Identification of Microbial Pathogens Using Metagenomic Next-Generation Sequencing and ID
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Changes to Virus Taxonomy 2004
Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales -
ICTV Code Assigned: 2011.001Ag Officers)
This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp . -
Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses
bioRxiv preprint doi: https://doi.org/10.1101/248203; this version posted February 21, 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 RUNNING TITLE: Environmental viromics for the detection of pathogens 2 Viromic analysis of wastewater input 3 to a river catchment reveals a diverse 4 assemblage of RNA viruses 5 Evelien M. Adriaenssens1,*, Kata Farkas2, Christian Harrison1, David L. Jones2, 6 Heather E. Allison1, Alan J. McCarthy1 7 1 Microbiology Research Group, Institute of Integrative Biology, University of 8 Liverpool, UK 9 2 School of Environment, Natural Resources and Geography, Bangor University, 10 Bangor, LL57 2UW, UK 11 * Corresponding author: [email protected] 12 1 bioRxiv preprint doi: https://doi.org/10.1101/248203; this version posted February 21, 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. 13 Abstract 14 Detection of viruses in the environment is heavily dependent on PCR-based 15 approaches that require reference sequences for primer design. While this strategy 16 can accurately detect known viruses, it will not find novel genotypes, nor emerging 17 and invasive viral species. In this study, we investigated the use of viromics, i.e. 18 high-throughput sequencing of the biosphere viral fraction, to detect human/animal 19 pathogenic RNA viruses in the Conwy river catchment area in Wales, UK. -
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 -
ICTV in San Francisco: a Report from the Plenary Session
Arch Virol (2006) 151: 413– 422 DOI 10.1007/s00705-005-0698-3 ICTV in San Francisco: a report from the Plenary Session M. A. Mayo1 and L. A. Ball2 1Scottish Crop Research Institute, Dundee, U.K. 2Department of Microbiology, University of Birmingham at Alabama, Birmingham, Alabama, U.S.A. Received October 19, 2005; accepted November 23, 2005 Published online December 29, 2005 c Springer-Verlag 2005 At the International Congress of Virology (ICV) in San Francisco in July 2005, the Inter- national Committee on Taxonomy of Viruses (ICTV) held a Plenary Session. This note summarizes the reports made to the meeting by the President and the chairs of the ICTV subcommittees acknowledged at the end of this note. It also reports the results of elections to positions on the ICTV Executive Committee (EC) and changes made to the statutes that govern how ICTV operates. President’s report The composition of the EC will change greatly after the Congress because three of the four officers, 5 of the 6 subcommittee chairs and 5 of the 8 elected members will change. The memberships of the ICTV EC for 2002 to 2005 and for 2005 to 2008 (following the results of the elections at the Plenary Session) are shown in Table 1. Meetings Since the International Congress of Virology held in Paris in 2002, the EC met in May 2003 at the Danforth Plant Science Center, St Louis, USA and in July 2004 at Queen’s University, Kingston, Ontario, Canada. Immediately after the Kingston meeting, ICTV organized and, with donated funds, spon- sored a 1-day Satellite Symposium on ‘Virus Evolution’ in association with the annual American Society forVirology (ASV) meeting held at McGill University in Montreal, Canada, on July 10, 2004. -
The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes?
viruses Review The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes? Anna-Ursula Happel 1,* , Arvind Varsani 2,3 , Christina Balle 1 , Jo-Ann Passmore 1,4,5 and Heather Jaspan 1,6,7 1 Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa; [email protected] (C.B.); [email protected] (J.-A.P.); [email protected] (H.J.) 2 The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA; [email protected] 3 Structural Biology Research Unit, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town 7925, South Africa 4 NRF-DST CAPRISA Centre of Excellence in HIV Prevention, 719 Umbilo Road, Congella, Durban 4013, South Africa 5 National Health Laboratory Service, Anzio Road, Observatory, Cape Town 7925, South Africa 6 Department of Pediatrics and Global Health, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195, USA 7 Seattle Children’s Research Institute, 307 Westlake Ave N, Seattle, WA 98109, USA * Correspondence: [email protected] Received: 12 June 2020; Accepted: 24 July 2020; Published: 30 July 2020 Abstract: Besides bacteria, fungi, protists and archaea, the vaginal ecosystem also contains a range of prokaryote- and eukaryote-infecting viruses, which are collectively referred to as the “virome”. Despite its well-described role in the gut and other environmental niches, the vaginal virome remains understudied. -
CONSERVED VIRUS PROTEIN FAMILIES in BACTERIOPHAGE GENOMES and in METAGENOMES of HUMANS by Xixu Cai Submitted to the Graduate De
CONSERVED VIRUS PROTEIN FAMILIES IN BACTERIOPHAGE GENOMES AND IN METAGENOMES OF HUMANS By Xixu Cai Submitted to the graduate degree program in Microbiology, Molecular Genetics and Immunology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Master of Arts. ________________________________ Chairperson, Arcady Mushegian, Ph.D. ________________________________ Joe Lutkenhaus, Ph.D. ________________________________ Philip Hardwidge, Ph.D. Date Defended: July 1st, 2011 The Thesis Committee for Xixu Cai certifies that this is the approved version of the following thesis: CONSERVED VIRUS PROTEIN FAMILIES IN BACTERIOPHAGE GENOMES AND IN METAGENOMES OF HUMANS ________________________________ Chairperson, Arcady Mushegian, Ph.D. Date approved: July 22, 2011 ii Abstract Viruses are likely to be the most abundant genomes in the biosphere, displaying remarkable molecular diversity. Their fast-evolving genomes and lack of universal marker genes make phylogenetic and taxonomic studies more difficult than with other organisms. A detailed determination of gene conservation between virus genomes should facilitate the study of virus evolution and function. Here we used sequence similarity methods to build a phage orthologous groups (POGs) resource. The number of POGs has grown significantly in the past decade, while the percentage of genes in phage genomes that have orthologs in other phages has also been increasing, and the percentage of unknown "ORFans" - phage genes that are not in POGs - is decreasing. Other properties of phage genomes remain stable, in particular the high fraction of genes that are never or only rarely observed in their cellular hosts. This suggests that despite the role of phages in transferring cellular genes, a large fraction of the genes in phage genomes maintain an evolutionary trajectory that is distinct from that of host genes. -
Archives of Virology
Archives of Virology Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018) --Manuscript Draft-- Manuscript Number: Full Title: Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018) Article Type: Virology Division News: Virus Taxonomy/Nomenclature Keywords: virus taxonomy; virus phylogeny; virus nomenclature; International Committee on Taxonomy of Viruses; International Code of Virus Classification and Nomenclature Corresponding Author: Arcady Mushegian National Science Foundation McLean, Virginia UNITED STATES Corresponding Author Secondary Information: Corresponding Author's Institution: National Science Foundation Corresponding Author's Secondary Institution: First Author: Andrew M.Q. King First Author Secondary Information: Order of Authors: Andrew M.Q. King Elliot J Lefkowitz Arcady R Mushegian Michael J Adams Bas E Dutilh Alexander E Gorbalenya Balázs Harrach Robert L Harrison Sandra Junglen Nick J Knowles Andrew M Kropinski Mart Krupovic Jens H Kuhn Max Nibert Luisa Rubino Sead Sabanadzovic Hélène Sanfaçon Stuart G Siddell Peter Simmonds Arvind Varsani Francisco Murilo Zerbini Andrew J Davison Powered by Editorial Manager® and ProduXion Manager® from Aries Systems Corporation Order of Authors Secondary Information: Funding Information: Medical Research Council Dr Andrew J Davison (MC_UU_12014/3) Nederlandse Organisatie voor -
Molecular Diagnosis of Infection-Related Cancers in Dermatopathology Melissa Pulitzer, MD
Molecular Diagnosis of Infection-Related Cancers in Dermatopathology Melissa Pulitzer, MD The association between viruses and skin cancer is increasingly recognized in a number of neoplasms, that is, cutaneous squamous cell carcinoma, Kaposi sarcoma, nasopharyngeal carcinoma, and Merkel cell carcinoma, as well as hematolymphoid malignancies such as adult T-cell leukemia/lymphoma and NK/T-cell lymphoma (nasal type) and post-transplant lymphoproliferative disorders. Molecular assays are increasingly used to diagnose and manage these diseases. In this review, molecular features of tumor viruses and related host responses are explored. The tests used to identify such features are summarized. Evalua- tion of the utility of these assays for diagnosis and/or management of specific tumor types is presented. Semin Cutan Med Surg 31:247-257 © 2012 Frontline Medical Communications KEYWORDS Insertional Mutagenesis, Oncogenic Virus, Skin Neoplasm, Merkel Cell Carci- noma, Epstein-Barr Virus, Squamous Cell Carcinoma, Adult T-Cell Leukemia-Lymphoma n the United States, approximately 10% of all cancers are virus (EBV), human papillomavirus (HPV), human T-cell lym- Ithought to be related to infection. Worldwide, infectious photropic virus type 1 (HTLV-1), human herpesvirus 8 (HHV- agents are associated with 20% of all cancers.1 Most of the im- 8), a Kaposi sarcoma-associated herpes virus (KSHV), and hu- plicated microorganisms that are recognized in this role are vi- man immunodeficiency virus (HIV) type 1.4 ruses, commonly referred to as “tumor viruses.” A smaller num- As human tumor viruses are prevalent, and as virus-driven ber of cancers may be associated with bacterial infection. neoplasms are increasingly identified with advancing tech- Viral infection is thought to initiate tumor transformation. -
Supplemental Material.Pdf
SUPPLEMENTAL MATERIAL A cloud-compatible bioinformatics pipeline for ultra-rapid pathogen identification from next-generation sequencing of clinical samples Samia N. Naccache1,2, Scot Federman1,2, Narayanan Veerarghavan1,2, Matei Zaharia3, Deanna Lee1,2, Erik Samayoa1,2, Jerome Bouquet1,2, Alexander L. Greninger4, Ka-Cheung Luk5, Barryett Enge6, Debra A. Wadford6, Sharon L. Messenger6, Gillian L. Genrich1, Kristen Pellegrino7, Gilda Grard8, Eric Leroy8, Bradley S. Schneider9, Joseph N. Fair9, Miguel A.Martinez10, Pavel Isa10, John A. Crump11,12,13, Joseph L. DeRisi4, Taylor Sittler1, John Hackett, Jr.5, Steve Miller1,2 and Charles Y. Chiu1,2,14* Affiliations: 1Department of Laboratory Medicine, UCSF, San Francisco, CA, USA 2UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA 3Department of Computer Science, University of California, Berkeley, CA, USA 4Department of Biochemistry, UCSF, San Francisco, CA, USA 5Abbott Diagnostics, Abbott Park, IL, USA 6Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA, USA 7Department of Family and Community Medicine, UCSF, San Francisco, CA, USA 8Viral Emergent Diseases Unit, Centre International de Recherches Médicales de Franceville, Franceville, Gabon 9Metabiota, Inc., San Francisco, CA, USA 10Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 11Division of Infectious Diseases and International Health and the Duke Global Health -
Genetic Assays for Detecting Viral Recombination Rate
(19) *EP003024948B1* (11) EP 3 024 948 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12Q 1/6827 (2018.01) C12Q 1/70 (2006.01) 15.01.2020 Bulletin 2020/03 (86) International application number: (21) Application number: 14829649.4 PCT/US2014/048301 (22) Date of filing: 25.07.2014 (87) International publication number: WO 2015/013681 (29.01.2015 Gazette 2015/04) (54) GENETIC ASSAYS FOR DETECTING VIRAL RECOMBINATION RATE GENETISCHE TESTS ZUR BESTIMMUNG EINER VIRALEN REKOMBINATIONSFREQUENZ DOSAGES GÉNÉTIQUES POUR DÉTERMINER UNE FREQUENCE DE LA RECOMBINATION VIRALE (84) Designated Contracting States: • A. D. TADMOR ET AL: "Probing Individual AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Environmental Bacteria for Viruses by Using GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Microfluidic Digital PCR", SCIENCE, vol. 333, no. PL PT RO RS SE SI SK SM TR 6038, 1 July 2011 (2011-07-01), pages 58-62, XP055344735, ISSN: 0036-8075, DOI: (30) Priority: 25.07.2013 US 201361858311 P 10.1126/science.1200758 -& A. D. TADMOR ET 01.11.2013 US 201361899027 P AL: "Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR - (43) Date of publication of application: Supporting Online Material", SCIENCE, vol. 333, 01.06.2016 Bulletin 2016/22 no. 6038, 30 June 2011 (2011-06-30), pages 1-48, XP055344921, ISSN: 0036-8075, DOI: (73) Proprietor: Bio-rad Laboratories, Inc. 10.1126/science.1200758 Hercules, CA 94547 (US) • K. -
Classification of Organisms
Classification of Organisms: Pathogenicity classification of RNA and DNA viruses Status May 2017 (CGM/170522-03) COGEM advice CGM/170522-03 Pathogenicity classification of RNA and DNA viruses COGEM advice CGM/170522-03 Dutch Regulations Genetically Modified Organisms In the Decree on Genetically Modified Organisms (GMO Decree) and its accompanying more detailed Regulations (GMO Regulations) genetically modified micro-organisms are grouped in four pathogenicity classes, ranging from the lowest pathogenicity Class 1 to the highest Class 4.1 The pathogenicity classifications are used to determine the containment level for working in laboratories with GMOs. A micro-organism of Class 1 should at least comply with one of the following conditions: a) the micro-organism does not belong to a species of which representatives are known to be pathogenic for humans, animals or plants, b) the micro-organism has a long history of safe use under conditions without specific containment measures, c) the micro-organism belongs to a species that includes representatives of class 2, 3 or 4, but the particular strain does not contain genetic material that is responsible for the virulence, d) the micro-organism has been shown to be non-virulent through adequate tests. A micro-organism is grouped in Class 2 when it can cause a disease in humans or animals whereby it is unlikely to spread within the population while an effective prophylaxis, treatment or control strategy exists, as well as an organism that can cause a disease in plants. A micro-organism is grouped in Class 3 when it can cause a serious disease in humans or animals whereby it is likely to spread within the population while an effective prophylaxis, treatment or control strategy exists.