Virosaurus a Reference to Explore and Capture Virus Genetic Diversity
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Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment
medRxiv preprint doi: https://doi.org/10.1101/19013763; this version posted December 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . 1 Host genomics of the HIV-1 reservoir size and its decay rate during 2 suppressive antiretroviral treatment 3 4 Christian W. Thorball1,*, Alessandro Borghesi1,2,*, Nadine Bachmann3,4, Chantal von 5 Siebenthal3.4, Valentina Vongrad3,4, Teja Turk3,4, Kathrin Neumann3,4, Niko Beerenwinkel5,6, 6 Jasmina Bogojeska7, Volker Roth8, Yik Lim Kok3,4, Sonali Parbhoo8,9, Mario Wieser8, Jürg 7 Böni4, Matthieu Perreau10, Thomas Klimkait11, Sabine Yerly12, Manuel Battegay13, Andri 8 Rauch14, Patrick Schmid15, Enos Bernasconi16, Matthias Cavassini17, Roger D. Kouyos3,4, 9 Huldrych F. Günthard3,4, Karin J. Metzner3,4, Jacques Fellay1,18,§ and the Swiss HIV Cohort 10 Study 11 12 1 School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland 13 2 Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy. 14 3 Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 15 Zurich, Switzerland. 16 4 Institute of Medical Virology, University of Zurich, Zurich, Switzerland. 17 5 Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. 18 6 SIB Swiss Institute of Bioinformatics, Basel, Switzerland. 19 7 IBM Research - Zurich, Rüschlikon, Switzerland. 20 8 Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland. 21 9 Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, 22 Cambridge, MA, USA. -
Regulation of Hematopoietic and Leukemic Stem Cells by the Immune System
Cell Death and Differentiation (2015) 22, 187–198 OPEN & 2015 Macmillan Publishers Limited All rights reserved 1350-9047/15 www.nature.com/cdd Review Regulation of hematopoietic and leukemic stem cells by the immune system C Riether1,4, CM Schu¨rch1,2,4 and AF Ochsenbein*,1,3 Hematopoietic stem cells (HSCs) are rare, multipotent cells that generate via progenitor and precursor cells of all blood lineages. Similar to normal hematopoiesis, leukemia is also hierarchically organized and a subpopulation of leukemic cells, the leukemic stem cells (LSCs), is responsible for disease initiation and maintenance and gives rise to more differentiated malignant cells. Although genetically abnormal, LSCs share many characteristics with normal HSCs, including quiescence, multipotency and self-renewal. Normal HSCs reside in a specialized microenvironment in the bone marrow (BM), the so-called HSC niche that crucially regulates HSC survival and function. Many cell types including osteoblastic, perivascular, endothelial and mesenchymal cells contribute to the HSC niche. In addition, the BM functions as primary and secondary lymphoid organ and hosts various mature immune cell types, including T and B cells, dendritic cells and macrophages that contribute to the HSC niche. Signals derived from the HSC niche are necessary to regulate demand-adapted responses of HSCs and progenitor cells after BM stress or during infection. LSCs occupy similar niches and depend on signals from the BM microenvironment. However, in addition to the cell types that constitute the HSC niche during homeostasis, in leukemia the BM is infiltrated by activated leukemia-specific immune cells. Leukemic cells express different antigens that are able to activate CD4 þ and CD8 þ T cells. -
Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
G C A T T A C G G C A T genes Article Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial 1, 2, 2 2, Thomas Junier *, Michael Huber * , Stefan Schmutz , Verena Kufner y, 2, 3, 3, 4, Osvaldo Zagordi y, Stefan Neuenschwander y, Alban Ramette y , Jakub Kubacki y , 4, 5, 6, 6, Claudia Bachofen y, Weihong Qi y, Florian Laubscher y, Samuel Cordey y , 6, 7, 8 1,9 8, Laurent Kaiser y, Christian Beuret y, Valérie Barbié , Jacques Fellay and Aitana Lebrand * 1 Global Health Institute, Swiss Federal Institute of Technology (ETH Lausanne) & SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland 2 Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland 3 Institute for Infectious Diseases, University of Bern, 3001 Bern, Switzerland 4 Institute of Virology, VetSuisse Faculty, University of Zurich, 8057 Zurich, Switzerland 5 Functional Genomics Center Zurich, Swiss Federal Institute of Technology (ETH Zurich) & University of Zurich, 8057 Zurich, Switzerland 6 Laboratory of Virology, University Hospitals of Geneva, 1205 Geneva, Switzerland; University of Geneva Medical School, 1206 Geneva, Switzerland 7 Biology Department, Spiez Laboratory, 3700 Spiez, Switzerland 8 Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, 1202 Geneva, Switzerland 9 Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, 1010 Lausanne, Switzerland * Correspondence: [email protected] (T.J.); [email protected] (M.H.); [email protected] (A.L.) These authors contributed equally. y Received: 30 July 2019; Accepted: 24 August 2019; Published: 28 August 2019 Abstract: Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. -
A Gene Increases the Severity of Common Colds Researchers Funded by the SNSF Have Discovered Mutations That Worsen Respiratory Infections Among Children
www.snsf.ch Wildhainweg 3, P.O. Box 8232, CH-3001 Berne Communication division +41 (0)31 308 22 22 [email protected] Berne, 17 July 2017 Press release A gene increases the severity of common colds Researchers funded by the SNSF have discovered mutations that worsen respiratory infections among children. Their study explain the mechanism involved. Colds that are not linked to influenza are generally benign. Still, 2% of each generation of children have to go to hospital following a virulent infection. "These respiratory problems are responsible for 20% of child mortality around the world", says Jacques Fellay, who has held an SNSF professorship since 2011. "It is truly a silent epidemic." An international research collaboration coordinated by Fellay has discovered the reason for some of these infections: they are caused by mutations of a gene that plays a part in recognising certain cold-inducing viruses. (*) "We have been able to confirm that a gene, called IFIH1, plays an important role in defending the body against the principal viruses responsible for respiratory infections among children", he explains. This gene normally helps in identifying the virus's RNA, a type of genetic information related to the DNA. "We have been able to isolate the mechanisms that prevent the immune systems of children with an IFIH mutation from successfully combating the viral infection." Hospitals in Switzerland and Australia The researchers collaborated with various paediatric wards in Swiss and Australian hospitals to study cases of children who needed intensive care after a severe respiratory infection (bronchiolitis or pneumonia) caused by a virus. -
Sequence Variation of Human Jc and Bk Polyomaviruses in the Pathogenesis of Polyomavirus-Associated Diseases
Hanna Liimatainen SEQUENCE VARIATION OF HUMAN JC AND BK POLYOMAVIRUSES IN THE PATHOGENESIS OF POLYOMAVIRUS-ASSOCIATED DISEASES POLYOMAVIRUS-ASSOCIATED OF THE PATHOGENESIS IN SEQUENCE VARIATION OF HUMAN JC AND BK POLYOMAVIRUSES AND BK JC HUMAN OF VARIATION SEQUENCE IN THE PATHOGENESIS OF POLYOMAVIRUS-ASSOCIATED DISEASES Hanna Liimatainen Faculty of Medicine University of Helsinki 2019 SEQUENCE VARIATION OF HUMAN JC AND BK POLYOMAVIRUSES IN THE PATHOGENESIS OF POLYOMAVIRUS-ASSOCIATED DISEASES HANNA LIIMATAINEN Department of Virology Medicum, Faculty of Medicine University of Helsinki and Department of Virology and Immunology Division of Clinical Microbiology Helsinki University Hospital Laboratory ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Medicine of the University of Helsinki, for public examination in Lecture Hall 1, Haartman Institute, on Friday 10th of January 2020, at 12 noon. Helsinki 2019 7ǗǜȨǚǖǣǙǝǚ Eeva Auvinen, PhD, Docent Department of Virology and Immunology Helsinki University Hospital Laboratory and Department of Virology Medicum, Faculty of Medicine University of Helsinki Helsinki, Finland 6ȨǖǣȨǕȨǚǙ Varpu Marjomäki, PhD, Docent Department of Biological and Environmental Science Nanoscience Center University of Jyväskylä Jyväskylä, Finland Matti Jalasvuori, PhD, Docent Department of Biological and Environmental Science Nanoscience Center University of Jyväskylä Jyväskylä, Finland 3ǜǜǝǞȨǞǘ Ugo Moens, PhD, Professor 1SPIGYPEV-RƽEQQEXMSR6IWIEVGL+VSYT 1-6+ Department of Medical Biology Faculty -
Commission Directive (Eu)
L 279/54 EN Offi cial Jour nal of the European Union 31.10.2019 COMMISSION DIRECTIVE (EU) 2019/1833 of 24 October 2019 amending Annexes I, III, V and VI to Directive 2000/54/EC of the European Parliament and of the Council as regards purely technical adjustments THE EUROPEAN COMMISSION, Having regard to the Treaty on the Functioning of the European Union, Having regard to Directive 2000/54/EC of the European Parliament and of the Council of 18 September 2000 on the protection of workers from risks related to exposure to biological agents at work (1), and in particular Article 19 thereof, Whereas: (1) Principle 10 of the European Pillar of Social Rights (2), proclaimed at Gothenburg on 17 November 2017, provides that every worker has the right to a healthy, safe and well-adapted working environment. The workers’ right to a high level of protection of their health and safety at work and to a working environment that is adapted to their professional needs and that enables them to prolong their participation in the labour market includes protection from exposure to biological agents at work. (2) The implementation of the directives related to the health and safety of workers at work, including Directive 2000/54/EC, was the subject of an ex-post evaluation, referred to as a REFIT evaluation. The evaluation looked at the directives’ relevance, at research and at new scientific knowledge in the various fields concerned. The REFIT evaluation, referred to in the Commission Staff Working Document (3), concludes, among other things, that the classified list of biological agents in Annex III to Directive 2000/54/EC needs to be amended in light of scientific and technical progress and that consistency with other relevant directives should be enhanced. -
Genomic Medicine Genomic Medicine Editorial
Swiss Re R isk Dialogue Series Risk Dialogue Series Genomic medicine Genomic medicine Editorial Recent decades have seen massive advancements in genomic medicine. This has resulted in establishing a wealth of disease associations with genetic variances in the genome. At the same time, the extensive use of genome analysis tools has resulted in a massive decrease in the cost of genome sequencing. Today, genetic testing companies are offering full genome sequencing for below USD 1000. The growing availability and utility of genetic information is becoming an increasingly important aspect of modern personalised medicine, due to the ability to deliver patient-tailored health care based on an individual’s genetic makeup. The emerging field of epigenetics, studying dynamically evolving changes in gene expression in response to environmental stresses, has added an additional layer of complexity to our understanding of the genome. As with genomic studies, current epigenetic research is rapidly evolving into potential clinical applications. The latest advances in genetic science will improve disease diagnosis and aid in guiding and applying personalised treatment and prevention plans. These advances include liquid biopsy, which identifies cancer cells or DNA in bodily fluids, requiring minimally invasive extraction; and the development of CRISPR technology, which allows precise and efficient gene editing in any organism. These new tools and techniques, combined with the growing availability of genomic information and new predictive methodologies, are entering clinical practice. They will challenge how we as insurers define disease; how we structure and price our policies; and how we sustainably provide our products and services to our customers. We wish you an enjoyable read. -
Role of Viruses in the Pathogenesis of Multiple Sclerosis
viruses Review Role of Viruses in the Pathogenesis of Multiple Sclerosis Rachael E. Tarlinton 1 , Ekaterina Martynova 2, Albert A. Rizvanov 2 , Svetlana Khaiboullina 3 and Subhash Verma 3,* 1 School of Veterinary Medicine and Science, University of Nottingham, Loughborough LE12 5RD, UK; [email protected] 2 Insititute of Fundamental Medicine and Biology Kazan Federal University, 420008 Kazan, Russia; [email protected] (E.M.); [email protected] (A.A.R.) 3 School of Medicine, University of Nevada, Reno, NV 89557, USA; [email protected] * Correspondence: [email protected] Received: 24 April 2020; Accepted: 10 June 2020; Published: 13 June 2020 Abstract: Multiple sclerosis (MS) is an immune inflammatory disease, where the underlying etiological cause remains elusive. Multiple triggering factors have been suggested, including environmental, genetic and gender components. However, underlying infectious triggers to the disease are also suspected. There is an increasing abundance of evidence supporting a viral etiology to MS, including the efficacy of interferon therapy and over-detection of viral antibodies and nucleic acids when compared with healthy patients. Several viruses have been proposed as potential triggering agents, including Epstein–Barr virus, human herpesvirus 6, varicella–zoster virus, cytomegalovirus, John Cunningham virus and human endogenous retroviruses. These viruses are all near ubiquitous and have a high prevalence in adult populations (or in the case of the retroviruses are actually part of the genome). They can establish lifelong infections with periods of reactivation, which may be linked to the relapsing nature of MS. In this review, the evidence for a role for viral infection in MS will be discussed with an emphasis on immune system activation related to MS disease pathogenesis. -
Leistungsverzeichnis Institut Für Virologie
Dokument-Nr.: [lk_vollstnr] Gültig seit: [lk_datfreigabe] Nächste Prüfung: [lk_datpruefung] Dokumentenart: [lk_dokart] [lk_doktitel] Institut für Virologie Universitätsklinikum Bonn (UKB) Direktor: Univ.-Prof. Dr. med. Hendrik Streeck Leistungsverzeichnis zur Virusdiagnostik Stand 01/2020 Die jeweils aktuellste Version des Leistungsverzeichnisses finden Sie auf unserer Homepage (http://www.ukb.uni-bonn.de → Institute → Virologie) Ansprechpartner: [lk_pruefungdurch] Freigabebereich: [lk_hgb] Dokument-Nr.: [lk_vollstnr] Herausgeber: Institut für Virologie Universitätsklinkum Bonn Prof. Dr. Anna M. Eis-Hübinger Dr. Souhaib Aldabbagh Sigmund-Freud-Str. 25 D-53127 Bonn e-mail: [email protected] Seite 2 von 65 Dokument-Nr.: [lk_vollstnr] Inhaltsverzeichnis Seitenzahl 1. Anschrift, Anfahrt, Lageplan 5 2. Dienstzeiten, Telefonnummern, Ansprechpartner 7 3. Abkürzungen 8 4. Hinweise zur Probenentnahme, -transport und -lagerung 10 4.1 Entnahme von Untersuchungsproben 10 4.2 Allgemeine Hinweise zu Transportgefäß, Transportzeit sowie Kriterien für die Ablehnung von Untersuchungsaufträgen 11 4.3 Probenmaterial-bezogene Hinweise zu Transportgefäß, Probenlagerung sowie Mindestprobenmenge 12 5. Untersuchungsanforderung und Anforderungsformular 15 6. Diagnostisches Angebot (Kurzfassung), Untersuchungsfrequenz und minimale Bearbeitungsdauer 19 7. Diagnostisches Angebot (Langfassung) 26 Adenoviren 26 Astroviren 26 BK Polyomavirus 27 Bocaviren 27 Chikungunya Virus 27 Coronaviren 27 Cytomegalievirus 28 Dengue Virus 29 Enteroviren 29 Enzephalitis-Panel -
Confident and Fast Metagenomics Classification Using Unique K-Mer
bioRxiv preprint doi: https://doi.org/10.1101/262956; this version posted February 9, 2018. 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 4.0 International license. 1 KrakenHLL: Confident and fast metagenomics classification using 2 unique k-mer counts 3 Breitwieser FP1 and Salzberg SL1,2 4 1 Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns 5 Hopkins School of Medicine, Baltimore, MD, United States 6 2 Departments of Biomedical Engineering, Computer Science and Biostatistics, Johns Hopkins 7 University, Baltimore, MD, United States 8 9 Abstract 10 Motivation: False positive identifications are a significant problem in metagenomics. Spurious 11 identifications can attract many reads that often aggregate in the genomes. Genome coverage 12 may be used to filter false positives, but fast k-mer based metagenomic classifiers only provide 13 read counts as metrics, and re-alignment is expensive. We propose using k-mer coverage, which 14 can be computed during classification, as proxy for genome base coverage. 15 Results: We present KrakenHLL, a metagenomics classifier that records the number of unique k- 16 mers as well as coverage for each taxon. KrakenHLL is based on the ultra-fast classification 17 engine Kraken and combines it with HyperLogLog cardinality estimators. We demonstrate that 18 more false-positive identifications can be filtered using the unique k-mer count, especially when 19 looking at species of low abundance. Further enhancements include mapping against multiple 20 databases, plasmid and strain identification using an extended taxonomy, and inclusion of over 21 100,000 additional viral strain sequences. -
Antibody Positivity in Psoriasis Patients
Journal Pre-proof The prevalence of Human polyomavirus 2 (HPyV2) antibody positivity in psoriasis patients OE Molloy (Conceptualization) (Methodology) (Data curation) (Visualization) (Writing - original draft) (Writing - review and editing), A Malara (Data curation), J Hassan (Investigation) (Writing - review and editing), M Lynch (Data curation), J Clowry (Data curation), K Hedman (Investigation), CF De Gascun (Conceptualization) (Resources) (Investigation) (Writing - review and editing), B Kirby (Conceptualization) (Methodology) (Writing - review and editing) (Supervision) PII: S1386-6532(20)30110-4 DOI: https://doi.org/10.1016/j.jcv.2020.104368 Reference: JCV 104368 To appear in: Journal of Clinical Virology Received Date: 15 January 2020 Revised Date: 7 April 2020 Accepted Date: 9 April 2020 Please cite this article as: Molloy O, Malara A, Hassan J, Lynch M, Clowry J, Hedman K, De Gascun C, Kirby B, The prevalence of Human polyomavirus 2 (HPyV2) antibody positivity in psoriasis patients, Journal of Clinical Virology (2020), doi: https://doi.org/10.1016/j.jcv.2020.104368 This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2020 Published by Elsevier. Title page The prevalence of Human polyomavirus 2 (HPyV2) antibody positivity in psoriasis patients. -
Role of Viruses in the Pathogenesis of Multiple Sclerosis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repository@Nottingham Viruses 2020, 12, x FOR PEER REVIEW 1 of 20 Review Role of viruses in the pathogenesis of Multiple Sclerosis Tarlinton Rachael1, Martynova Ekaterina2, Rizvanov Albert2, Khaiboullina Svetlana3, Verma Subhash3 1School of Veterinary Medicine and Science, University of Nottingham, UK 2Kazan Federal University, Kazan, Russia 3University of Nevada, Reno, USA Corresponding author: Verma Subhash, Ph.D. Associate Professor, E-mail: [email protected] Abstract: Multiple sclerosis (MS) is an immune inflammatory disease, where the underlying etiological cause remains elusive. Multiple triggering factors have been suggested including environmental, genetic and gender components. However underlying infectious triggers to the disease are also suspected. There is an increasing abundance of evidence supporting a viral etiology to MS, including the efficacy of interferon therapy and over detection of viral antibodies and nucleic acids when compared with healthy patients. Several viruses have been proposed as potential triggering agents, including Epstein-Barr virus, Human herpesvirus 6, Varicella-zoster virus, Cytomegalovirus, John Cunningham virus and Human endogenous retroviruses. These viruses are all near ubiquitous and have a high prevalence in adult populations (or in the case of the retroviruses are actually part of the genome). They can establish lifelong infections with periods of reactivation, which may be linked to the relapsing nature of MS. In this review, the evidence for a role for viral infection in MS will be discussed with an emphasis on immune system activation related to MS disease pathogenesis. Keywords: Multiple sclerosis; human herpesvirus-6; varicella-zoster virus; Cytomegalovirus; John Cunningham virus; human endogenous retroviruses; Epstein-Barr virus 1.