DOCSLIB.ORG

Seasonal Dynamics and Relative Persistence Potential of the Enteric Species of Enterovirus in Wastewater

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Seasonal Dynamics and Relative Persistence Potential of the Enteric Species of Enterovirus in Wastewater A dissertation submitted to the Graduate School Of the University of Cincinnati In partial fulfillment of the requirements for the degree of Doctor of Philosophy In the Department of Biological Sciences Of the McMicken College of Arts and Sciences By Nichole E. Brinkman B.S., Biological Sciences Northern Kentucky University, Highland Heights, Kentucky, December 1999 M.S., Biological Sciences University of Cincinnati, Cincinnati, Ohio, March 2007 Committee Chair: Dr. Brian Kinkle ABSTRACT Human enteroviruses (EV) are a large group of enteric pathogens containing approximately 104 serotypes, which cluster into four different species (EV-A-D). They can be transmitted from infected to susceptible individuals via a person-to-person route, contaminated food and water used for recreation, shellfish harvesting, or drinking. Assessments of public health risk due to exposure to waterborne enteroviruses require, in part, an understanding of the levels of these pathogens in water sources. Two key factors in determining their occurrence in water are 1) knowing the extent of the diversity of this group present in a particular water source and 2) the ability of individual members to persist in water. Data published to date regarding presence and persistence potential of enteroviruses has been limited to poliovirus, and members of one of the four enterovirus species, leaving the majority of serotypes uncharacterized. The objectives for this project were to assess the diversity of enteroviruses present in wastewater and evaluate the influence that the persistence potential may have on the diversity profile. Towards this end, a method to concentrate representative enterovirus species was identified and determined to equally recover enterovirus species from primary effluent of wastewater. This method was then applied to monthly wastewater samples collected locally over a one year period for deep sequencing of enteroviruses present. This culture-independent, next- generation sequencing approach allowed for hundreds to thousands of enterovirus genomic sequences in each sample to be identified. Analysis of these sequences revealed that members of EV-A, EV-B and EV-C are present in each month of the year, while EV-D is present sporadically. EV-C is present in relatively low abundance year-round, while EV-A and EV-B alternate in predominance in a pattern that coincides with season. Investigation into the persistence potential of enteroviruses in wastewater shows that persistence cannot be described by species, but is serotype dependent. Poliovirus (EV-C) and enterovirus 70 (EV-D) were ii observed to be most persistent, while CVA10 (EV-A) was least persistent. The members of EV- B examined (CVA9, CVB1 and echovirus 30) showed moderate levels of persistence. The work described here provides a new perspective of the diversity profile of enterovirus present in wastewater and begins to decode the relative persistence potential of, until now, unrepresented members. iii iv ACKNOWLEDGEMENTS I would like to thank my advisors, Brian Kinkle and Shay Fout, for their continued support and guidance throughout my tenure as a graduate student. I would also like to thank the remaining members of my committee, Eric Villegas, Nick Ashbolt and Dennis Grogan for their time, guidance and support. I am very grateful to Scott Keely for his assistance with statistical and bioinformatic analyses that was critical in several parts of the research presented here. In addition, his continued passion for science and relentless discussions about many scientific topics has made me a better scientist. I also thank several colleagues in my branch at the EPA, Shannon Griffin, Jennifer Cashdollar and Eunice Varughese for the many discussions we had about the research contained in this dissertation. These women are awesome lab mates and I am grateful to work with such dedicated civil servants. I would also like to thank my management at EPA, especially Ann Grimm, for their support of my pursuit of this degree. I also thank my family, especially my daughter Sydney, for their support and patience. I will always be grateful for their love and support. v TABLE OF CONTENTS ABSTRACT .................................................................................................................................... II ACKNOWLEDGEMENTS ........................................................................................................... V LIST OF TABLES ....................................................................................................................... VII LIST OF FIGURES ................................................................................................................... VIII LIST OF ABBREVIATIONS ........................................................................................................ X CHAPTER 1 GENERAL INTRODUCTION ............................................................................... 1 CHAPTER 2 EVALUATION OF METHODS USING CELITE TO CONCENTRATE NOROVIRUS, ADENOVIRUS AND ENTEROVIRUS FROM WASTEWATER ................... 29 ABSTRACT .................................................................................................................................. 30 INTRODUCTION ........................................................................................................................... 31 MATERIALS AND METHODS ....................................................................................................... 33 RESULTS ..................................................................................................................................... 41 DISCUSSION ................................................................................................................................ 47 REFERENCES .............................................................................................................................. 53 CHAPTER 3 SEASONAL DYNAMICS OF ENTERIC ENTEROVIRUS SPECIES IN WASTEWATER........................................................................................................................... 57 ABSTRACT .................................................................................................................................. 58 INTRODUCTION ........................................................................................................................... 59 MATERIALS AND METHODS ....................................................................................................... 61 RESULTS ..................................................................................................................................... 67 DISCUSSION ................................................................................................................................ 73 REFERENCES .............................................................................................................................. 78 CHAPTER 4 COMPARATIVE ATTENUATION PROFILES OF ENTERIC ENTEROVIRUS SPECIES IN WASTEWATER ..................................................................................................... 85 ABSTRACT .................................................................................................................................. 86 INTRODUCTION ........................................................................................................................... 87 MATERIALS AND METHODS ....................................................................................................... 89 RESULTS ..................................................................................................................................... 95 DISCUSSION .............................................................................................................................. 110 REFERENCES ............................................................................................................................ 117 CHAPTER 5 GENERAL CONCLUSIONS .............................................................................. 123 APPENDIX A ............................................................................................................................. 134 APPENDIX B ............................................................................................................................. 143 APPENDIX C ............................................................................................................................. 148 vi List of Tables Table 1.1. Human enteric enterovirus species and serotypes ......................................................... 6 Table 1.2. Top 5 serotypes of each enterovirus species reported to NESS over 39 years ........... 12 Table 2.1: Concentrations of indigenous enteric viruses in a composite primary effluent sample ....................................................................................................................................................... 47 Table 3.1. Analysis of reads obtained from 454 sequencing of VP1 ........................................... 68 Table 3.2. Analysis of reads obtained from 454 sequencing of VP4 ........................................... 69 Table 3.3. Read assignments to other viruses ............................................................................... 69 Table 4.1. Enterovirus serotypes .................................................................................................
Recommended publications
  • Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats

    Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats

    viruses Article Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats Laura M. Bergner 1,2,* , Nardus Mollentze 1,2 , Richard J. Orton 2 , Carlos Tello 3,4, Alice Broos 2, Roman Biek 1 and Daniel G. Streicker 1,2 1 Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; [email protected] (N.M.); [email protected] (R.B.); [email protected] (D.G.S.) 2 MRC–University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK; [email protected] (R.J.O.); [email protected] (A.B.) 3 Association for the Conservation and Development of Natural Resources, Lima 15037, Peru; [email protected] 4 Yunkawasi, Lima 15049, Peru * Correspondence: [email protected] Abstract: The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely Citation: Bergner, L.M.; Mollentze, applied to viruses at the time of their discovery. Here, we characterized viral genomes detected N.; Orton, R.J.; Tello, C.; Broos, A.; through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) Biek, R.; Streicker, D.G. and used these data as a case study in evaluating zoonotic potential using molecular sequencing Characterizing and Evaluating the data.
  • Intestinal Virome Changes Precede Autoimmunity in Type I Diabetes-Susceptible Children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D

    Intestinal Virome Changes Precede Autoimmunity in Type I Diabetes-Susceptible Children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D

    Correction MEDICAL SCIENCES Correction for “Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D. Kostic, Tiffany W. Poon, Hera Vlamakis, Heli Siljander, Taina Härkönen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Jorma Ilonen, David Wang, Mikael Knip, Ramnik J. Xavier, and Herbert W. Virgin, which was first published July 10, 2017; 10.1073/pnas.1706359114 (Proc Natl Acad Sci USA 114: E6166–E6175). The authors wish to note the following: “After publication, we discovered that certain patient-related information in the spreadsheets placed online had information that could conceiv- ably be used to identify, or at least narrow down, the identity of children whose fecal samples were studied. The article has been updated online to remove these potential privacy concerns. These changes do not alter the conclusions of the paper.” Published under the PNAS license. Published online November 19, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1817913115 E11426 | PNAS | November 27, 2018 | vol. 115 | no. 48 www.pnas.org Downloaded by guest on September 26, 2021 Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children Guoyan Zhaoa,1, Tommi Vatanenb,c, Lindsay Droita, Arnold Parka, Aleksandar D. Kosticb,2, Tiffany W. Poonb, Hera Vlamakisb, Heli Siljanderd,e, Taina Härkönend,e, Anu-Maaria Hämäläinenf, Aleksandr Peetg,h, Vallo Tillmanng,h, Jorma Iloneni, David Wanga,j, Mikael Knipd,e,k,l, Ramnik J. Xavierb,m, and
  • Arenaviridae Astroviridae Filoviridae Flaviviridae Hantaviridae

    Arenaviridae Astroviridae Filoviridae Flaviviridae Hantaviridae

    Hantaviridae 0.7 Filoviridae 0.6 Picornaviridae 0.3 Wenling red spikefish hantavirus Rhinovirus C Ahab virus * Possum enterovirus * Aronnax virus * * Wenling minipizza batfish hantavirus Wenling filefish filovirus Norway rat hunnivirus * Wenling yellow goosefish hantavirus Starbuck virus * * Porcine teschovirus European mole nova virus Human Marburg marburgvirus Mosavirus Asturias virus * * * Tortoise picornavirus Egyptian fruit bat Marburg marburgvirus Banded bullfrog picornavirus * Spanish mole uluguru virus Human Sudan ebolavirus * Black spectacled toad picornavirus * Kilimanjaro virus * * * Crab-eating macaque reston ebolavirus Equine rhinitis A virus Imjin virus * Foot and mouth disease virus Dode virus * Angolan free-tailed bat bombali ebolavirus * * Human cosavirus E Seoul orthohantavirus Little free-tailed bat bombali ebolavirus * African bat icavirus A Tigray hantavirus Human Zaire ebolavirus * Saffold virus * Human choclo virus *Little collared fruit bat ebolavirus Peleg virus * Eastern red scorpionfish picornavirus * Reed vole hantavirus Human bundibugyo ebolavirus * * Isla vista hantavirus * Seal picornavirus Human Tai forest ebolavirus Chicken orivirus Paramyxoviridae 0.4 * Duck picornavirus Hepadnaviridae 0.4 Bildad virus Ned virus Tiger rockfish hepatitis B virus Western African lungfish picornavirus * Pacific spadenose shark paramyxovirus * European eel hepatitis B virus Bluegill picornavirus Nemo virus * Carp picornavirus * African cichlid hepatitis B virus Triplecross lizardfish paramyxovirus * * Fathead minnow picornavirus
  • Viruses and Type 1 Diabetes: from Enteroviruses to the Virome

    Viruses and Type 1 Diabetes: from Enteroviruses to the Virome

    microorganisms Review Viruses and Type 1 Diabetes: From Enteroviruses to the Virome Sonia R. Isaacs 1,2 , Dylan B. Foskett 1,2 , Anna J. Maxwell 1,2, Emily J. Ward 1,3, Clare L. Faulkner 1,2, Jessica Y. X. Luo 1,2, William D. Rawlinson 1,2,3,4 , Maria E. Craig 1,2,5,6 and Ki Wook Kim 1,2,* 1 Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; [email protected] (S.R.I.); [email protected] (D.B.F.); [email protected] (A.J.M.); [email protected] (E.J.W.); [email protected] (C.L.F.); [email protected] (J.Y.X.L.); [email protected] (W.D.R.); [email protected] (M.E.C.) 2 Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia 3 Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia 4 Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia 5 Institute of Endocrinology and Diabetes, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia 6 Faculty of Medicine and Health, Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2006, Australia * Correspondence: [email protected]; Tel.: +61-2-9382-9096 Abstract: For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes.
  • Parechovirus B)

    Parechovirus B)

    Department of Virology Faculty of Medicine, University of Helsinki Doctoral Program in Biomedicine Doctoral School in Health Sciences DISTRIBUTION AND CLINICAL ASSOCIATIONS OF LJUNGAN VIRUS (PARECHOVIRUS B) CRISTINA FEVOLA ACADEMIC DISSERTATION To be presented for public examination with the permission of the Faculty of Medicine, University of Helsinki, in lecture hall LS1, on 11 01 19, at noon Helsinki 2019 Supervisors: Anne J. Jääskeläinen, PhD, Docent, Department of Virology University of Helsinki and Helsinki University Hospital Helsinki, Finland Antti Vaheri, MD, PhD, Professor Department of Virology Faculty of Medicine, University of Helsinki Finland & Heidi C. Hauffe, RhSch, DPhil (Oxon), Researcher Department of Biodiversity and Molecular Ecology Research and Innovation Centre, Fondazione Edmund Mach San Michele all’Adige, TN Italy Reviewers: Laura Kakkola, PhD, Docent Institute of Biomedicine Faculty of Medicine, University of Turku Turku, Finland & Petri Susi, PhD, Docent Institute of Biomedicine Faculty of Medicine, University of Turku Turku, Finland Official opponent: Detlev Krüger, MD, PhD, Professor Institute of Medical Virology Helmut-Ruska-Haus University Hospital Charité Berlin, Germany Cover photo: Cristina Fevola, The Pala group (Italian: Pale di San Martino), a mountain range in the Dolomites, in Trentino Alto Adige, Italy. ISBN 978-951-51-4748-6 (paperback) ISBN 978-951-51-4749-3 (PDF, available at http://ethesis.helsinki.fi) Unigrafia Oy, Helsinki, Finland 2019 To you the reader, for being curious. Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less. Marie Curie TABLE OF CONTENTS LIST OF ORIGINAL PUBLICATIONS ................................................................................................. 5 LIST OF ABBREVIATIONS ...............................................................................................................
  • A Potential Drug Target for Inhibiting Virus Replication

    A Potential Drug Target for Inhibiting Virus Replication

    Old Dominion University ODU Digital Commons Chemistry & Biochemistry Theses & Dissertations Chemistry & Biochemistry Winter 2018 Structure of the Picornavirus Replication Platform: A Potential Drug Target for Inhibiting Virus Replication Meghan Suzanne Warden Old Dominion University, [email protected] Follow this and additional works at: https://digitalcommons.odu.edu/chemistry_etds Part of the Biochemistry Commons, Chemistry Commons, Epidemiology Commons, and the Physiology Commons Recommended Citation Warden, Meghan S.. "Structure of the Picornavirus Replication Platform: A Potential Drug Target for Inhibiting Virus Replication" (2018). Doctor of Philosophy (PhD), Dissertation, Chemistry & Biochemistry, Old Dominion University, DOI: 10.25777/wyvk-8b21 https://digitalcommons.odu.edu/chemistry_etds/22 This Dissertation is brought to you for free and open access by the Chemistry & Biochemistry at ODU Digital Commons. It has been accepted for inclusion in Chemistry & Biochemistry Theses & Dissertations by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. STRUCTURE OF THE PICORNAVIRUS REPLICATION PLATFORM: A POTENTIAL DRUG TARGET FOR INHIBITING VIRUS REPLICATION by Meghan Suzanne Warden B.S. May 2011, Lambuth University A Dissertation Submitted to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY CHEMISTRY OLD DOMINION UNIVERSITY December 2018 Approved by: Steven M. Pascal (Director) Lesley H. Greene (Member) Hameeda Sultana (Member) James W. Lee (Member) John B. Cooper (Member) ABSTRACT STRUCTURE OF THE PICORNAVIRUS REPLICATION PLATFORM: A POTENTIAL DRUG TARGET FOR INHIBITING VIRUS REPLICATION Meghan Suzanne Warden Old Dominion University, 2018 Director: Dr. Steven M. Pascal Picornaviruses are small, positive-stranded RNA viruses, divided into twelve different genera.
  • Emerging Encephalitis ESCMID Online Lecture Library © by Author

    Emerging Encephalitis ESCMID Online Lecture Library © by Author

    Emerging encephalitis Nipah, Enterovirus 71, West Nile, and others … © by author O. Epaulard Department of Infectious Diseases ESCMID OnlineGrenoble Lecture University HospitalLibrary Unit of Virus - host cell interactions UMI 3265 UJF-EMBL-CNRS Declaration of interest • No contradictory interest © by author ESCMID Online Lecture Library Menu • General considerations • Flaviviruses West Nile virus • Henipaviruses © by author • Enterovirus 71 • ESCMIDHEV Online Lecture Library DNA viruses RNA viruses © by author ESCMID Online Lecture Library Hepeviridae Rubivirus Alphavirus Caliciviridae Flavivirus (HEV) (Rubella) (Chikungunya, O Nyong- (Norwalk) (YF, Dengue, JE, Nyong, Am. Eq. Enc.) WNV, TBE) Togaviridae Hepacivirus Enterovirus (HCV) (Coxsackie, echovirus, …) Flaviviridae Hepatovirus (HAV) picornaviridae Rabies Rhinovirus Rhabdoviridae Parechovirus RNA viruses Coronaviridae Morbillivirus Filoviridae (measles) (Marburg, Ebola) Paramyxoviridae© by author Orthomyxoviridae RubulavirusESCMIDPneumovirus OnlineBunyaviridae Lecture Library (mumps) (RSV) Henipavirus Retroviridae (Nipah, Hendra) Hantaviruses influenza Hepeviridae Rubivirus Alphavirus Flavivirus Caliciviridae (HEV) (Rubella) (Chikungunya, O Nyong- (Y (Norwalk) F, Dengue, JE, Nyong, Am. Eq. Enc.) TBE, WNV) Enterovirus Togaviridae Hepacivirus (Coxsackie, echovirus, …) (HCV) Hepatovirus Flaviviridae (HAV) picornaviridae Rhinovirus Rabies Rhabdoviridae Parechovirus RNA viruses Coronaviridae Morbillivirus Filoviridae (measles) (Marburg, Ebola) Paramyxoviridae© by author Orthomyxoviridae
  • Parechovirus Infection: a Rare Cause of Neonatal Encephalitis

    Parechovirus Infection: a Rare Cause of Neonatal Encephalitis

    SWISS SOCIETY OF NEONATOLOGY Parechovirus infection: a rare cause of neonatal encephalitis August 2018 Truant AS, Fischer-Fumeaux CJ, Truttmann AC, Heiniger C, Llor J, Rosato L, Faignart N, Asner S, Matthias Roth-Kleiner M, Clinic of Neonatology (TAS, FCJ, TAC, RKM), Pediatric Neurology Unit (FN), Pediatric Infectiology Unit (AS), Department Woman-Mother-Child, University Hospital and University of Lausanne, Lausanne, Switzerland, Department of Pediatrics (HC, RL), Hôpital Neuchâtelois, Neuchâtel, Switzerland, Department of Pediatrics (LJ), Cantonal Hospital of Valais, Sion, Switzerland Title figure: Human parechovirus type 3 (source: www.nature.com). © Swiss Society of Neonatology, Thomas M Berger, Webmaster 3 Human Parechovirus (HPeV) infections show a variety INTRODUCTION of clinical manifestations. Infections in early child- hood are often severe, mostly leading to sepsis and/or meningitis. As Enterovirus (EV), Parechovirus belongs to the family of Picornaviridae. Their clinical and mor- phological properties are similar. However, HPeVs were shown to be distinct from EVs and other Picornavirus groups in several features of their genome organi- zation, structure and replication. While EVs are found in individuals of all ages, HPeVs mainly infect children under 5 years of age, especially young infants. Neonatal presentations are less well described and recognized. We present two patients with neonatal encephalitis. 4 CASE REPORT 1 This female infant was born in a regional hospital at 38 0/7 weeks of gestation after a pregnancy compli- cated by gestational diabetes. She developed respira- tory distress, which resolved after 72 hours of CPAP and was felt to be consistent with transient tachypnea of the newborn and lung immaturity. On day of life 7, her condition again deteriorated with fever (up to 39.1°C), followed by irritability and central apnea with desaturations two days later.
  • Viruses in Food: Scientific Advice to Support Risk Management Activities

    Viruses in Food: Scientific Advice to Support Risk Management Activities

    M I C R O B I O L O G I C A L R I S K A S S E S S M E N T S E R I E S ISSN1726-5274 13 VIRUSES IN FOOD: SCIENTIFIC ADVICE TO SUPPORT RISK MANAGEMENT ACTIVITIES MEETING REPORT For further information on the joint FAO/WHO activities on microbiological risk assessment, please contact: Nutrition and Consumer Protection Division Food and Agriculture Organization of the United Nations Viale delle Terme di Caracalla 00153 Rome, Italy Fax: +39 06 57054593 E-mail: [email protected] Web site: http://www.fao.org/ag/agn or Department of Food Safety, Zoonoses and Foodborne Disease World Health Organization 20, Avenue Appia CH-1211 Geneva 27 Switzerland Fax: +41 22 7914807 E-mail: [email protected] Web site: http://www.who.int/foodsafety The designations employed and the presentation of material in this information product do not imply the expression of any opinion whatsoever on the part of the Food and Agriculture Organization of the United Nations (FAO) or of the World Health Organization (WHO) concerning the legal or development status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. The views expressed herein are those of the authors and do not necessarily represent those of FAO nor of WHO nor of their affiliated organization(s). All reasonable precautions have been taken by FAO and WHO to verify the information contained in this publication. However, the published material is being distributed without warranty of any kind, either expressed or implied.
  • Wastewater Surveillance for Infectious Disease: a Systematic Review

    Wastewater Surveillance for Infectious Disease: a Systematic Review

    medRxiv preprint doi: https://doi.org/10.1101/2021.07.26.21261155; this version posted July 29, 2021. 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 . Title: Wastewater surveillance for infectious disease: a systematic review Authors: Pruthvi Kilaru MPH1, Dustin Hill PhD1,2, Kathryn Anderson MD/PhD3, Mary B. Collins PhD4, Hyatt Green PhD5, Brittany L. Kmush PhD1, David A. Larsen PhD*1 1. Department of Public Health, Syracuse University, Syracuse, NY, USA 2. Graduate Program in Environmental Science, SUNY ESF, Syracuse, NY, USA 3. Department of Medicine, SUNY Upstate, Syracuse, NY, USA 4. Department of Environmental Studies, SUNY ESF, Syracuse, NY, USA 5. Department of Environmental Biology, SUNY ESF, Syracuse, NY, USA * Correspondence to: Dr. David Larsen, Department of Public Health, Syracuse University, Syracuse, NY, 13244, USA Abstract: Wastewater surveillance of SARS-CoV-2 has shown to be a valuable source of information regarding SARS-CoV-2 transmission and COVID-19 cases. Though the method has been used for several decades to track other infectious diseases, there has not been a comprehensive review outlining all of the pathogens surveilled through wastewater. The aim of this study is to identify what infectious diseases have been previously studied via wastewater surveillance prior to the COVID-19 Pandemic and identify common characteristics between the studies, as well as identify current gaps in knowledge. Peer-reviewed articles published as of August 1, 2020 that examined wastewater for communicable and infectious human pathogens on 2 or more occasions were included in the study.
  • Genomic Characterization of Sebokele Virus 1 (SEBV1) Reveals a New Candidate Species Among the Genus Parechovirus

    Genomic Characterization of Sebokele Virus 1 (SEBV1) Reveals a New Candidate Species Among the Genus Parechovirus

    Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the genus Parechovirus. Marie-Line Joffret, Christiane Bouchier, Marc Grandadam, Hervé Zeller, Corinne Maufrais, Hervé Bourhy, Philippe Desprès, Francis Delpeyroux, Laurent Dacheux To cite this version: Marie-Line Joffret, Christiane Bouchier, Marc Grandadam, Hervé Zeller, Corinne Maufrais, etal.. Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the genus Parechovirus.. Journal of General Virology, Microbiology Society, 2013, 94 (Pt_7), pp.1547-53. 10.1099/vir.0.053157-0. pasteur-01435337 HAL Id: pasteur-01435337 https://hal-pasteur.archives-ouvertes.fr/pasteur-01435337 Submitted on 13 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License 1 Title 2 Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the 3 genus Parechovirus 4 5 Running title 6 Molecular characterization of Sebokele virus 1 7 8 Contents category : Short communication 9 10 Authors and affiliations 11 Joffret ML1,2, Bouchier C3, Grandadam M4, Zeller H5, Maufrais C6, Bourhy H7, Despres P8, 12 Delpeyroux F1,2, Dacheux L7*.
  • Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

    Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

    viruses Article Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach 1, , , 1, 1,2 Xavier Fernandez-Cassi * y z, Sandra Martínez-Puchol y , Marcelle Silva-Sales , Thais Cornejo 3, Rosa Bartolome 3, Silvia Bofill-Mas 1 and Rosina Girones 1 1 Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain; [email protected] (S.M.-P.); marcelle.fi[email protected] (M.S.-S.); Sbofi[email protected] (S.B.-M.); [email protected] (R.G.) 2 Laboratory of Virology and Cell Culture, Tropical Pathology and Public Health Institute, Federal University of Goiás, Goiânia, GO 74605-050, Brazil 3 Hospital Universitari Vall d’Hebron, Microbiology Service, 08035 Barcelona, Spain; [email protected] (T.C.); [email protected] (R.B.) * Correspondence: [email protected] These authors contributed equally to this work. y Present address: Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental z Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. Academic Editor: Lennart Svensson Received: 4 November 2020; Accepted: 8 December 2020; Published: 13 December 2020 Abstract: Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections.