprehensive review under contract by the following: Raphael Freitas de Souza, Faculty of Dentistry, McGill University Paul Allison, Faculty of Dentistry, McGill University Lilian Aboud, Faculty of Dentistry, McGill University Martin Morris, Library, McGill University March 31, 2021 1 Contents Evidence to support safe return to clinical practice by oral health professionals in Canada during the COVID-19 pandemic: A report prepared for the Office of the Chief Dental Officer of Canada. .................................................................................................................................. 1 Foreword to the second update ............................................................................................. 4 Introduction ............................................................................................................................. 5 Project goal............................................................................................................................. 5 Specific objectives .................................................................................................................. 6 Methods used to identify and include relevant literature ...................................................... -
Patogenicidad Microbiana En Medicina Veterinaria Volumen: Virología
Patogenicidad microbiana en Medicina Veterinaria Volumen: Virología Fabiana A. Moredo, Alejandra E. Larsen, Nestor O. Stanchi (Coordinadores) FACULTAD DE CIENCIAS VETERINARIAS PATOGENICIDAD MICROBIANA EN MEDICINA VETERINARIA VOLUMEN: VIROLOGÍA Fabiana A. Moredo Alejandra E. Larsen Nestor O. Stanchi (Coordinadores) Facultad de Ciencias Veterinarias 1 A nuestras familias 2 Agradecimientos Nuestro agradecimiento a todos los colegas docentes de la Facultad de Ciencias Veterinarias y en especial a la Universidad Nacional de La Plata por darnos esta oportunidad. 3 Índice VOLUMEN 2 Virología Capítulo 1 Características generales de los virus Cecilia M. Galosi, Nadia A. Fuentealba____________________________________________6 Capítulo 2 Arterivirus Germán E. Metz y María M. Abeyá______________________________________________28 Capítulo 3 Herpesvirus Cecilia M. Galosi, María E. Bravi, Mariela R. Scrochi ________________________________37 Capítulo 4 Orthomixovirus Guillermo H. Sguazza y María E. Bravi___________________________________________49 Capítulo 5 Paramixovirus Marco A. Tizzano____________________________________________________________61 Capítulo 6 Parvovirus Nadia A Fuentealba, María S. Serena____________________________________________71 Capítulo 7 Retrovirus Carlos J. Panei, Viviana Cid de la Paz____________________________________________81 Capítulo 8 Rhabdovirus Marcelo R. Pecoraro, Leandro Picotto____________________________________________92 Capítulo 9 Togavirus María G. Echeverría, María Laura Susevich______________________________________104 -
Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA)
viruses Review Electron Microscopy in Discovery of Novel and Emerging Viruses from the Collection of the World Reference Center for Emerging Viruses and Arboviruses (WRCEVA) Vsevolod L. Popov 1,2,3,4,5,*, Robert B. Tesh 1,2,3,4,5, Scott C. Weaver 2,3,4,5,6 and Nikos Vasilakis 1,2,3,4,5,* 1 Department of Pathology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; [email protected] 2 Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA; [email protected] 3 Institute for Human Infection and Immunity, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA 4 Center for Tropical Diseases, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA 5 World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA 6 Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA * Correspondence: [email protected] (V.L.P.); [email protected] (N.V.); Tel.: +1-409-747-2423 (V.L.P.); +1-409-747-0650 (N.V.) Received: 30 April 2019; Accepted: 24 May 2019; Published: 25 May 2019 Abstract: Since the beginning of modern virology in the 1950s, transmission electron microscopy (TEM) has been an important and widely used technique for discovery, identification and characterization of new viruses. Using TEM, viruses can be differentiated by their ultrastructure: shape, size, intracellular location and for some viruses, by the ultrastructural cytopathic effects and/or specific structures forming in the host cell during their replication. -
Using Label Free Proteomics and RNA Sequencing to Investigate the Human Respiratory Syncytial Virus and the Effects of the Antiviral Ribavirin
Using label free proteomics and RNA sequencing to investigate the human respiratory syncytial virus and the effects of the antiviral ribavirin Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Waleed A. Aljabr November 2016 i AUTHOR’S DECLARATION Apart from the help and advice acknowledged, this thesis represents the unaided work of the author ………………………………………………. Waleed Abdurhaman Suliman Aljabr November 2016 This research was carried out in the Department of Infection Biology and Institute of Infection and Global Health, University of Liverpool ii DEDICATION I dedicate this work to my parents who pray me constantly and inspire me. A dedication also goes to my brothers, sisters and my daughters (Leen, Almas and Yara) and my son (Luay) who were always encouraging and supportive throughout my PhD. Finally, special thanks go to my wife (Amal) for her encouragement and support during this time and for looking after my children. iii ACKNOWLEDGEMENTS In the name of Allah, the Most Gracious, the Most Merciful. All Thanks to Allah the Creator of the universe and the mastermind of everything. I would like to express my sincere gratitude to my supervisor Prof Julian Hiscox for the continuous support of my PhD study and research, for his motivation, enthusiasm, patience and wide knowledge. This work would not have been possible without the help and support of my principle supervisor. Very special thanks to my second supervisor Prof James Stuart for his support and encouragement. I am also indebted to my PhD advisors, Prof Stuart Carter and Dr Jane Hodgkinson who have been invaluable on both an academic and a personal level, for which I am extremely grateful.