1
|
Runstadler JA, Puryear WB. The virus is out of the barn: the emergence of HPAI as a pathogen of avian and mammalian wildlife around the globe. Am J Vet Res 2024; 85:ajvr.24.01.0018. [PMID: 38593825 DOI: 10.2460/ajvr.24.01.0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Highly pathogenic avian influenza (HPAI) has persisted as a One Health threat whose current circulation and impact are addressed in the companion Currents in One Health by Puryear and Runstadler, JAVMA, May 2024. Highly pathogenic avian influenza emerged as a by-product of agricultural practices and adapted to endemic circulation in wild bird species. Over more than 20 years, continued evolution in a complex ecology involving multiple hosts has produced a lineage that expanded globally over the last 2 years. Understanding the continued evolution and movement of HPAI relies on understanding how the virus is infecting different hosts in different contexts. This includes understanding the environmental factors and the natural ecology of viral transmission that impact host exposure and ultimately evolutionary trajectories. Particularly with the rapid host expansion, increased spillover to mammalian hosts, and novel clinical phenotypes in infected hosts, despite progress in understanding the impact of specific mutations to HPAI viruses that are associated with spillover potential, the threat to public health is poorly understood. Active research is focusing on new approaches to understanding the relationship of viral genotype to phenotype and the implementation of research and surveillance pipelines to make sense of the enormous potential for diverse HPAI viruses to emerge from wild reservoirs amid global circulation.
Collapse
Affiliation(s)
| | - Wendy B Puryear
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA
| |
Collapse
|
2
|
Puryear WB, Runstadler JA. High-pathogenicity avian influenza in wildlife: a changing disease dynamic that is expanding in wild birds and having an increasing impact on a growing number of mammals. J Am Vet Med Assoc 2024; 262:601-609. [PMID: 38599231 DOI: 10.2460/javma.24.01.0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/12/2023] [Indexed: 04/12/2024]
Abstract
While diverse strains of low-pathogenicity avian influenza have circulated in wild birds for a long period of time, there has previously been little pathology in wild birds, ducks have been the primary and largely asymptomatic wild reservoir, and spillover into mammals has been limited and rare. In recent years, a high-pathogenicity avian influenza (HPAI) virus has emerged on the global scene and shifted the previously established dogmas for influenza infection. High-pathogenicity avian influenza has expanded into wildlife in unprecedented numbers and species diversity, with unmatched disease severity for influenza in wildlife. As the disease ecology of influenza has shifted with this new variant, significant efforts are underway to understand disease course, pathology, and species susceptibility. Here we focus primarily on the impact that HPAI has had in wild mammals while framing these novel spillovers within the context of significantly expanding disease in avian species and geography. The clinical and pathology presentations of HPAI in these atypical hosts are discussed, as well as prognosis and risk for continued spillover. The companion Currents in One Health by Runstadler and Puryear, AJVR, May 2024, provides further context on viral reservoirs and possible routes of direct or environmental transmission and risk assessment of viral variants that are emerging within wildlife.
Collapse
|
3
|
Rasmussen AL, Gronvall GK, Lowen AC, Goodrum F, Alwine J, Andersen KG, Anthony SJ, Baines J, Banerjee A, Broadbent AJ, Brooke CB, Campos SK, Caposio P, Casadevall A, Chan GC, Cliffe AR, Collins-McMillen D, Connell N, Damania B, Daugherty MD, Debbink K, Dermody TS, DiMaio D, Duprex WP, Emerman M, Galloway DA, Garry RF, Goldstein SA, Greninger AL, Hartman AL, Hogue BG, Horner SM, Hotez PJ, Jung JU, Kamil JP, Karst SM, Laimins L, Lakdawala SS, Landais I, Letko M, Lindenbach B, Liu SL, Luftig M, McFadden G, Mehle A, Morrison J, Moscona A, Mühlberger E, Munger J, Münger K, Murphy E, Neufeldt CJ, Nikolich JZ, O'Connor CM, Pekosz A, Permar SR, Pfeiffer JK, Popescu SV, Purdy JG, Racaniello VR, Rice CM, Runstadler JA, Sapp MJ, Scott RS, Smith GA, Sorrell EM, Speranza E, Streblow D, Tibbetts SA, Toth Z, Van Doorslaer K, Weiss SR, White EA, White TM, Wobus CE, Worobey M, Yamaoka S, Yurochko A. Correction for Rasmussen et al., "Virology-the path forward". J Virol 2024; 98:e0007424. [PMID: 38334328 PMCID: PMC10949460 DOI: 10.1128/jvi.00074-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
|
4
|
Rasmussen AL, Gronvall GK, Lowen AC, Goodrum F, Alwine J, Andersen KG, Anthony SJ, Baines J, Banerjee A, Broadbent AJ, Brooke CB, Campos SK, Caposio P, Casadevall A, Chan GC, Cliffe AR, Collins-McMillen D, Connell N, Damania B, Daugherty MD, Debbink K, Dermody TS, DiMaio D, Duprex WP, Emerman M, Galloway DA, Garry RF, Goldstein SA, Greninger AL, Hartman AL, Hogue BG, Horner SM, Hotez PJ, Jung JU, Kamil JP, Karst SM, Laimins L, Lakdawala SS, Landais I, Letko M, Lindenbach B, Liu SL, Luftig M, McFadden G, Mehle A, Morrison J, Moscona A, Mühlberger E, Munger J, Münger K, Murphy E, Neufeldt CJ, Nikolich JZ, O'Connor CM, Pekosz A, Permar SR, Pfeiffer JK, Popescu SV, Purdy JG, Racaniello VR, Rice CM, Runstadler JA, Sapp MJ, Scott RS, Smith GA, Sorrell EM, Speranza E, Streblow D, Tibbetts SA, Toth Z, Van Doorslaer K, Weiss SR, White EA, White TM, Wobus CE, Worobey M, Yamaoka S, Yurochko A. Virology-the path forward. J Virol 2024; 98:e0179123. [PMID: 38168672 PMCID: PMC10804978 DOI: 10.1128/jvi.01791-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US.
Collapse
Affiliation(s)
- Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Canada
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Gigi K. Gronvall
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Felicia Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - James Alwine
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Simon J. Anthony
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, California, USA
| | - Joel Baines
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Andrew J. Broadbent
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Samuel K. Campos
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gary C. Chan
- Department of Microbiology and Immunology, SUNY Upstate Medical Center, Syracuse, New York, USA
| | - Anna R. Cliffe
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | | | - Nancy Connell
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Blossom Damania
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA
| | - Kari Debbink
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Terence S. Dermody
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - W. Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael Emerman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Denise A. Galloway
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Amy L. Hartman
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Stacy M. Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Peter J. Hotez
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jae U. Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Stephanie M. Karst
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Lou Laimins
- Department of Microbiology, Ohio State University, Wooster, Ohio, USA
| | - Seema S. Lakdawala
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Igor Landais
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, USA
| | - Shan-Lu Liu
- Department of Microbiology, Ohio State University, Wooster, Ohio, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, Ohio State University, Wooster, Ohio, USA
| | - Micah Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Grant McFadden
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Anne Moscona
- Department of Microbiology and Immunology, Columbia University, New York, New York, USA
- Department of Physiology, Columbia University, New York, New York, USA
- Department of Biophysics, Columbia University, New York, New York, USA
| | - Elke Mühlberger
- Department of Virology, Immunology, and Microbiology, Boston University, Boston, Massachusetts, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York, USA
| | - Karl Münger
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Eain Murphy
- Department of Microbiology and Immunology, SUNY Upstate Medical Center, Syracuse, New York, USA
| | | | - Janko Z. Nikolich
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- Aegis Consortium for a Pandemic-Free Future, University of Arizona, Tucson, Arizona, USA
| | | | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Sallie R. Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Julie K. Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Saskia V. Popescu
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - John G. Purdy
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Vincent R. Racaniello
- Department of Microbiology and Immunology, Columbia University, New York, New York, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, USA
| | - Martin J. Sapp
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Rona S. Scott
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Gregory A. Smith
- Department of Microbiology, Ohio State University, Wooster, Ohio, USA
| | - Erin M. Sorrell
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Emily Speranza
- Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port St. Lucie, Florida, USA
| | - Daniel Streblow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Scott A. Tibbetts
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | | | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth A. White
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy M. White
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Satoko Yamaoka
- Department of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew Yurochko
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| |
Collapse
|
5
|
Kuhn JH, Abe J, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Kumar Baranwal V, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Blair CD, Blasdell KR, Blouin AG, Bradfute SB, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Kumar Chaturvedi K, Chooi KM, Crane A, Dal Bó E, Carlos de la Torre J, de Souza WM, de Swart RL, Debat H, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, Laura García M, García-Sastre A, Garrison AR, Gaskin TR, Gong W, Gonzalez JPJ, de Bellocq J, Griffiths A, Groschup MH, Günther I, Günther S, Hammond J, Hasegawa Y, Hayashi K, Hepojoki J, Higgins CM, Hongō S, Horie M, Hughes HR, Hume AJ, Hyndman TH, Ikeda K, Jiāng D, Jonson GB, Junglen S, Klempa B, Klingström J, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Lǐ J, Li JM, Liu R, Lukashevich IS, MacDiarmid RM, Maes P, Marklewitz M, Marshall SH, Marzano SYL, McCauley JW, Mirazimi A, Mühlberger E, Nabeshima T, Naidu R, Natsuaki T, Navarro B, Navarro JA, Neriya Y, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Ochoa-Corona FM, Okada T, Palacios G, Pallás V, Papa A, Paraskevopoulou S, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Pérez DR, Pfaff F, Plemper RK, Postler TS, Rabbidge LO, Radoshitzky SR, Ramos-González PL, Rehanek M, Resende RO, Reyes CA, Rodrigues TCS, Romanowski V, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sadiq S, Salvato MS, Sasaya T, Schwemmle M, Sharpe SR, Shi M, Shimomoto Y, Kavi Sidharthan V, Sironi M, Smither S, Song JW, Spann KM, Spengler JR, Stenglein MD, Takada A, Takeyama S, Tatara A, Tesh RB, Thornburg NJ, Tian X, Tischler ND, Tomitaka Y, Tomonaga K, Tordo N, Tu C, Turina M, Tzanetakis IE, Maria Vaira A, van den Hoogen B, Vanmechelen B, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Waltzek TB, Whitfield AE, Wolf YI, Xia H, Xylogianni E, Yanagisawa H, Yano K, Ye G, Yuan Z, Zerbini FM, Zhang G, Zhang S, Zhang YZ, Zhao L, Økland AL. Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota). J Gen Virol 2023; 104:001864. [PMID: 37622664 PMCID: PMC10721048 DOI: 10.1099/jgv.0.001864] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 05/26/2023] [Indexed: 08/26/2023] Open
Abstract
In April 2023, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by one new family, 14 new genera, and 140 new species. Two genera and 538 species were renamed. One species was moved, and four were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Collapse
Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Junya Abe
- Ornamental Plants and Vegetables Research Center, Agricultural Research Department, Hokkaido Research Organization, Takikawa, Hokkaido, Japan
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Sergey V. Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - María A. Ayllón
- Centro de Biotecnología y Genómica de Plantas; Departamento de Biotecnología-Biología Vegetal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón; Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Greifswald, Germany
| | - Matthew J. Ballinger
- Department of Biological Sciences, Mississippi State University, Starkville, MS,, Mississippi State, USA
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Éric Bergeron
- Division of High-Consequence Pathogens and Pathology, Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nadine Biedenkopf
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Carol D. Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R. Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, USA
| | - Paul A. Brown
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J. Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | | | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Bloemfontein, South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N. Charrel
- Unite des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Krishna Kumar Chaturvedi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - William M. de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Rik L. de Swart
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Córdoba, Argentina
| | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, Maisons-Alfort, France
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - J. Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W. Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Toufic Elbeaino
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Koray Ergünay
- Department of Medical Microbiology, Virology Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution–National Museum of Natural History (NMNH), Washington, DC, USA
| | - Guozhong Feng
- China National Rice Research Institute, Hangzhou, PR China
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas R. Gaskin
- Brandenburg State Office of Rural Development, Agriculture and Land Consolidation (LELF), Frankfurt, Germany
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Wenjie Gong
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonoses Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Jean-Paul J. Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, USA
| | | | - Anthony Griffiths
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ines Günther
- Division Phytomedicine, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Stephan Günther
- Department of Virology, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Yusuke Hasegawa
- Department of Clinical Plant Science, Hosei University, Koganei, Tokyo, 184-8584, Japan
| | - Kazusa Hayashi
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Colleen M. Higgins
- The School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Seiji Hongō
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University; International Research Center for Infectious Diseases, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Adam J. Hume
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Timothy H. Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Kenichi Ikeda
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, PR China
| | - Gilda B. Jonson
- International Rice Research Institute, College, Los Baños, 4032, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin 10117, Germany
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Kenji Kubota
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, Washington, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit; Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jun-Min Li
- Institute of Plant Virology, Ningbo University, Ningbo, PR China
| | - Ran Liu
- Illumina (China), Beijing, PR China
| | - Igor S. Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited; School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Sergio H. Marshall
- Instituto de Biología-Laboratorio de Genética Molecular-Pontificia Universidad Católica de ValparaísoCampus Curauma, Valparaíso, Chile
| | - Shin-Yi L. Marzano
- United States Department of Agriculture, Agricultural Research Service, Toledo, OH, USA
| | | | | | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Chobanian and Avedisian School of Medicine; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | | | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - José A. Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Yutaro Neriya
- School of Agriculture, Utsunomiya University, Utsunomiya, Japan
| | | | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Francisco M. Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics. Stillwater, Oklahoma State University, Oklahoma, USA
| | - Tomoyuki Okada
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universitat Politècnica de Valencia, Valencia, Spain
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Colin R. Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - Janusz T. Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Daniel R. Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Richard K. Plemper
- Center for Translational Antiviral Research, Georgia State University Institute for Biomedical Sciences, Atlanta, GA, USA
| | - Thomas S. Postler
- Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, Brooklyn, NY, USA
| | - Lee O. Rabbidge
- The New Zealand Institute for Plant and Food Research Limited; The School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Sheli R. Radoshitzky
- Division of Antivirals, Office of Infectious Diseases, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | | | - Marius Rehanek
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato O. Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A. Reyes
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Thaís C. S. Rodrigues
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Jonathan A. Runstadler
- Department of Infectious Disease & Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, Mississippi State, USA
| | - Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Maria S. Salvato
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Stephen R. Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, PR China
| | | | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS “E. Medea”, Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M. Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R. Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sawana Takeyama
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Akio Tatara
- Faculty of Agricultural Production and Management, Shizuoka Professional University of Agriculture, Shizuoka, Japan
| | - Robert B. Tesh
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | | | - Xin Tian
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
| | - Nicole D. Tischler
- Laboratorio de Virología Molecular, Centro Ciencia & Vida, Fundación Ciencia & Vida and Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Yasuhiro Tomitaka
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Keizō Tomonaga
- Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur de Guinée, BP 4416, Conakry, Guinea
| | - Changchun Tu
- College of Veterinary Medicine, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, PR China
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Ioannis E. Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | | | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Nikos Vasilakis
- The University of Texas Medical Branch at Galveston, Galveston, TX,, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Thomas B. Waltzek
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Anna E. Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - Evanthia Xylogianni
- Plant Pathology Laboratory, Department of Crop Science, School of Agricultural Production, Infrastructure and Environment, Agricultural University of Athens, Votanikos, Athens, Greece
| | | | - Kazutaka Yano
- Kochi Agricultural Research Center, Nankoku, Kochi, Japan
| | - Gongyin Ye
- Institute of Insect Sciences, Zhejiang University, Hangzhou, PR China
| | - Zhiming Yuan
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
| | - F. Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Guilin Zhang
- Center for Disease Control and Prevention of Xinjiang Military Command Area, Urumqi, Xinjiang, PR China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, PR China
- Guangxi Academy of Specialty Crops, Guilin, Guangxi, PR China
| | - Yong-Zhen Zhang
- School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, PR China
| | - Lu Zhao
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | | |
Collapse
|
6
|
Pakpour S, Vojnits K, Alousi S, Khalid MF, Fowler JD, Wang Y, Tan AM, Lam MI, Zhao M, Calderon E, Luka GS, Hoorfar M, Kazemian N, Isazadeh S, Ashkarran AA, Runstadler JA, Mahmoudi M. Magnetic Levitation System Isolates and Purifies Airborne Viruses. ACS Nano 2023. [PMID: 37417775 DOI: 10.1021/acsnano.3c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Detection of viable viruses in the air is critical in order to determine the level of risk associated with the airborne diffusion of viruses. Different methods have been developed for the isolation, purification, and detection of viable airborne viruses, but they require an extensive processing time and often present limitations including low physical efficiency (i.e., the amount of collected viruses), low biological efficiency (i.e., the number of viable viruses), or a combination of all. To mitigate such limitations, we have employed an efficient technique based on the magnetic levitation (Maglev) technique with a paramagnetic solution and successfully identified distinct variations in levitation and density characteristics among bacteria (Escherichia coli), phages (MS2), and human viruses (SARS-CoV-2 and influenza H1N1). Notably, the Maglev approach enabled a significant enrichment of viable airborne viruses in air samples. Furthermore, the enriched viruses obtained through Maglev exhibited high purity, rendering them suitable for direct utilization in subsequent analyses such as reverse transcription-polymerase chain reaction (RT-PCR) or colorimetric assays. The system is portable, easy to use, and cost-efficient and can potentially provide proactive surveillance data for monitoring future outbreaks of airborne infectious diseases and allow for the induction of various preventative and mitigative measures.
Collapse
Affiliation(s)
- Sepideh Pakpour
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Kinga Vojnits
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Sahar Alousi
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Muhammad Faizan Khalid
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - James D Fowler
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Yongliang Wang
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao City, 130012, People's Republic of China
| | - Andrea Marie Tan
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Man In Lam
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Michael Zhao
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Enrique Calderon
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - George S Luka
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Mina Hoorfar
- Department of Mechanical Engineering, University of Victoria, Victoria, British Columbia V8W 2Y2, Canada
| | - Negin Kazemian
- School of Engineering, University of British Columbia, Kelowna, British Columbia V1V 1V7, Canada
| | - Siavash Isazadeh
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Ali Akbar Ashkarran
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University, Medford, Massachusetts 02155, United States
| | - Morteza Mahmoudi
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, Michigan 48824, United States
| |
Collapse
|
7
|
Gass JD, Hill NJ, Damodaran L, Naumova EN, Nutter FB, Runstadler JA. Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016-Early 2022. Int J Environ Res Public Health 2023; 20:6030. [PMID: 37297634 PMCID: PMC10252585 DOI: 10.3390/ijerph20116030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses across continents and characterized ecological and environmental predictors of virus spread between geographic regions by constructing a Bayesian phylodynamic generalized linear model (phylodynamic-GLM). The findings demonstrate localized epidemics of H5Nx throughout Europe in the first several years of the epizootic, followed by a singular branching point where H5N1 viruses were introduced to North America, likely via stopover locations throughout the North Atlantic. Once in the United States (US), H5Nx viruses spread at a greater rate between US-based regions as compared to prior spread in Europe. We established that geographic proximity is a predictor of virus spread between regions, implying that intercontinental transport across the Atlantic Ocean is relatively rare. An increase in mean ambient temperature over time was predictive of reduced H5Nx virus spread, which may reflect the effect of climate change on declines in host species abundance, decreased persistence of the virus in the environment, or changes in migratory patterns due to ecological alterations. Our data provide new knowledge about the spread and directionality of H5Nx virus dispersal in Europe and the US during an actively evolving intercontinental outbreak, including predictors of virus movement between regions, which will contribute to surveillance and mitigation strategies as the outbreak unfolds, and in future instances of uncontained avian spread of HPAI viruses.
Collapse
Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, Boston, MA 02125, USA
| | | | - Elena N. Naumova
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02155, USA
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
| |
Collapse
|
8
|
Runstadler JA, Lowen AC, Kayali G, Tompkins SM, Albrecht RA, Fouchier RAM, Stallknecht DE, Lakdawala SS, Goodrum FD, Casadevall A, Enquist LW, Alwine JC, Imperiale MJ, Schultz-Cherry S, Webby RJ. Field Research Is Essential to Counter Virological Threats. J Virol 2023; 97:e0054423. [PMID: 37166327 DOI: 10.1128/jvi.00544-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The interface between humans and wildlife is changing and, with it, the potential for pathogen introduction into humans has increased. Avian influenza is a prominent example, with an ongoing outbreak showing the unprecedented expansion of both geographic and host ranges. Research in the field is essential to understand this and other zoonotic threats. Only by monitoring dynamic viral populations and defining their biology in situ can we gather the information needed to ensure effective pandemic preparation.
Collapse
Affiliation(s)
- Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Boston, Massachusetts, USA
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, USA
| | - Ghazi Kayali
- Human-Link DMCC, Dubai, UAE
- University of Texas School of Public Health, Houston, Texas, USA
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
| | - S Mark Tompkins
- Center for Vaccines and Immunology, University of Georgia, Athens, Georgia, USA
- Center for Influenza Disease and Emergence Research (CIDER) CEIRR, Athens, Georgia, USA
| | - Randy A Albrecht
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ron A M Fouchier
- Center for Research on Influenza Pathogenesis and Transmission (CRIPT) CEIRR, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - David E Stallknecht
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Seema S Lakdawala
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Penn Center of Excellence for Influenza Research and Response (Penn-CEIRR), Philadelphia, Pennsylvania, USA
| | - Felicia D Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Lynn W Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - James C Alwine
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael J Imperiale
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stacey Schultz-Cherry
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard J Webby
- St Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, Tennessee, USA
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
9
|
Gass JD, Dusek RJ, Hall JS, Hallgrimsson GT, Halldórsson HP, Vignisson SR, Ragnarsdottir SB, Jónsson JE, Krauss S, Wong SS, Wan XF, Akter S, Sreevatsan S, Trovão NS, Nutter FB, Runstadler JA, Hill NJ. Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones. Mol Ecol 2023; 32:198-213. [PMID: 36239465 PMCID: PMC9797457 DOI: 10.1111/mec.16738] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/31/2022]
Abstract
Influenza A viruses (IAV) circulate endemically among many wild aquatic bird populations that seasonally migrate between wintering grounds in southern latitudes to breeding ranges along the perimeter of the circumpolar arctic. Arctic and subarctic zones are hypothesized to serve as ecologic drivers of the intercontinental movement and reassortment of IAVs due to high densities of disparate populations of long distance migratory and native bird species present during breeding seasons. Iceland is a staging ground that connects the East Atlantic and North Atlantic American flyways, providing a unique study system for characterizing viral flow between eastern and western hemispheres. Using Bayesian phylodynamic analyses, we sought to evaluate the viral connectivity of Iceland to proximal regions and how inter-species transmission and reassortment dynamics in this region influence the geographic spread of low and highly pathogenic IAVs. Findings demonstrate that IAV movement in the arctic and subarctic reflects wild bird migration around the perimeter of the circumpolar north, favouring short-distance flights between proximal regions rather than long distance flights over the polar interior. Iceland connects virus movement between mainland Europe and North America, consistent with the westward migration of wild birds from mainland Europe to Northeastern Canada and Greenland. Though virus diffusion rates were similar among avian taxonomic groups in Iceland, gulls play an outsized role as sinks of IAVs from other avian hosts prior to onward migration. These data identify patterns of virus movement in northern latitudes and inform future surveillance strategies related to seasonal and emergent IAVs with potential public health concern.
Collapse
Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | | | | | | | | | - Solvi Runar Vignisson
- University of Iceland’s Research Centre in Suðurnes
- Suðurnes Science and Learning Center
| | | | | | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Sook-San Wong
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | - Sadia Akter
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | | | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Nichola J. Hill
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
- Department of Biology, University of Massachusetts, Boston
| |
Collapse
|
10
|
Ramsey ME, Faugno AJ, Puryear WB, Lee BC, Foss AD, Lambert LH, Nargi FE, Bopp GP, Lee LP, Rudzinski CM, Ervin BL, Runstadler JA, Hill NS. Characterization of SARS-CoV-2 Aerosols Dispersed During Noninvasive Respiratory Support of Patients With COVID-19. Respir Care 2023; 68:8-17. [PMID: 36566031 PMCID: PMC9993517 DOI: 10.4187/respcare.10340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND In the midst of the COVID-19 pandemic, noninvasive respiratory support (NRS) therapies such as high-flow nasal cannula (HFNC) and noninvasive ventilation (NIV) were central to respiratory care. The extent to which these treatments increase the generation and dispersion of infectious respiratory aerosols is not fully understood. The objective of this study was to characterize SARS-CoV-2 aerosol dispersion from subjects with COVID-19 undergoing NRS therapy. METHODS Several different aerosol sampling devices were used to collect air samples in the vicinity of 31 subjects with COVID-19, most of whom were receiving NRS therapy, primarily HFNC. Aerosols were collected onto filters and analyzed for the presence of SARS-CoV-2 RNA. Additional measurements were collected in an aerosol chamber with healthy adult subjects using respiratory therapy devices under controlled and reproducible conditions. RESULTS Fifty aerosol samples were collected from subjects receiving HFNC or NIV therapy, whereas 6 samples were collected from subjects not receiving NRS. Only 4 of the 56 aerosol samples were positive for SARS-CoV-2 RNA, and all positive samples were collected using a high air flow scavenger mask collection device placed in close proximity to the subject. The chamber measurements with healthy subjects did not show any significant increase in aerosol dispersion caused by the respiratory therapy devices compared to baseline. CONCLUSIONS Our findings demonstrate very limited detection of SARS-CoV-2-containing aerosols in the vicinity of subjects with COVID-19 receiving NRS therapies in the clinical setting. These results, combined with controlled chamber measurements showing that HFNC and NIV device usage was not associated with increased aerosol dispersion, suggest that NRS therapies do not result in increased dispersal of aerosols in the clinical setting.
Collapse
Affiliation(s)
- Meghan E Ramsey
- Biotechnology and Human Systems Division, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, Massachusetts
| | - Anthony J Faugno
- Critical Care and Sleep Division, Tufts Medical Center, Boston, Massachusetts
| | - Wendy B Puryear
- Cummings School of Veterinary Medicine, Tufts University, Grafton, Massachusetts
| | - Brian C Lee
- Biotechnology and Human Systems Division, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, Massachusetts
| | - Alexa D Foss
- Cummings School of Veterinary Medicine, Tufts University, Grafton, Massachusetts
| | - Lester H Lambert
- Critical Care and Sleep Division, Tufts Medical Center, Boston, Massachusetts
| | - Frances E Nargi
- Biotechnology and Human Systems Division, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, Massachusetts
| | - Gregory P Bopp
- Biotechnology and Human Systems Division, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, Massachusetts
| | - Lauren P Lee
- Biotechnology and Human Systems Division, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, Massachusetts
| | - Christina M Rudzinski
- Biotechnology and Human Systems Division, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, Massachusetts
| | - Benjamin L Ervin
- Biotechnology and Human Systems Division, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, Massachusetts
| | | | - Nicholas S Hill
- Critical Care and Sleep Division, Tufts Medical Center, Boston, Massachusetts.
| |
Collapse
|
11
|
Gass JD, Waite KB, Hill NJ, Dalton KR, Sawatzki K, Runstadler JA, Davis MF. A standardized instrument quantifying risk factors associated with bi-directional transmission of SARS-CoV-2 and other zoonotic pathogens: The COVID-19 human-animal interactions survey (CHAIS). One Health 2022; 15:100422. [PMID: 35910303 PMCID: PMC9327186 DOI: 10.1016/j.onehlt.2022.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022] Open
Abstract
Similar to many zoonotic pathogens which transmit from animals to humans, SARS-CoV-2 (CoV-2), the virus responsible for the COVID-19 pandemic, most likely originated in Rhinolophus bats before spreading among humans globally. Early into the pandemic, reports of CoV-2 diagnoses in animals from various countries emerged. While most CoV-2 positive animals were confirmed to have been in close contact with CoV-2 positive humans, there has been a paucity of published evidence to-date describing risk factors associated with CoV-2 transmission among humans and animals. The COVID-19 Human-Animal Interactions Survey (CHAIS) was developed to provide a standardized instrument describing human-animal interactions during the pandemic and to evaluate behavioral, spatiotemporal, and biological risk factors associated with bi-directional zoonotic transmission of CoV-2 within shared environments, predominantly households with limited information about human-wildlife or human-livestock interactions. CHAIS measures four broad domains of transmission risk: 1) risk and intensity of infection in human hosts, 2) spatial characteristics of shared environments, 3) behaviors and human-animal interactions, and 4) susceptible animal subpopulations. Following the development of CHAIS, with a One Health approach, a multidisciplinary group of experts (n = 20) was invited to review and provide feedback on the survey for content validity. Expert feedback was incorporated into two final survey formats—an extended version and an abridged version for which specific core questions addressing zoonotic and reverse zoonotic transmission were identified. Both versions are modularized, with each section having the capacity to serve as independent instruments, allowing researchers to customize the survey based on context and research-specific needs. Further adaptations for studies seeking to investigate other zoonotic pathogens with similar routes of transmission (i.e. respiratory, direct contact) are also possible. The CHAIS instrument is a standardized human-animal interaction survey developed to provide important data on risk factors that guide transmission of CoV-2, and other similar pathogens, among humans and animals. The CHAIS instrument is a standardized instrument evaluating risk factors for bi-directional CoV-2 zoonotic transmission It evaluates settings where humans and animals share close contact, mainly households It is highly adaptable for investigating other zoonotic pathogens such as influenza viruses It will enable pooling of data across studies for meta-analyses to improve predictive models It can help inform public health prevention and mitigation measures
Collapse
Affiliation(s)
- Jonathon D Gass
- Dept. of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, United States
| | - Kaitlin B Waite
- Dept. of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, United States
| | - Nichola J Hill
- Department of Biology, University of Massachusetts Boston, United States
| | - Kathryn R Dalton
- Dept. of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, United States
| | - Kaitlin Sawatzki
- Dept. of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, United States
| | - Jonathan A Runstadler
- Dept. of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, United States
| | - Meghan F Davis
- Dept. of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, United States.,Dept. of Molecular and Comparative Pathobiology; Division of Infectious Diseases, Johns Hopkins School of Medicine, United States
| | | |
Collapse
|
12
|
Kuhn JH, Adkins S, Alkhovsky SV, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bandte M, Beer M, Bejerman N, Bergeron É, Biedenkopf N, Bigarré L, Blair CD, Blasdell KR, Bradfute SB, Briese T, Brown PA, Bruggmann R, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Candresse T, Carson J, Casas I, Chandran K, Charrel RN, Chiaki Y, Crane A, Crane M, Dacheux L, Bó ED, de la Torre JC, de Lamballerie X, de Souza WM, de Swart RL, Dheilly NM, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Drexler JF, Duprex WP, Dürrwald R, Easton AJ, Elbeaino T, Ergünay K, Feng G, Feuvrier C, Firth AE, Fooks AR, Formenty PBH, Freitas-Astúa J, Gago-Zachert S, García ML, García-Sastre A, Garrison AR, Godwin SE, Gonzalez JPJ, de Bellocq JG, Griffiths A, Groschup MH, Günther S, Hammond J, Hepojoki J, Hierweger MM, Hongō S, Horie M, Horikawa H, Hughes HR, Hume AJ, Hyndman TH, Jiāng D, Jonson GB, Junglen S, Kadono F, Karlin DG, Klempa B, Klingström J, Koch MC, Kondō H, Koonin EV, Krásová J, Krupovic M, Kubota K, Kuzmin IV, Laenen L, Lambert AJ, Lǐ J, Li JM, Lieffrig F, Lukashevich IS, Luo D, Maes P, Marklewitz M, Marshall SH, Marzano SYL, McCauley JW, Mirazimi A, Mohr PG, Moody NJG, Morita Y, Morrison RN, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Neriya Y, Netesov SV, Neumann G, Nowotny N, Ochoa-Corona FM, Palacios G, Pallandre L, Pallás V, Papa A, Paraskevopoulou S, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Pérez DR, Pfaff F, Plemper RK, Postler TS, Pozet F, Radoshitzky SR, Ramos-González PL, Rehanek M, Resende RO, Reyes CA, Romanowski V, Rubbenstroth D, Rubino L, Rumbou A, Runstadler JA, Rupp M, Sabanadzovic S, Sasaya T, Schmidt-Posthaus H, Schwemmle M, Seuberlich T, Sharpe SR, Shi M, Sironi M, Smither S, Song JW, Spann KM, Spengler JR, Stenglein MD, Takada A, Tesh RB, Těšíková J, Thornburg NJ, Tischler ND, Tomitaka Y, Tomonaga K, Tordo N, Tsunekawa K, Turina M, Tzanetakis IE, Vaira AM, van den Hoogen B, Vanmechelen B, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Whitfield AE, Williams JV, Wolf YI, Yamasaki J, Yanagisawa H, Ye G, Zhang YZ, Økland AL. 2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2022; 167:2857-2906. [PMID: 36437428 PMCID: PMC9847503 DOI: 10.1007/s00705-022-05546-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Collapse
Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Greifswald, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, Starkville, MS, USA
| | - Martina Bandte
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Éric Bergeron
- Division of High-Consequence Pathogens and Pathology, Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nadine Biedenkopf
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Laurent Bigarré
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Carol D Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Paul A Brown
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Republic of South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | - Jeremy Carson
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Yuya Chiaki
- Division of Fruit Tree and Tea Pest Control Research, Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Mark Crane
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | - Laurent Dacheux
- Institut Pasteur, Université Paris Cité, Unit Lyssavirus Epidemiology and Neuropathology, National Reference Center for Rabies, WHO Collaborating Center for Reference and Research on Rabies, Paris, France
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - William M de Souza
- World Reference Center for Emerging Viruses and Arboviruses and Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Rik L de Swart
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, Maisons-Alfort, France
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Toufic Elbeaino
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Koray Ergünay
- Department of Medical Microbiology, Virology Unit, Hacettepe University Faculty of Medicine, Ankara, Turkey
- Walter Reed Biosystematics Unit (WRBU), Smithsonian Institution, Museum Support Center, Suitland, MD, USA
- One Health Branch, Walter Reed Army Institute of Research (WRAIR), Silver Spring, MD, USA
- Department of Entomology, Smithsonian Institution-National Museum of Natural History (NMNH), Washington, DC, USA
| | - Guozhong Feng
- China National Rice Research Institute, Hangzhou, China
| | | | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Scott E Godwin
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, USA
| | | | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Melanie M Hierweger
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Seiji Hongō
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Izumisano, Osaka, Japan
| | | | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Adam J Hume
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China
| | - Gilda B Jonson
- International Rice Research Institute, College, Los Baños, 4032, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Fujio Kadono
- Clinical Plant Science Center, Hosei University, Tokyo, Japan
| | - David G Karlin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Michel C Koch
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jarmila Krásová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Kenji Kubota
- Institute for Plant Protection, NARO, Tsukuba, Ibaraki, Japan
| | - Ivan V Kuzmin
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jun-Min Li
- Institute of Plant Virology, Ningbo University, Ningbo, China
| | | | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Dongsheng Luo
- Institut Pasteur, Université Paris Cité, Unit Lyssavirus Epidemiology and Neuropathology, Paris, France
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Sergio H Marshall
- Instituto de Biología-Laboratorio de Genética Molecular-Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service, Toledo, OH, USA
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Peter G Mohr
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | - Nick J G Moody
- CSIRO Australian Centre for Disease Preparedness, East Geelong, VIC, Australia
| | | | - Richard N Morrison
- Centre for Aquatic Animal Health and Vaccines, Department of Natural Resources and Environment Tasmania, Launceston, TAS, Australia
| | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | | | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Yutaro Neriya
- School of Agriculture, Utsunomiya University, Utsunomiya, Japan
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Francisco M Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics. Stillwater, Oklahoma State University, Oklahoma, USA
| | - Gustavo Palacios
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurane Pallandre
- French Agency for Food, Environmental and Occupational Heath Safety ANSES, Laboratory of Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidat Politècnica de Valencia, Valencia, Spain
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Methods Development and Research Infrastructure, Bioinformatics and Systems Biology, Robert Koch Institute, Berlin, Germany
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | | | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | | | - Richard K Plemper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | | | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, MD, USA
| | | | - Marius Rehanek
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Unversidad Nacional de La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, Facultad de Ciencias Exactas, Unversidad Nacional de La Plata, Buenos Aires, Argentina
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Artemis Rumbou
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease & Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Melanie Rupp
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Heike Schmidt-Posthaus
- Institute for Fish and Wildlife Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Torsten Seuberlich
- Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Stephen R Sharpe
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, China
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Jana Těšíková
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Nicole D Tischler
- Laboratorio de Virología Molecular, Centro Ciencia & Vida, Fundación Ciencia & Vida and Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Yasuhiro Tomitaka
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Keizō Tomonaga
- Institute for Life and Medical Sciences (LiMe), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur de Guinée, BP 4416, Conakry, Guinea
| | | | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR, USA
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Torino, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Nikos Vasilakis
- The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Junki Yamasaki
- Environmental Agriculture Promotion Division, Department of Agricultural Development, Kochi Prefectural Government, Kochi, Kochi, Japan
| | | | - Gongyin Ye
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, China Center for Disease Control and Prevention, Beijing, China
| | | |
Collapse
|
13
|
Gass JD, Kellogg HK, Hill NJ, Puryear WB, Nutter FB, Runstadler JA. Epidemiology and Ecology of Influenza A Viruses among Wildlife in the Arctic. Viruses 2022; 14:v14071531. [PMID: 35891510 PMCID: PMC9315492 DOI: 10.3390/v14071531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host–pathogen–environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.
Collapse
Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
- Correspondence:
| | - Hunter K. Kellogg
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA;
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| |
Collapse
|
14
|
Hill NJ, Bishop MA, Trovão NS, Ineson KM, Schaefer AL, Puryear WB, Zhou K, Foss AD, Clark DE, MacKenzie KG, Gass JD, Borkenhagen LK, Hall JS, Runstadler JA. Ecological divergence of wild birds drives avian influenza spillover and global spread. PLoS Pathog 2022; 18:e1010062. [PMID: 35588106 PMCID: PMC9119557 DOI: 10.1371/journal.ppat.1010062] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/01/2022] [Indexed: 01/21/2023] Open
Abstract
The diversity of influenza A viruses (IAV) is primarily hosted by two highly divergent avian orders: Anseriformes (ducks, swans and geese) and Charadriiformes (gulls, terns and shorebirds). Studies of IAV have historically focused on Anseriformes, specifically dabbling ducks, overlooking the diversity of hosts in nature, including gull and goose species that have successfully adapted to human habitats. This study sought to address this imbalance by characterizing spillover dynamics and global transmission patterns of IAV over 10 years at greater taxonomic resolution than previously considered. Furthermore, the circulation of viral subtypes in birds that are either host-adapted (low pathogenic H13, H16) or host-generalist (highly pathogenic avian influenza—HPAI H5) provided a unique opportunity to test and extend models of viral evolution. Using Bayesian phylodynamic modelling we uncovered a complex transmission network that relied on ecologically divergent bird hosts. The generalist subtype, HPAI H5 was driven largely by wild geese and swans that acted as a source for wild ducks, gulls, land birds, and domestic geese. Gulls were responsible for moving HPAI H5 more rapidly than any other host, a finding that may reflect their long-distance, pelagic movements and their immuno-naïve status against this subtype. Wild ducks, long viewed as primary hosts for spillover, occupied an optimal space for viral transmission, contributing to geographic expansion and rapid dispersal of HPAI H5. Evidence of inter-hemispheric dispersal via both the Pacific and Atlantic Rims was detected, supporting surveillance at high latitudes along continental margins to achieve early detection. Both neutral (geographic expansion) and non-neutral (antigenic selection) evolutionary processes were found to shape subtype evolution which manifested as unique geographic hotspots for each subtype at the global scale. This study reveals how a diversity of avian hosts contribute to viral spread and spillover with the potential to improve surveillance in an era of rapid global change. Our study provides novel insights into the biology of influenza A virus (IAV), which is timely in view of the unusually large number of animal and human cases of highly pathogenic avian influenza (HPAI) H5 across Europe, Asia, Africa and North America. Currently we face challenges with predicting how the avian reservoir will influence IAV spread because the mechanisms by which different subtypes disperse are not well understood. Our study sought to address this knowledge gap by systematically comparing the evolutionary dynamics that drive IAV transmission across subtypes and bird hosts with the goal of identifying spillover pathways at the wild-domestic interface. By analyzing the evolution of IAV over 10 years at greater taxonomic resolution than previously considered, we uncovered a complex transmission network that relied on ecologically divergent bird hosts. Domestic birds were responsible for slow but steady range expansion of HPAI H5, while wild birds such as geese, swans, gulls and ducks contibuted to rapid but episodic dispersal via uniquely different pathways. By assessing how virus-host systems are coupled, findings from this study have the potential to refine and enhance global surveillance and outbreak prediction.
Collapse
Affiliation(s)
- Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, Massachusetts, United States of America
- * E-mail:
| | - Mary Anne Bishop
- Prince William Sound Science Center, Cordova, Alaska, United States of America
| | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Katherine M. Ineson
- U.S. Fish and Wildlife Service, Hadley, Massachusetts, United States of America
| | - Anne L. Schaefer
- Prince William Sound Science Center, Cordova, Alaska, United States of America
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Katherine Zhou
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Alexa D. Foss
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Daniel E. Clark
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, United States of America
| | - Kenneth G. MacKenzie
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, United States of America
| | - Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Laura K. Borkenhagen
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| | - Jeffrey S. Hall
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine Tufts University, North Grafton, Massachusetts, United States of America
| |
Collapse
|
15
|
Ineson KM, Hill NJ, Clark DE, MacKenzie KG, Whitney JJ, Laskaris Y, Ronconi RA, Ellis JC, Giroux JF, Lair S, Stevens S, Puryear WB, Runstadler JA. Age and season predict influenza A virus dynamics in urban gulls: consequences for natural hosts in unnatural landscapes. Ecol Appl 2022; 32:e2497. [PMID: 34783416 DOI: 10.1002/eap.2497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/01/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Gulls are ubiquitous in urban areas due to a growing reliance on anthropogenic feeding sites, which has led to changes in their abundance, distribution, and migration ecology, with implications for disease transmission. Gulls offer a valuable model for testing hypotheses regarding the dynamics of influenza A virus (IAV) - for which gulls are a natural reservoir in urban areas. We sampled sympatric populations of Ring-billed (Larus delawarensis), Herring (L. argentatus), and Great Black-backed Gulls (L. marinus) along the densely populated Atlantic rim of North America to understand how IAV transmission is influenced by drivers such as annual cycle, host species, age, habitat type, and their interplay. We found that horizontal transmission, rather than vertical transmission, played an outsized role in the amplification of IAV due to the convergence of gulls from different breeding grounds and age classes. We detected overlapping effects of age and season in our prevalence model, identifying juveniles during autumn as the primary drivers of the seasonal epidemic in gulls. Gulls accumulated immunity over their lifespan, however short-term fluctuations in seroprevalence were observed, suggesting that migration may impose limits on the immune system to maintain circulating antibodies. We found that gulls in coastal urban habitats had higher viral prevalence than gulls captured inland, correlating with higher richness of waterbird species along the coast, a mechanism supported by our movement data. The peak in viral prevalence in newly fledged gulls that are capable of long-distance movement has important implications for the spread of pathogens to novel hosts during the migratory season as well as for human health as gulls increasingly utilize urban habitats.
Collapse
Affiliation(s)
- Katherine M Ineson
- Department of Natural Resources & the Environment, University of New Hampshire, Durham, New Hampshire, 03824, USA
| | - Nichola J Hill
- Department of Biology, University of Massachusetts, Boston, Massachusetts, 02125, USA
| | - Daniel E Clark
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, 01583, USA
| | - Kenneth G MacKenzie
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, 01583, USA
| | - Jillian J Whitney
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, 01583, USA
| | - Yianni Laskaris
- US Fish and Wildlife Service, Galloway, New Jersey, 08205, USA
| | - Robert A Ronconi
- Canadian Wildlife Service, Environment and Climate Change Canada, Dartmouth, Nova Scotia, B2Y 2N6, Canada
| | - Julie C Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, Kennett Square, Pennsylvania, 19348, USA
| | - Jean-François Giroux
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, H3C 3P8, Canada
| | - Stéphane Lair
- Centre québécois sur la santé des animaux sauvages/Canadian Wildlife Health Cooperative, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, J2S 2M2, Canada
| | - Skyler Stevens
- Division of Mathematics, Physical, and Natural Sciences, University of New Mexico, Gallup, New Mexico, 87301, USA
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts, 01536, USA
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts, 01536, USA
| |
Collapse
|
16
|
Kuhn JH, Adkins S, Agwanda BR, Kubrusli RA, Alkhovsky (Aльxoвcкий Cepгeй Bлaдимиpoвич) SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao (曹孟籍) M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki (千秋祐也) Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Bó ED, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara (海老原秀喜) H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu (付晶晶) J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han (韩彤) T, Hepojoki J, Hewson R, Hong (洪健) J, Hong (洪霓) N, Hongo S, Horie (堀江真行) M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng (姜道宏) D, Jonson GB, Junglen S, Kadono (上遠野冨士夫) F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō (近藤秀樹) H, Koonin EV, Krupovic M, Kubota (久保田健嗣) K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li (李邵蓉) S, Li (李龙辉) L, Lǐ (李建荣) J, Liu (刘华珍) H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki (夏秋知英) T, Navarro JA, Netesov (Heтёcoв Cepгeй Bиктopoвич) SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa (Άννα Παπά) A, Paraskevopoulou (Παρασκευοπούλου Σοφία) S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi (亓立莹) L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya (笹谷孝英) T, Schulze AD, Schwemmle M, Shi (施莽) M, Shí (石晓宏) X, Shí (石正丽) Z, Shimomoto (下元祥史) Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song (송진원) JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada (高田礼人) A, Takeuchi (竹内繁治) S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka (冨高保弘) Y, Tomonaga (朝長啓造) K, Tordo N, Torto B, Towner JS, Tsuda (津田新哉) S, Tu (涂长春) C, Turina M, Tzanetakis I, Uchida J, Usugi (宇杉富雄) T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis (Νίκος Βασιλάκης) N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang (王林发) LF, Wang (王国平) G, Wang (王雁翔) Y, Wang (王亚琴) YQ, Waqas M, Wèi (魏太云) T, Wen (温少华) S, Whitfield AE, Williams JV, Wolf YI, Wu (吴建祥) JX, Xu (徐雷) L, Yanagisawa (栁澤広宣) H, Yang (杨彩霞) C, Yang (杨作坤) Z, Zerbini FM, Zhai (翟立峰) L, Zhang YZ, Zhang (张松) S, Zhang (张靖国) J, Zhang (张哲) Z, Zhou (周雪平) X. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3567-3579. [PMID: 34786611 PMCID: PMC11078012 DOI: 10.1007/s00705-021-05266-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National
Institute of Allergy and Infectious Diseases, National Institutes of Health,
Frederick, MD, USA
| | - Scott Adkins
- United States Department of Agriculture, Agricultural
Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R. Agwanda
- Zoology Department, National Museums of Kenya, Nairobi,
Kenya
- Jomo Kenyatta University of Agriculture &
Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington
University School of Medicine, St. Louis, MO, USA
| | | | - María A. Ayllón
- Centro de Biotecnología y Genómica de
Plantas, Universidad Politécnica de Madrid—Instituto Nacional de
Investigación y Tecnología Agraria y Alimentaria, Campus de
Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología
Vegetal, Escuela Técnica Superior de Ingeniería Agronómica,
Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid,
Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of
Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of
Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases,
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health,
Greifswald-Insel Riems, Germany
| | - Matthew J. Ballinger
- Department of Biological Sciences, Mississippi State
University, Mississippi State, MS, USA
| | - Christopher F. Basler
- Center for Microbial Pathogenesis, Institute for
Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD,
USA
| | - Martin Beer
- Institute of Diagnostic Virology,
Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J. Bennett
- Genomics and Bioinformatics Department, Biological
Defense Research Directorate, Naval Medical Research Center–Frederick, Fort
Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of
High-Consequence Pathogens and Pathology, Centers for Disease Control and
Prevention, Atlanta, GA, USA
| | - Brian H. Bird
- School of Veterinary Medicine, One Health Institute,
University of California, Davis, Davis, CA, USA
| | - Carol D. Blair
- Department of Microbiology, Immunology and Pathology,
Colorado State University, Fort Collins, CO, USA
| | - Kim R. Blasdell
- Commonwealth Scientific and Industrial Research
Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC,
Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University,
Middlesbrough TS1 3BX, UK
- National Horizons Centre, Teesside University,
Darlington DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center,
Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research
Center, Seattle, WA, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of
Epidemiology, Mailman School of Public Health, Columbia University, New York, NY,
USA
| | - Paul A. Brown
- Laboratory of Ploufragan-Plouzané-Niort, French
Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan,
France
| | - Judith K. Brown
- School of Plant Sciences, University of Arizona, Tucson,
AZ, USA
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD, USA
| | - Michael J. Buchmeier
- Department of Molecular Biology and Biochemistry,
University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas
Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service
and Division of Virology, University of the Free State, Bloemfontein, Republic of
South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao (曹孟籍)
- National Citrus Engineering and Technology Research
Center, Citrus Research Institute, Southwest University, Beibei, Chongqing,
People’s Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National
Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert
Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N. Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD
190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Yuya Chiaki (千秋祐也)
- Grape and Persimmon Research Station, Institute of Fruit
tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and
International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate,
Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales,
Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The
Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD
190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L. de Swart
- Department Viroscience, Erasmus MC, University Medical
Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto
Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba,
Argentina
- Unidad de Fitopatología y Modelización
Agrícola, Consejo Nacional de Investigaciones Científicas y
Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health
Laboratory, 94704 Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante,
Consiglio Nazionale delle Ricerche, Turin, Italy
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation,
The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari,
Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg,
Marburg, Germany
| | - Michael A. Drebot
- Zoonotic Diseases and Special Pathogens, National
Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J. Felix Drexler
- Institute of Virology,
Charité-Universitätsmedizin Berlin, Corporate Member of Freie
Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G. Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA
Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear
Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W. Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh,
PA, USA
| | | | - John M. Dye
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | | | | | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology,
Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W. Ferguson
- School of Veterinary Medicine, St. George’s
University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin,
Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular
Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu (付晶晶)
- College of Life Science and Engineering, Shenyang
University, Shenyang, Liaoning, People’s Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal
Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin,
Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin
Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and
Prevention, Chinese Center for Disease Control and Prevention, Beijing,
People’s Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología
Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R. Garrison
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für
ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J. Gonzalez
- Department of Microbiology and Immunology, Division of
Biomedical Graduate Research Organization, School of Medicine, Georgetown
University, Washington, DC 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging
Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA,
USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of
Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases,
Friedric h-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic
Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for
Tropical Medicine, Hamburg, Germany
| | - Roy A. Hall
- Australian Infectious Diseases Research Centre, School of
Chemistry and Molecular Biosciences, The University of Queensland, Brisbane,
Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States
Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD,
USA
| | - Tong Han (韩彤)
- College of Life Science and Engineering, Shenyang
University, Shenyang, Liaoning, People’s Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum,
Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty,
University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London,
UK
| | - Jiang Hong (洪健)
- Analysis Center of Agrobiology and Environmental
Sciences, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ni Hong (洪霓)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University
Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie (堀江真行)
- Hakubi Center for Advanced Research, Kyoto University,
Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of
Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | | | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins,
CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H. Hyndman
- School of Veterinary Medicine, Murdoch University,
Murdoch, WA, Australia
| | - M. Ilyas
- Entomology and Plant Pathology, North Carolina State
University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng (姜道宏)
- State Key Laboratory of Agricultural Microbiology,
Huazhong Agricultural University, Wuhan, Hubei Province, People’s Republic of
China
| | - Gilda B. Jonson
- Rice Breeding Innovations Platform, International Rice
Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology,
Charité-Universitätsmedizin Berlin, Corporate Member of Free
University Berlin, Humboldt-University Berlin, and Berlin Institute of Health,
Berlin, Germany
- German Centre for Infection Research, Berlin,
Germany
| | - Fujio Kadono (上遠野冨士夫)
- Department of Clinical Plant Science, Faculty of
Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H. Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada,
Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak
Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine
Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm,
Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious
Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular
Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō (近藤秀樹)
- Institute of Plant Science and Resources, Okayama
University, Kurashiki, Japan
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris,
France
| | | | - Gael Kurath
- US Geological Survey Western Fisheries Research Center,
Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases
unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals
Leuven, Leuven, Belgium
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins,
CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai, New York, NY, USA
| | | | - Eric M. Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French
National Research Institute for Sustainable Development (IRD), Montpellier,
France
| | - Shaorong Li (李邵蓉)
- Fisheries and Oceans Canada, Pacific Biological
Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Longhui Li (李龙辉)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Jiànróng Lǐ (李建荣)
- Department of Veterinary Biosciences, College of
Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu (刘华珍)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Igor S. Lukashevich
- Department of Pharmacology and Toxicology, School of
Medicine, and the Center for Predictive Medicine for Biodefense and Emerging
Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases
unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology,
Charité-Universitätsmedizin Berlin, Corporate Member of Free
University Berlin, Humboldt-University Berlin, and Berlin Institute of Health,
Berlin, Germany
- German Center for Infection Research (DZIF), Berlin,
Germany
| | - Sergio H. Marshall
- Pontificia Universidad Católica de
Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L. Marzano
- United States Department of Agriculture, Agricultural
Research Service, Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology
Laboratory, Liège University, Liege, Belgium
| | | | - Michael Melzer
- Plant and Environmental Protection Sciences, University
of Hawai’i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada,
Nanaimo, BC, Canada
| | - Tobi J. Ming
- Molecular Genetics, Pacific Biological Station,
Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J. Mordecai
- Department of Medicine, Univeristy of British Columbia,
Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging
Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA,
USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural
Research and Extension Center, Washington State University, Prosser, WA, USA
| | | | - José A. Navarro
- Instituto de Biología Molecular y Celular de
Plantas, Universitat Politècnica de València-Consejo Superior de
Investigaciones Científicas, Valencia, Spain
| | | | - Gabriele Neumann
- Influenza Research Institute, Department of
Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary
Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of
Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de
Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad
Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health
Center, Budapest, Hungary
| | - Anna Papa (Άννα Παπά)
- National Reference Centre for Arboviruses and
Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle
University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou (Παρασκευοπούλου Σοφία)
- Institute of Virology,
Charité-Universitätsmedizin Berlin, corporate member of Freie
Universität Berlin, Humboldt-Universität zu Berlin, and Berlin
Institute of Health, Berlin, Germany
| | - Adam C. Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI,
USA
| | - Colin R. Parrish
- Baker Institute for Animal Health, College of
Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A. Patterson
- Fisheries and Oceans Canada, Resource and Environmental
Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and
Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz,
Rio de Janeiro, Brazil
| | - Janusz T. Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases,
National Institute for Communicable Diseases of the National Health Laboratory
Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of
Veterinary Medicine and Biomedical Sciences, Texas A&M University, College
Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Daniel R. Pérez
- Department of Population Health, College of Veterinary
Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S. Postler
- Department of Microbiology and Immunology, Vagelos
College of Physicians and Surgeons, Columbia University Irving Medical Center, New
York, NY 10032, USA
| | - Liying Qi (亓立莹)
- Jiangxi Academy of Agricultural Sciences, Nanchang,
Jiangxi, People’s Republic of China
| | | | - Renato O. Resende
- Departamento de Biologia Celular, Universidade de
Brasília, Brasília, Brazil
| | - Carina A. Reyes
- Instituto de Biotecnología y Biología
Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K. Rima
- Centre for Experimental Medicine, School of Medicine,
Dentistry and Biomedical Sciences, The Queen’s University of Belfast,
Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología
Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología
Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de
Investigaciones Científico Tecnológico—Universidad Nacional de
La Plata, La Plata, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory
Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology,
Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la
Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health,
Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North
Grafton, MA 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology,
Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS,
USA
| | | | - Maria S. Salvato
- Institute of Human Virology, University of Maryland
School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology,
Nairobi, Kenya
| | - Takahide Sasaya (笹谷孝英)
- Western Region Agricultural Research Center, National
Agriculture and Food Research Organization, Fukuyama, Japan
| | - Angela D. Schulze
- Molecular Genetics Lab, Pacific Biological Station,
Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical
Center-University Freiburg, Freiburg, Germany
| | - Mang Shi (施莽)
- Sun Yat-sen University, Shenzhen, People’s
Republic of China
| | - Xiǎohóng Shí (石晓宏)
- MRC-University of Glasgow Centre for Virus Research,
Glasgow, Scotland, UK
| | - Zhènglì Shí (石正丽)
- CAS Key Laboratory of Special Pathogens, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei, People’s Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental
Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G. Siddell
- School of Cellular and Molecular Medicine, University
of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford,
Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS
“E. Medea”, Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plant
and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire,
UK
| | - Jin-Won Song (송진원)
- Department of Microbiology, College of Medicine, Korea
University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health,
Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R. Spengler
- Viral Special Pathogens Branch, Division of
High-Consequence Pathogens and Pathology, Centers for Disease Control and
Prevention, Atlanta, USA
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology,
College of Veterinary Medicine and Biomedical Sciences, Colorado State University,
Fort Collins, CO, USA
| | - David M. Stone
- Centre for Environment, Fisheries and Aquaculture
Science, Weymouth, Dorset, UK
| | | | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences,
Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries,
University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada,
Nanaimo, BC, Canada
| | - Ayato Takada (高田礼人)
- Division of Global Epidemiology, Research Center for
Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | - Amy Teffer
- Department of Forest Sciences, University of British
Columbia, Vancouver, Canada
| | - Robert B. Tesh
- The University of Texas Medical Branch, Galveston, TX,
USA
| | | | | | - Keizō Tomonaga (朝長啓造)
- Institute for Frontier Life and Medical Sciences
(inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO
Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference
Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology,
Nairobi, Kenya
| | - Jonathan S. Towner
- Viral Special Pathogens Branch, Division of
High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic
Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA,
USA
- Institut Pasteur de Guinée, Conakry,
Guinea
| | - Shinya Tsuda (津田新哉)
- Department of Clinical Plant Science, Faculty of
Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu (涂长春)
- Changchun Veterinary Research Institute, Chinese
Academy of Agricultural Sciences, Changchun, Jilin Province, People’s
Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council
of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis Tzanetakis
- Department of Entomology and Plant Pathology, Division
of Agriculture, University of Arkansas System,, Fayetteville, AR 72701, USA
| | | | - Tomio Usugi (宇杉富雄)
- Central Region Agricultural Research Center, NARO,
Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University
Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied
Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona
State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of
Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South
Africa
| | | | - Martin Verbeek
- Wageningen University and Research, Biointeractions and
Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National
Institute of Allergy and Infectious Diseases, National Institutes of Health,
Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures
Center, Fort Detrick, Frederick, MD, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences,
University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang (王林发)
- Programme in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore, Singapore
| | - Guoping Wang (王国平)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Yanxiang Wang (王雁翔)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Ya-qin Wang (王亚琴)
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety
Control in Hubei Province, College of Plant Science and Technology, Huazhong
Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Tàiyún Wèi (魏太云)
- Fujian Province Key Laboratory of Plant Virology,
Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou,
Fujian, People’s Republic of China
| | - Shaohua Wen (温少华)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Anna E. Whitfield
- Department of Entomology and Plant Pathology, North
Carolina State University, Raleigh, NC, USA
| | - John V. Williams
- School of Medicine, University of Pittsburgh,
Pittsburgh, PA, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiang-xiang Wu (吴建祥)
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Lei Xu (徐雷)
- Jiangxi Academy of Agricultural Sciences, Nanchang,
Jiangxi, People’s Republic of China
| | | | - Caixia Yang (杨彩霞)
- College of Life Science and Engineering, Shenyang
University, Shenyang, Liaoning, People’s Republic of China
| | - Zuokun Yang (杨作坤)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - F. Murilo Zerbini
- epartamento de Fitopatologia, Instituto de
Biotecnologia Aplicada à Agropecuária, Universidade Federal de
Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai (翟立峰)
- Key Laboratory of Horticultural Plant Biology, Ministry
of Education, Wuhan 430070, Hubei, People’s Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and
Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing,
People’s Republic of China
- Shanghai Public Health Clinical Center & Institutes
of Biomedical Sciences, Fudan University, Shanghai, People’s Republic of
China
| | - Song Zhang (张松)
- National Citrus Engineering and Technology Research
Center, Citrus Research Institute, Southwest University, Beibei, Chongqing,
People’s Republic of China
| | - Jinguo Zhang (张靖国)
- National Sand Pear Germplasm Repository in Wuchang,
Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan,
Hubei, People’s Republic of China
| | - Zhe Zhang (张哲)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Xueping Zhou (周雪平)
- State Key Laboratory for Biology of Plant Diseases and
Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural
Sciences, Beijing, People’s Republic of China
| |
Collapse
|
17
|
Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li S, Li L, Lǐ J, Liu H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa A, Paraskevopoulou S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya T, Schulze AD, Schwemmle M, Shi M, Shí X, Shí Z, Shimomoto Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada A, Takeuchi S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka Y, Tomonaga K, Tordo N, Torto B, Towner JS, Tsuda S, Tu C, Turina M, Tzanetakis IE, Uchida J, Usugi T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang LF, Wang G, Wang Y, Wang Y, Waqas M, Wèi T, Wen S, Whitfield AE, Williams JV, Wolf YI, Wu J, Xu L, Yanagisawa H, Yang C, Yang Z, Zerbini FM, Zhai L, Zhang YZ, Zhang S, Zhang J, Zhang Z, Zhou X. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3513-3566. [PMID: 34463877 PMCID: PMC8627462 DOI: 10.1007/s00705-021-05143-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Collapse
Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R Agwanda
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture & Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, Davis, CA, USA
| | - Carol D Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Republic of South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuya Chiaki
- Grape and Persimmon Research Station, Institute of Fruit tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W Ferguson
- School of Veterinary Medicine, St. George's University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin, Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD, USA
| | - Tong Han
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London, UK
| | - Jiang Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - John S Hu
- University of Hawaii, Honolulu, HI, USA
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - M Ilyas
- Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Gilda B Jonson
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research, Berlin, Germany
| | - Fujio Kadono
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Kenji Kubota
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Longhui Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service , Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liege, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | - Michael Melzer
- Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Tobi J Ming
- Molecular Genetics, Pacific Biological Station, Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J Mordecai
- Department of Medicine, Univeristy of British Columbia, Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Adam C Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A Patterson
- Fisheries and Oceans Canada, Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz, Rio de Janeiro, Brazil
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Angela D Schulze
- Molecular Genetics Lab, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shigeharu Takeuchi
- Japan Plant Protection Association Kochi Experiment Station, Konan, Kochi, Japan
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Amy Teffer
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Yasuhiro Tomitaka
- Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, Japan
| | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), , Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Shinya Tsuda
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People's Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System,, Fayetteville, AR, 72701, USA
| | | | - Tomio Usugi
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People's Republic of China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiangxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Caixia Yang
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei , People's Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, People's Republic of China
| | - Zhe Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| |
Collapse
|
18
|
Abstract
Background: There is great interest in understanding the viral genomic predictors of phenotypic traits that allow influenza A viruses to adapt to or become more virulent in different hosts. Machine learning techniques have demonstrated promise in addressing this critical need for other pathogens because the underlying algorithms are especially well equipped to uncover complex patterns in large datasets and produce generalizable predictions for new data. As the body of research where these techniques are applied for influenza A virus phenotype prediction continues to grow, it is useful to consider the strengths and weaknesses of these approaches to understand what has prevented these models from seeing widespread use by surveillance laboratories and to identify gaps that are underexplored with this technology. Methods and Results: We present a systematic review of English literature published through 15 April 2021 of studies employing machine learning methods to generate predictions of influenza A virus phenotypes from genomic or proteomic input. Forty-nine studies were included in this review, spanning the topics of host discrimination, human adaptability, subtype and clade assignment, pandemic lineage assignment, characteristics of infection, and antiviral drug resistance. Conclusions: Our findings suggest that biases in model design and a dearth of wet laboratory follow-up may explain why these models often go underused. We, therefore, offer guidance to overcome these limitations, aid in improving predictive models of previously studied influenza A virus phenotypes, and extend those models to unexplored phenotypes in the ultimate pursuit of tools to enable the characterization of virus isolates across surveillance laboratories.
Collapse
Affiliation(s)
- Laura K Borkenhagen
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| | - Martin W Allen
- Department of Computer Science, School of Engineering, Tufts University, Medford, MA, USA
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, USA
| |
Collapse
|
19
|
Kuhn JH, Adkins S, Alioto D, Alkhovsky SV, Amarasinghe GK, Anthony SJ, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Bartonička T, Basler C, Bavari S, Beer M, Bente DA, Bergeron É, Bird BH, Blair C, Blasdell KR, Bradfute SB, Breyta R, Briese T, Brown PA, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Buzkan N, Calisher CH, Cao M, Casas I, Chamberlain J, Chandran K, Charrel RN, Chen B, Chiumenti M, Choi IR, Clegg JCS, Crozier I, da Graça JV, Dal Bó E, Dávila AMR, de la Torre JC, de Lamballerie X, de Swart RL, Di Bello PL, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolja VV, Dolnik O, Drebot MA, Drexler JF, Dürrwald R, Dufkova L, Dundon WG, Duprex WP, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Fernandes J, Fooks AR, Formenty PBH, Forth LF, Fouchier RAM, Freitas-Astúa J, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gbakima A, Goldstein T, Gonzalez JPJ, Griffiths A, Groschup MH, Günther S, Guterres A, Hall RA, Hammond J, Hassan M, Hepojoki J, Hepojoki S, Hetzel U, Hewson R, Hoffmann B, Hongo S, Höper D, Horie M, Hughes HR, Hyndman TH, Jambai A, Jardim R, Jiāng D, Jin Q, Jonson GB, Junglen S, Karadağ S, Keller KE, Klempa B, Klingström J, Kobinger G, Kondō H, Koonin EV, Krupovic M, Kurath G, Kuzmin IV, Laenen L, Lamb RA, Lambert AJ, Langevin SL, Lee B, Lemos ERS, Leroy EM, Li D, Lǐ J, Liang M, Liú W, Liú Y, Lukashevich IS, Maes P, Marciel de Souza W, Marklewitz M, Marshall SH, Martelli GP, Martin RR, Marzano SYL, Massart S, McCauley JW, Mielke-Ehret N, Minafra A, Minutolo M, Mirazimi A, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro B, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Nylund A, Økland AL, Oliveira RC, Palacios G, Pallas V, Pályi B, Papa A, Parrish CR, Pauvolid-Corrêa A, Pawęska JT, Payne S, Pérez DR, Pfaff F, Radoshitzky SR, Rahman AU, Ramos-González PL, Resende RO, Reyes CA, Rima BK, Romanowski V, Robles Luna G, Rota P, Rubbenstroth D, Runstadler JA, Ruzek D, Sabanadzovic S, Salát J, Sall AA, Salvato MS, Sarpkaya K, Sasaya T, Schwemmle M, Shabbir MZ, Shí X, Shí Z, Shirako Y, Simmonds P, Širmarová J, Sironi M, Smither S, Smura T, Song JW, Spann KM, Spengler JR, Stenglein MD, Stone DM, Straková P, Takada A, Tesh RB, Thornburg NJ, Tomonaga K, Tordo N, Towner JS, Turina M, Tzanetakis I, Ulrich RG, Vaira AM, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, Wahl V, Walker PJ, Wang H, Wang J, Wang X, Wang LF, Wèi T, Wells H, Whitfield AE, Williams JV, Wolf YI, Wú Z, Yang X, Yáng X, Yu X, Yutin N, Zerbini FM, Zhang T, Zhang YZ, Zhou G, Zhou X. 2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2020; 165:3023-3072. [PMID: 32888050 PMCID: PMC7606449 DOI: 10.1007/s00705-020-04731-2] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/04/2020] [Indexed: 12/13/2022]
Abstract
In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Collapse
Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Simon J Anthony
- Mailman School of Public Health, Columbia University, New York, NY, USA
- EcoHealth Alliance, New York, NY, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Tomáš Bartonička
- Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Christopher Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Dennis A Bente
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
| | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, CA, USA
| | - Carol Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | - Steven B Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Department of Epidemiology, Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas, Medical Branch at Galveston, Galveston, TX, USA
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service, University of the Free State, Bloemfontein, Republic of South Africa
| | - Nihal Buzkan
- Department of Plant Protection, Faculty of Agriculture, Kahramanmaras Sütçü Imam University, Avsar Campus, 46060, Kahramanmaras, Turkey
| | | | - Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - John Chamberlain
- Virology and Pathogenesis Group, National Infection Service, Public Health England, Porton Down, UK
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Biao Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, TX, USA
| | - Elena Dal Bó
- CIDEFI. Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Alberto M R Dávila
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ-IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Patrick L Di Bello
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | | | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | | | | | - Leonie F Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Ron A M Fouchier
- Department Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | | | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aiah Gbakima
- Metabiota, Inc. Sierra Leone, Freetown, Sierra Leone
| | - Tracey Goldstein
- One Health Institute, Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Martin H Groschup
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Hamburg, Germany
| | - Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- United States Department of Agriculture, Agricultural Research Service, USNA, Floral and Nursery Plants Research Unit, Beltsville, MD, USA
| | - Mohamed Hassan
- Department of Agricultural Botany, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Vetsuisse Faculty, Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Satu Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Mobidiag Ltd, Espoo, Finland
| | - Udo Hetzel
- Institute of Veterinary Pathology, University of Zuerich, Zurich, Switzerland
| | - Roger Hewson
- Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Bernd Hoffmann
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Seiji Hongo
- Department of Infectious Diseases, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Dirk Höper
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - Amara Jambai
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qi Jin
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Gilda B Jonson
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Serpil Karadağ
- Republic Of Turkey Ministry Of Agriculture And Forestry, Pistachio Research Institute, Gaziantep, Turkey
| | - Karen E Keller
- United States Department of Agriculture, Agricultural Research Service, Horticulture Crops Research Unit, Corvallis, OR, USA
| | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Ivan V Kuzmin
- US Department of Agriculture, Animal and Plant Health Inspection, National Veterinary Services Laboratories, Diagnostic Virology Laboratory, Ames, USA
| | - Lies Laenen
- Zoonotic Infectious Diseases Unit, KU Leuven, Rega Institute, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Robert A Lamb
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Howard Hughes Medical Institute, Northwestern University, Evanston, IL, USA
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elba R S Lemos
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Dexin Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Mifang Liang
- Key Laboratory for Medical Virology, NHFPC, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wénwén Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yàn Liú
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, The Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- Department of Agricultural Biotechnology, Center for Fungal Pathogenesis, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Giovanni P Martelli
- Department of Plant, Soil and Food Sciences, University "Aldo Moro", Bari, Italy
| | - Robert R Martin
- United States Department of Agriculture, Horticultural Crops Research Unit, Corvallis, OR, USA
| | - Shin-Yi L Marzano
- Department of Biology and Microbiology, Department of Plant Sciences, South Dakota State University, Brookings, SD, USA
| | - Sébastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liège, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | | | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - Maria Minutolo
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante-Consiglio Nazionale delle ricerche (Institute for Sustainable Plant Protection-National Research Council), Bari, Italy
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Department of Pathobiological Sciences, Influenza Research Institute, University of Wisconsin-Madison, Madison, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Are Nylund
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Arnfinn L Økland
- Fish Disease Research Group, Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Renata C Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Rio de Janeiro, RJ, Brasil
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Colin R Parrish
- College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Sheli R Radoshitzky
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Aziz-Ul Rahman
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Daniel Ruzek
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Jiří Salát
- Veterinary Research Institute, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005, Ceske Budejovice, Czech Republic
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kamil Sarpkaya
- Department of Forestry Engineering, Faculty of Forestry, Karabuk University (UNIKA), Karabük, Turkey
| | - Takahide Sasaya
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Japan
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Muhammad Z Shabbir
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Sophie Smither
- CBR Division, Dstl, Porton Down, Salisbury, Wiltshire, UK
| | - Teemu Smura
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten M Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Institut Pasteur, Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV and CCHFV, Paris, France
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Ioannis Tzanetakis
- Division of Agriculture, Department of Entomology and Plant Pathology, University of Arkansas System, Fayetteville, AR, 72701, USA
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Südufer 10, 17493, Greifswald-Insel Riems, Germany
- German Center of Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 73 Strada delle Cacce, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Hui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB-Fondation Mérieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Heather Wells
- Mailman School of Public Health, Center for Infection and Immunity, Columbia University, New York, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Zhìqiáng Wú
- MOH Key Laboratory of Systems Biology of Pathogens, IPB, CAMS, Beijing, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xīnglóu Yáng
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Xuejie Yu
- Wuhan University School of Health Sciences, Wuhan, China
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
- Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangdong, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
20
|
Seifried BM, Qi W, Yang YJ, Mai DJ, Puryear WB, Runstadler JA, Chen G, Olsen BD. Glycoprotein Mimics with Tunable Functionalization through Global Amino Acid Substitution and Copper Click Chemistry. Bioconjug Chem 2020; 31:554-566. [PMID: 32078297 DOI: 10.1021/acs.bioconjchem.9b00601] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glycoproteins and their mimics are challenging to produce because of their large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein a new approach to protein bioconjugate synthesis is demonstrated that can approach the functionalization densities of natural glycoproteins through oligosaccharide grafting. Global amino acid substitution is used to replace the methionine residues in a methionine-enriched elastin-like polypeptide with homopropargylglycine (HPG); the substitution was found to replace 93% of the 41 methionines in the protein sequence as well as broaden and increase the thermoresponsive transition. A series of saccharides were conjugated to the recombinant protein backbones through copper(I)-catalyzed alkyne-azide cycloaddition to determine reactivity trends, with 83-100% glycosylation of HPGs. Only an acetyl-protected sialyllactose moiety showed a lower level of 42% HPG glycosylation that is attributed to steric hindrance. The recombinant glycoproteins reproduced the key biofunctional properties of their natural counterparts such as viral inhibition and lectin binding.
Collapse
Affiliation(s)
- Brian M Seifried
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wenjing Qi
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Yun Jung Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Danielle J Mai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, United States
| | - Guosong Chen
- The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| | - Bradley D Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Macromolecular Science, Fudan University, Shanghai 200000, China
| |
Collapse
|
21
|
Cummings CO, Hill NJ, Puryear WB, Rogers B, Mukherjee J, Leibler JH, Rosenbaum MH, Runstadler JA. Evidence of Influenza A in Wild Norway Rats ( Rattus norvegicus) in Boston, Massachusetts. Front Ecol Evol 2019; 7:36. [PMID: 34660611 PMCID: PMC8519512 DOI: 10.3389/fevo.2019.00036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Influenza A virus (IAV) is known to circulate among human and animal reservoirs, yet there are few studies that address the potential for urban rodents to carry and shed IAV. Rodents are often used as influenza models in the lab, but the few field studies that have looked for evidence of IAV in rodents have done so primarily in rural areas following outbreaks of IAV in poultry. This study sought to assess the prevalence of IAV recovered from wild Norway rats in a dense urban location (Boston). To do this, we sampled the oronasal cavity, paws, and lungs of Norway rats trapped by the City of Boston's Inspectional Services from December 2016 to September 2018. All samples were screened by real-time, reverse transcriptase PCR targeting the conserved IAV matrix segment. A total of 163 rats were trapped, 18 of which (11.04%) were RT-PCR positive for IAV in either oronasal swabs (9), paw swabs (9), both (2), or lung homogenates (2). A generalized linear model indicated that month and geographic location were correlated with IAV-positive PCR status of rats. A seasonal trend in IAV-PCR status was observed with the highest prevalence occurring in the winter months (December-January) followed by a decline over the course of the year, reaching its lowest prevalence in September. Sex and weight of rats were not significantly associated with IAV-PCR status, suggesting that rodent demography is not a primary driver of infection. This pilot study provides evidence of the need to further investigate the role that wild rats may play as reservoirs or mechanical vectors for IAV circulation in urban environments across seasons.
Collapse
Affiliation(s)
- Charles O. Cummings
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| | - Nichola J. Hill
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| | - Benjamin Rogers
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| | - Jean Mukherjee
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| | - Jessica H. Leibler
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, United States
| | - Marieke H. Rosenbaum
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| |
Collapse
|
22
|
Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol 2019; 37:160-168. [PMID: 30718881 PMCID: PMC6587591 DOI: 10.1038/s41587-018-0006-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 12/18/2018] [Indexed: 01/24/2023]
Abstract
Metagenomic sequencing has the potential to transform microbial detection and characterization, but new tools are needed to improve its sensitivity. Here we present CATCH, a computational method to enhance nucleic acid capture for enrichment of diverse microbial taxa. CATCH designs optimal probe sets, with a specified number of oligonucleotides, that achieve full coverage of, and scale well with, known sequence diversity. We focus on applying CATCH to capture viral genomes in complex metagenomic samples. We design, synthesize, and validate multiple probe sets, including one that targets the whole genomes of the 356 viral species known to infect humans. Capture with these probe sets enriches unique viral content on average 18-fold, allowing us to assemble genomes that could not be recovered without enrichment, and accurately preserves within-sample diversity. We also use these probe sets to recover genomes from the 2018 Lassa fever outbreak in Nigeria and to improve detection of uncharacterized viral infections in human and mosquito samples. The results demonstrate that CATCH enables more sensitive and cost-effective metagenomic sequencing.
Collapse
Affiliation(s)
- Hayden C. Metsky
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0001 2341 2786grid.116068.8Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Katherine J. Siddle
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | | | - James Qu
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - David K. Yang
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Patrick Brehio
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andrew Goldfarb
- 000000041936754Xgrid.38142.3cFaculty of Arts and Sciences, Harvard University, Cambridge, MA USA
| | - Anne Piantadosi
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA
| | - Shirlee Wohl
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Amber Carter
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Aaron E. Lin
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Kayla G. Barnes
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA
| | - Damien C. Tully
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Bjӧrn Corleis
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Scott Hennigan
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Giselle Barbosa-Lima
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yasmine R. Vieira
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lauren M. Paul
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Amanda L. Tan
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Kimberly F. Garcia
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Leda A. Parham
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Philomena Eromon
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria
| | - Onikepe A. Folarin
- grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Augustine Goba
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
| | | | - Etienne Simon-Lorière
- 0000 0001 2353 6535grid.428999.7Evolutionary Genomics of RNA Viruses, Virology Department, Institut Pasteur, Paris, France
| | - Lisa Hensley
- 0000 0001 2164 9667grid.419681.3Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Frederick, MD USA
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Eva Harris
- 0000 0001 2181 7878grid.47840.3fDivision of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Douglas S. Kwon
- 0000 0004 0386 9924grid.32224.35Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA USA ,0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Todd M. Allen
- 0000 0004 0489 3491grid.461656.6The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA USA
| | - Jonathan A. Runstadler
- 0000 0004 1936 7531grid.429997.8Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA USA
| | - Sandra Smole
- 0000 0004 0378 6934grid.416511.6Massachusetts Department of Public Health, Boston, MA USA
| | - Fernando A. Bozza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thiago M. L. Souza
- 0000 0001 0723 0931grid.418068.3Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sharon Isern
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Scott F. Michael
- 0000 0001 0647 2963grid.255962.fDepartment of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL USA
| | - Ivette Lorenzana
- 0000 0001 2297 2829grid.10601.36Instituto de Investigacion en Microbiologia, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Lee Gehrke
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Microbiology and Immunobiology, Harvard Medical School, Boston, MA USA
| | - Irene Bosch
- 0000 0001 2341 2786grid.116068.8Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Gregory Ebel
- 0000 0004 1936 8083grid.47894.36Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO USA
| | - Donald S. Grant
- Lassa Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone ,0000 0001 2290 9707grid.442296.fCollege of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | - Christian T. Happi
- 000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria ,grid.442553.1African Center of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s University, Ede, Nigeria ,grid.442553.1Department of Biological Sciences, College of Natural Sciences, Redeemer’s University, Ede, Nigeria
| | - Daniel J. Park
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Andreas Gnirke
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Pardis C. Sabeti
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA ,000000041936754Xgrid.38142.3cDepartment of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA USA ,0000 0001 2167 1581grid.413575.1Howard Hughes Medical Institute, Chevy Chase, MD USA
| | | |
Collapse
|
23
|
Desforges JP, Bandoro C, Shehata L, Sonne C, Dietz R, Puryear WB, Runstadler JA. Environmental contaminant mixtures modulate in vitro influenza infection. Sci Total Environ 2018; 634:20-28. [PMID: 29626767 DOI: 10.1016/j.scitotenv.2018.03.321] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 05/17/2023]
Abstract
Environmental chemicals, particularly organochlorinated contaminants (OCs), are associated with a ranged of adverse health effects, including impairment of the immune system and antiviral immunity. Influenza A virus (IAV) is an infectious disease of major global public health concern and exposure to OCs can increase the susceptibility, morbidity, and mortality to disease. It is however unclear how pollutants are interacting and affecting the outcome of viral infections at the cellular level. In this study, we investigated the effects of a mixture of environmentally relevant OCs on IAV infectivity upon in vitro exposure in Madin Darby Canine Kidney (MDCK) cells and human lung epithelial cells (A549). Exposure to OCs reduced IAV infectivity in MDCK and A549 cells during both short (18-24h) and long-term (72h) infections at 0.05 and 0.5ppm, and effects were more pronounced in cells co-treated with OCs and IAV than pre-treated with OCs prior to IAV (p<0.001). Pre-treatment of host cells with OCs did not affect IAV cell surface attachment or entry. Visualization of IAV by transmission electron microscopy revealed increased envelope deformations and fewer intact virions during OC exposure. Taken together, our results suggest that disruption of IAV infection upon in vitro exposure to OCs was not due to host-cell effects influencing viral attachment and entry, but perhaps mediated by direct effects on viral particles or cellular processes involved in host-virus interactions. In vitro infectivity studies such as ours can shed light on the complex processes underlying host-pathogen-pollutant interactions.
Collapse
Affiliation(s)
- Jean-Pierre Desforges
- Department of Bioscience, Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark.
| | - Christopher Bandoro
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, 200 Westboro Road, North Grafton, MA 01536, United States; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Laila Shehata
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Christian Sonne
- Department of Bioscience, Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, 200 Westboro Road, North Grafton, MA 01536, United States
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, 200 Westboro Road, North Grafton, MA 01536, United States
| |
Collapse
|
24
|
Lerner JE, Ono K, Hernandez KM, Runstadler JA, Puryear WB, Polito MJ. Evaluating the use of stable isotope analysis to infer the feeding ecology of a growing US gray seal (Halichoerus grypus) population. PLoS One 2018; 13:e0192241. [PMID: 29466372 PMCID: PMC5821315 DOI: 10.1371/journal.pone.0192241] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 01/18/2018] [Indexed: 11/19/2022] Open
Abstract
Gray seals (Halichoerus grypus) have been rapidly recolonizing the Northeast US coast, eliciting concern from the fishing industry. However, the ecological effect of this recovery is still unknown and as such, research is needed to better understand how the diet composition of gray seals in US waters will contribute to the ecological impact. While previous research on seal diets has focused on the analysis of hard prey remains, stable isotope analysis presents an alternative method that can be used to describe marine mammal diets when direct observation is impossible. To address this issue, we used stable isotope analysis of gray seal pup vibrissae and lanugo from Monomoy Island, Cape Cod, MA during the 2015/2016 winter breeding season to estimate adult female diet composition during pregnancy. Stable isotope mixing models (SIMM) suggested adult female gray seals were consuming greater amounts of cephalopod prey and less sand lance than previously indicated from analysis of hard prey remains. However, using SIMMs to estimate the diet composition of gray seals remains difficult due to the large number of isotopically similar prey species and uncertainty in tissue-specific, stable isotope trophic enrichment factors. Even so, by combining prey sources into ecologically informative groups and integrating prior information into SIMMs it is possible to obtain additional insights into the diet of this generalist predator.
Collapse
Affiliation(s)
- Jacob E. Lerner
- University of New England, Department of Marine Sciences, Biddeford, Maine, United States of America
| | - Kathryn Ono
- University of New England, Department of Marine Sciences, Biddeford, Maine, United States of America
| | - Keith M. Hernandez
- Lousiana State University, Department of Oceanography and Coastal Sciences, Baton Rouge, Louisiana, United States of America
| | - Jonathan A. Runstadler
- Tufts University, Cummings School of Veterinary Medicine, Boston, Massachusetts, United States of America
| | - Wendy B. Puryear
- Tufts University, Cummings School of Veterinary Medicine, Boston, Massachusetts, United States of America
| | - Michael J. Polito
- Lousiana State University, Department of Oceanography and Coastal Sciences, Baton Rouge, Louisiana, United States of America
| |
Collapse
|
25
|
Hill NJ, Hussein ITM, Davis KR, Ma EJ, Spivey TJ, Ramey AM, Puryear WB, Das SR, Halpin RA, Lin X, Fedorova NB, Suarez DL, Boyce WM, Runstadler JA. Reassortment of Influenza A Viruses in Wild Birds in Alaska before H5 Clade 2.3.4.4 Outbreaks. Emerg Infect Dis 2018; 23:654-657. [PMID: 28322698 PMCID: PMC5367406 DOI: 10.3201/eid2304.161668] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Sampling of mallards in Alaska during September 2014-April 2015 identified low pathogenic avian influenza A virus (subtypes H5N2 and H1N1) that shared ancestry with highly pathogenic reassortant H5N2 and H5N1 viruses. Molecular dating indicated reassortment soon after interhemispheric movement of H5N8 clade 2.3.4.4, suggesting genetic exchange in Alaska or surrounds before outbreaks.
Collapse
|
26
|
Spivey TJ, Lindberg MS, Meixell BW, Smith KR, Puryear WB, Davis KR, Runstadler JA, Stallknecht DE, Ramey AM. Maintenance of influenza A viruses and antibody response in mallards (Anas platyrhynchos) sampled during the non-breeding season in Alaska. PLoS One 2017; 12:e0183505. [PMID: 28837606 PMCID: PMC5570339 DOI: 10.1371/journal.pone.0183505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/04/2017] [Indexed: 11/25/2022] Open
Abstract
Prevalence of influenza A virus (IAV) infections in northern-breeding waterfowl has previously been reported to reach an annual peak during late summer or autumn; however, little is known about IAV infection dynamics in waterfowl populations persisting at high-latitude regions such as Alaska, during winter. We captured mallards (Anas platyrhynchos) throughout the non-breeding season (August–April) of 2012–2015 in Fairbanks and Anchorage, the two largest cities in Alaska, to assess patterns of IAV infection and antibody production using molecular methods and a standard serologic assay. In addition, we used virus isolation, genetic sequencing, and a virus microneutralization assay to characterize viral subtypes and to evaluate the immune response of mallards captured on multiple occasions through time. We captured 923 mallards during three successive sampling years: Fairbanks in 2012/13 and 2013/14, and Anchorage in 2014/15. Prevalence varied by age, season, and year/site with high and relatively stable estimates throughout the non-breeding season. Infected birds were detected in all locations/seasons except early-winter in Fairbanks during 2013/14. IAVs with 17 combinations of hemagglutinin (H1–5, H7–9, H11, H12) and neuraminidase (N1–6, N8, N9) subtypes were isolated. Antibodies to IAVs were detected throughout autumn and winter for all sampling locations and years, however, seroprevalence was higher among adults and varied among years. Mallards exhibited individual heterogeneity with regard to immune response, providing instances of both seroconversion and seroreversion to detected viral subtypes. The probability that an individual transitioned from one serostatus to another varied by age, with juvenile mallards having higher rates of seroconversion and seroreversion than adults. Our study provides evidence that a diversity of IAVs circulate in populations of mallards wintering at urban locations in Alaska, and we suggest waterfowl wintering at high-latitudes may play an important role in maintenance of viruses across breeding seasons.
Collapse
Affiliation(s)
- Timothy J. Spivey
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
- * E-mail:
| | - Mark S. Lindberg
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska, United States of America
| | - Brandt W. Meixell
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
| | - Kyle R. Smith
- Alaska Department of Fish and Game, Anchorage, Alaska, United States of America
| | - Wendy B. Puryear
- Department of Biological Engineering & Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kimberly R. Davis
- Department of Biological Engineering & Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jonathan A. Runstadler
- Department of Biological Engineering & Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - David E. Stallknecht
- College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Andrew M. Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
| |
Collapse
|
27
|
Hill NJ, Runstadler JA. A Bird's Eye View of Influenza A Virus Transmission: Challenges with Characterizing Both Sides of a Co-Evolutionary Dynamic. Integr Comp Biol 2016; 56:304-16. [PMID: 27252222 PMCID: PMC5964799 DOI: 10.1093/icb/icw055] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In nature, wild birds and influenza A viruses (IAV) are continually co-evolving, locked into a back-and-forth of resistance and conquest that has approached a stable equilibrium over time. This co-evolutionary relationship between bird host and IAV may appear stable at the organismal level, but is highly dynamic at the molecular level manifesting in a constant trade-off between transmissibility and virulence of the virus. Characterizing both sides of the host-virus dynamic has presented a challenge for ecologists and virologists alike, despite the potential for this approach to provide insights into which conditions destabilize the equilibrium state resulting in outbreaks or mortality of hosts in extreme cases. The use of different methods that are either host-centric or virus-centric has made it difficult to reconcile the disparate fields of host ecology and virology for investigating and ultimately predicting wild bird-mediated transmission of IAV. This review distills some of the key lessons learned from virological and ecological studies and explores the promises and pitfalls of both approaches. Ultimately, reconciling ecological and virological approaches hinges on integrating scales for measuring host-virus interactions. We argue that prospects for finding common scales for measuring wild bird-influenza dynamics are improving due to advances in genomic sequencing, host-tracking technology and remote sensing data, with the unit of time (months, year, or seasons) providing a starting point for crossover.
Collapse
Affiliation(s)
- Nichola J Hill
- Massachusetts Institute of Technology, Division of Comparative Medicine & Department of Biological Engineering, 77 Massachusetts Ave, Cambridge 02139
| | - Jonathan A Runstadler
- Massachusetts Institute of Technology, Division of Comparative Medicine & Department of Biological Engineering, 77 Massachusetts Ave, Cambridge 02139
| |
Collapse
|
28
|
Meixell BW, Arnold TW, Lindberg MS, Smith MM, Runstadler JA, Ramey AM. Detection, prevalence, and transmission of avian hematozoa in waterfowl at the Arctic/sub-Arctic interface: co-infections, viral interactions, and sources of variation. Parasit Vectors 2016; 9:390. [PMID: 27387437 PMCID: PMC4936110 DOI: 10.1186/s13071-016-1666-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/23/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The epidemiology of avian hematozoa at high latitudes is still not well understood, particularly in sub-Arctic and Arctic habitats, where information is limited regarding seasonality and range of transmission, co-infection dynamics with parasitic and viral agents, and possible fitness consequences of infection. Such information is important as climate warming may lead to northward expansion of hematozoa with unknown consequences to northern-breeding avian taxa, particularly populations that may be previously unexposed to blood parasites. METHODS We used molecular methods to screen blood samples and cloacal/oropharyngeal swabs collected from 1347 ducks of five species during May-August 2010, in interior Alaska, for the presence of hematozoa, Influenza A Virus (IAV), and IAV antibodies. Using models to account for imperfect detection of parasites, we estimated seasonal variation in prevalence of three parasite genera (Haemoproteus, Plasmodium, Leucocytozoon) and investigated how co-infection with parasites and viruses were related to the probability of infection. RESULTS We detected parasites from each hematozoan genus in adult and juvenile ducks of all species sampled. Seasonal patterns in detection and prevalence varied by parasite genus and species, age, and sex of duck hosts. The probabilities of infection for Haemoproteus and Leucocytozoon parasites were strongly positively correlated, but hematozoa infection was not correlated with IAV infection or serostatus. The probability of Haemoproteus infection was negatively related to body condition in juvenile ducks; relationships between Leucocytozoon infection and body condition varied among host species. CONCLUSIONS We present prevalence estimates for Haemoproteus, Leucocytozoon, and Plasmodium infections in waterfowl at the interface of the sub-Arctic and Arctic and provide evidence for local transmission of all three parasite genera. Variation in prevalence and molecular detection of hematozoa parasites in wild ducks is influenced by seasonal timing and a number of host traits. A positive correlation in co-infection of Leucocytozoon and Haemoproteus suggests that infection probability by parasites in one or both genera is enhanced by infection with the other, or that encounter rates of hosts and genus-specific vectors are correlated. Using size-adjusted mass as an index of host condition, we did not find evidence for strong deleterious consequences of hematozoa infection in wild ducks.
Collapse
Affiliation(s)
- Brandt W. Meixell
- />Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN 55108 USA
- />U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508 USA
| | - Todd W. Arnold
- />Department of Fisheries, Wildlife, and Conservation Biology, University of Minnesota, St. Paul, MN 55108 USA
| | - Mark S. Lindberg
- />Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775 USA
| | - Matthew M. Smith
- />U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508 USA
| | - Jonathan A. Runstadler
- />Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Andrew M. Ramey
- />U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508 USA
| |
Collapse
|
29
|
Hill NJ, Ma EJ, Meixell BW, Lindberg MS, Boyce WM, Runstadler JA. Transmission of influenza reflects seasonality of wild birds across the annual cycle. Ecol Lett 2016; 19:915-25. [PMID: 27324078 DOI: 10.1111/ele.12629] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/04/2016] [Indexed: 11/30/2022]
Abstract
Influenza A Viruses (IAV) in nature must overcome shifting transmission barriers caused by the mobility of their primary host, migratory wild birds, that change throughout the annual cycle. Using a phylogenetic network of viral sequences from North American wild birds (2008-2011) we demonstrate a shift from intraspecific to interspecific transmission that along with reassortment, allows IAV to achieve viral flow across successive seasons from summer to winter. Our study supports amplification of IAV during summer breeding seeded by overwintering virus persisting locally and virus introduced from a wide range of latitudes. As birds migrate from breeding sites to lower latitudes, they become involved in transmission networks with greater connectivity to other bird species, with interspecies transmission of reassortant viruses peaking during the winter. We propose that switching transmission dynamics may be a critical strategy for pathogens that infect mobile hosts inhabiting regions with strong seasonality.
Collapse
Affiliation(s)
- Nichola J Hill
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eric J Ma
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brandt W Meixell
- Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, MN, 55108, USA.,U.S. Geological Survey, Alaska Science Center, Anchorage, AK, 99508, USA
| | - Mark S Lindberg
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Walter M Boyce
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Jonathan A Runstadler
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| |
Collapse
|
30
|
Abstract
Reticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in transmission between different host species. Moreover, as host evolutionary distance increases, reassortment is increasingly favored. We conclude that the greater the quantitative difference between ecological niches, the greater the importance of reticulate evolutionary processes in overcoming niche barriers.
Collapse
Affiliation(s)
- Eric J Ma
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
| | - Nichola J Hill
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Justin Zabilansky
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kyle Yuan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jonathan A Runstadler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
31
|
Bahl J, Pham TT, Hill NJ, Hussein ITM, Ma EJ, Easterday BC, Halpin RA, Stockwell TB, Wentworth DE, Kayali G, Krauss S, Schultz-Cherry S, Webster RG, Webby RJ, Swartz MD, Smith GJD, Runstadler JA. Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential. PLoS Pathog 2016; 12:e1005620. [PMID: 27166585 PMCID: PMC4864295 DOI: 10.1371/journal.ppat.1005620] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 04/18/2016] [Indexed: 12/21/2022] Open
Abstract
Despite evidence for avian influenza A virus (AIV) transmission between wild and domestic ecosystems, the roles of bird migration and poultry trade in the spread of viruses remain enigmatic. In this study, we integrate ecosystem interactions into a phylogeographic model to assess the contribution of wild and domestic hosts to AIV distribution and persistence. Analysis of globally sampled AIV datasets shows frequent two-way transmission between wild and domestic ecosystems. In general, viral flow from domestic to wild bird populations was restricted to within a geographic region. In contrast, spillover from wild to domestic populations occurred both within and between regions. Wild birds mediated long-distance dispersal at intercontinental scales whereas viral spread among poultry populations was a major driver of regional spread. Viral spread between poultry flocks frequently originated from persistent lineages circulating in regions of intensive poultry production. Our analysis of long-term surveillance data demonstrates that meaningful insights can be inferred from integrating ecosystem into phylogeographic reconstructions that may be consequential for pandemic preparedness and livestock protection.
Collapse
Affiliation(s)
- Justin Bahl
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, Texas, United States of America
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Truc T. Pham
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, Texas, United States of America
| | - Nichola J. Hill
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Islam T. M. Hussein
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Eric J. Ma
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bernard C. Easterday
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Rebecca A. Halpin
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - David E. Wentworth
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ghazi Kayali
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Robert G. Webster
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Michael D. Swartz
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, Texas, United States of America
| | - Gavin J. D. Smith
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | - Jonathan A. Runstadler
- Division of Comparative Medicine, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| |
Collapse
|
32
|
Hussein ITM, Ma EJ, Hill NJ, Meixell BW, Lindberg M, Albrecht RA, Bahl J, Runstadler JA. A point mutation in the polymerase protein PB2 allows a reassortant H9N2 influenza isolate of wild-bird origin to replicate in human cells. Infect Genet Evol 2016; 41:279-288. [PMID: 27101787 DOI: 10.1016/j.meegid.2016.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/08/2016] [Accepted: 04/10/2016] [Indexed: 12/09/2022]
Abstract
H9N2 influenza A viruses are on the list of potentially pandemic subtypes. Therefore, it is important to understand how genomic reassortment and genetic polymorphisms affect phenotypes of H9N2 viruses circulating in the wild bird reservoir. A comparative genetic analysis of North American H9N2 isolates of wild bird origin identified a naturally occurring reassortant virus containing gene segments derived from both North American and Eurasian lineage ancestors. The PB2 segment of this virus encodes 10 amino acid changes that distinguish it from other H9 strains circulating in North America. G590S, one of the 10 amino acid substitutions observed, was present in ~12% of H9 viruses worldwide. This mutation combined with R591 has been reported as a marker of pathogenicity for human pandemic 2009 H1N1 viruses. Screening by polymerase reporter assay of all the natural polymorphisms at these two positions identified G590/K591 and S590/K591 as the most active, with the highest polymerase activity recorded for the SK polymorphism. Rescued viruses containing these two polymorphic combinations replicated more efficiently in MDCK cells and they were the only ones tested that were capable of establishing productive infection in NHBE cells. A global analysis of all PB2 sequences identified the K591 signature in six viral HA/NA subtypes isolated from several hosts in seven geographic locations. Interestingly, introducing the K591 mutation into the PB2 of a human-adapted H3N2 virus did not affect its polymerase activity. Our findings demonstrate that a single point mutation in the PB2 of a low pathogenic H9N2 isolate could have a significant effect on viral phenotype and increase its propensity to infect mammals. However, this effect is not universal, warranting caution in interpreting point mutations without considering protein sequence context.
Collapse
Affiliation(s)
- Islam T M Hussein
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric J Ma
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nichola J Hill
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brandt W Meixell
- U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508, USA
| | - Mark Lindberg
- Institute of Arctic Biology, University of Alaska Fairbanks, AK 99775, USA
| | - Randy A Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Justin Bahl
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX, USA
| | - Jonathan A Runstadler
- Department of Biological Engineering and Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
33
|
Ramos I, Mansour M, Wohlbold TJ, Ermler ME, Hirsh A, Runstadler JA, Fernandez-Sesma A, Krammer F. Hemagglutinin Receptor Binding of a Human Isolate of Influenza A(H10N8) Virus. Emerg Infect Dis 2016; 21:1197-201. [PMID: 26079843 PMCID: PMC4480385 DOI: 10.3201/eid2107.141755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Three cases of influenza A(H10N8) virus infection in humans have been reported; 2 of these infected persons died. Characterization of the receptor binding pattern of H10 hemagglutinin from avian and human isolates showed that both interact weakly with human-like receptors and maintain strong affinity for avian-like receptors.
Collapse
|
34
|
Tang S, Puryear WB, Seifried BM, Dong X, Runstadler JA, Ribbeck K, Olsen BD. Antiviral Agents from Multivalent Presentation of Sialyl Oligosaccharides on Brush Polymers. ACS Macro Lett 2016; 5:413-418. [PMID: 35614714 DOI: 10.1021/acsmacrolett.5b00917] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bioinspired brush polymers containing α-2,6-linked sialic acids at the side chain termini were synthesized by protection-group-free, ring-opening metathesis polymerization. Polymers showed strain-selective antiviral activity through multivalent presentation of the sialosides. The multivalent effect was further controlled by independently varying the degree of polymerization, the number density of sialic acids, and the length of side chains in the brush polymers. Optimizing the three-dimensional sialoside spacing for better binding to hemagglutinin trimers was of critical importance to enhance the multivalent effect and the antiviral activity determined by hemagglutination inhibition assays and in vitro infection assays. By taking advantage of their structural similarities with native mucins, these brush polymers can be used as model systems to dissect the intricate design principles in natural mucins.
Collapse
Affiliation(s)
- Shengchang Tang
- Department of Chemical Engineering, ‡Department of Biological Engineering, and §Division of Comparative
Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Wendy B. Puryear
- Department of Chemical Engineering, ‡Department of Biological Engineering, and §Division of Comparative
Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Brian M. Seifried
- Department of Chemical Engineering, ‡Department of Biological Engineering, and §Division of Comparative
Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Xuehui Dong
- Department of Chemical Engineering, ‡Department of Biological Engineering, and §Division of Comparative
Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jonathan A. Runstadler
- Department of Chemical Engineering, ‡Department of Biological Engineering, and §Division of Comparative
Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Katharina Ribbeck
- Department of Chemical Engineering, ‡Department of Biological Engineering, and §Division of Comparative
Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley D. Olsen
- Department of Chemical Engineering, ‡Department of Biological Engineering, and §Division of Comparative
Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
35
|
Bui VN, Ogawa H, Hussein ITM, Hill NJ, Trinh DQ, AboElkhair M, Sultan S, Ma E, Saito K, Watanabe Y, Runstadler JA, Imai K. Genetic characterization of a rare H12N3 avian influenza virus isolated from a green-winged teal in Japan. Virus Genes 2015; 50:316-20. [PMID: 25557930 DOI: 10.1007/s11262-014-1162-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 12/18/2014] [Indexed: 11/24/2022]
Abstract
This study reports on the genetic characterization of an avian influenza virus, subtype H12N3, isolated from an Eurasian green-winged teal (Anas crecca) in Japan in 2009. The entire genome sequence of the isolate was analyzed, and phylogenetic analyses were conducted to characterize the evolutionary history of the isolate. Phylogenetic analysis of the hemagglutinin and neuraminidase genes indicated that the virus belonged to the Eurasian-like avian lineage. Molecular dating indicated that this H12 virus is likely a multiple reassortant influenza A virus. This is the first reported characterization of influenza A virus subtype H12N3 isolated in Japan and these data contribute to the accumulation of knowledge on the genetic diversity and generation of novel influenza A viruses.
Collapse
Affiliation(s)
- Vuong Nghia Bui
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, 2-11 Inada, Obihiro, Hokkaido, 080-8555, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Vernau KM, Runstadler JA, Brown EA, Cameron JM, Huson HJ, Higgins RJ, Ackerley C, Sturges BK, Dickinson PJ, Puschner B, Giulivi C, Shelton GD, Robinson BH, DiMauro S, Bollen AW, Bannasch DL. Genome-wide association analysis identifies a mutation in the thiamine transporter 2 (SLC19A3) gene associated with Alaskan Husky encephalopathy. PLoS One 2013; 8:e57195. [PMID: 23469184 PMCID: PMC3587633 DOI: 10.1371/journal.pone.0057195] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/18/2013] [Indexed: 11/28/2022] Open
Abstract
Alaskan Husky Encephalopathy (AHE) has been previously proposed as a mitochondrial encephalopathy based on neuropathological similarities with human Leigh Syndrome (LS). We studied 11 Alaskan Husky dogs with AHE, but found no abnormalities in respiratory chain enzyme activities in muscle and liver, or mutations in mitochondrial or nuclear genes that cause LS in people. A genome wide association study was performed using eight of the affected dogs and 20 related but unaffected control AHs using the Illumina canine HD array. SLC19A3 was identified as a positional candidate gene. This gene controls the uptake of thiamine in the CNS via expression of the thiamine transporter protein THTR2. Dogs have two copies of this gene located within the candidate interval (SLC19A3.2 – 43.36–43.38 Mb and SLC19A3.1 – 43.411–43.419 Mb) on chromosome 25. Expression analysis in a normal dog revealed that one of the paralogs, SLC19A3.1, was expressed in the brain and spinal cord while the other was not. Subsequent exon sequencing of SLC19A3.1 revealed a 4bp insertion and SNP in the second exon that is predicted to result in a functional protein truncation of 279 amino acids (c.624 insTTGC, c.625 C>A). All dogs with AHE were homozygous for this mutation, 15/41 healthy AH control dogs were heterozygous carriers while 26/41 normal healthy AH dogs were wild type. Furthermore, this mutation was not detected in another 187 dogs of different breeds. These results suggest that this mutation in SLC19A3.1, encoding a thiamine transporter protein, plays a critical role in the pathogenesis of AHE.
Collapse
Affiliation(s)
- Karen M Vernau
- University of California Davis, Davis, California, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Hill NJ, Takekawa JY, Ackerman JT, Hobson KA, Herring G, Cardona CJ, Runstadler JA, Boyce WM. Migration strategy affects avian influenza dynamics in mallards (Anas platyrhynchos). Mol Ecol 2012; 21:5986-99. [PMID: 22971007 DOI: 10.1111/j.1365-294x.2012.05735.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 06/02/2012] [Accepted: 06/18/2012] [Indexed: 11/30/2022]
Abstract
Studies of pathogen transmission typically overlook that wildlife hosts can include both migrant and resident populations when attempting to model circulation. Through the application of stable isotopes in flight feathers, we estimated the migration strategy of mallards (Anas platyrhynchos) occurring on California wintering grounds. Our study demonstrates that mallards- a principal host of avian influenza virus (AIV) in nature, contribute differently to virus gene flow depending on migration strategy. No difference in AIV prevalence was detected between resident (9.6%), intermediate-distance (9.6%) and long-distance migrants (7.4%). Viral diversity among the three groups was also comparable, possibly owing to viral pool mixing when birds converge at wetlands during winter. However, migrants and residents contributed differently to the virus gene pool at wintering wetlands. Migrants introduced virus from northern breeding grounds (Alaska and the NW Pacific Rim) into the wintering population, facilitating gene flow at continental scales, but circulation of imported virus appeared to be limited. In contrast, resident mallards acted as AIV reservoirs facilitating year-round circulation of limited subtypes (i.e. H5N2) at lower latitudes. This study supports a model of virus exchange in temperate regions driven by the convergence of wild birds with separate geographic origins and exposure histories.
Collapse
Affiliation(s)
- Nichola J Hill
- US Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA 94592, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Hill NJ, Takekawa JY, Cardona CJ, Meixell BW, Ackerman JT, Runstadler JA, Boyce WM. Cross-seasonal patterns of avian influenza virus in breeding and wintering migratory birds: a flyway perspective. Vector Borne Zoonotic Dis 2011; 12:243-53. [PMID: 21995264 DOI: 10.1089/vbz.2010.0246] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The spread of avian influenza viruses (AIV) in nature is intrinsically linked with the movements of wild birds. Wild birds are the reservoirs for the virus and their migration may facilitate the circulation of AIV between breeding and wintering areas. This cycle of dispersal has become widely accepted; however, there are few AIV studies that present cross-seasonal information. A flyway perspective is critical for understanding how wild birds contribute to the persistence of AIV over large spatial and temporal scales, with implications for how to focus surveillance efforts and identify risks to public health. This study characterized spatio-temporal infection patterns in 10,389 waterfowl at two important locations within the Pacific Flyway--breeding sites in Interior Alaska and wintering sites in California's Central Valley during 2007-2009. Among the dabbling ducks sampled, the northern shoveler (Anas clypeata) had the highest prevalence of AIV at both breeding (32.2%) and wintering (5.2%) locations. This is in contrast to surveillance studies conducted in other flyways that have identified the mallard (Anas platyrhynchos) and northern pintail (Anas acuta) as hosts with the highest prevalence. A higher diversity of AIV subtypes was apparent at wintering (n=42) compared with breeding sites (n=17), with evidence of mixed infections at both locations. Our study suggests that wintering sites may act as an important mixing bowl for transmission among waterfowl in a flyway, creating opportunities for the reassortment of the virus. Our findings shed light on how the dynamics of AIV infection of wild bird populations can vary between the two ends of a migratory flyway.
Collapse
Affiliation(s)
- Nichola J Hill
- Western Ecological Research Center, San Francisco Bay Estuary Field Station, U.S. Geological Survey, Vallejo, California, USA
| | | | | | | | | | | | | |
Collapse
|
39
|
Reeves AB, Pearce JM, Ramey AM, Meixell BW, Runstadler JA. Interspecies transmission and limited persistence of low pathogenic avian influenza genomes among Alaska dabbling ducks. Infect Genet Evol 2011; 11:2004-10. [PMID: 21964597 DOI: 10.1016/j.meegid.2011.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 08/24/2011] [Accepted: 09/06/2011] [Indexed: 12/09/2022]
Abstract
The reassortment and geographic distribution of low pathogenic avian influenza (LPAI) virus genes are well documented, but little is known about the persistence of intact LPAI genomes among species and locations. To examine persistence of entire LPAI genome constellations in Alaska, we calculated the genetic identities among 161 full-genome LPAI viruses isolated across 4 years from five species of duck: northern pintail (Anas acuta), mallard (Anas platyrhynchos), American green-winged teal (Anas crecca), northern shoveler (Anas clypeata) and American wigeon (Anas americana). Based on pairwise genetic distance, highly similar LPAI genomes (>99% identity) were observed within and between species and across a range of geographic distances (up to and >1000 km), but most often between isolates collected 0-10 km apart. Highly similar viruses were detected between years, suggesting inter-annual persistence, but these were rare in our data set with the majority occurring within 0-9 days of sampling. These results identify LPAI transmission pathways in the context of species, space and time, an initial perspective into the extent of regional virus distribution and persistence, and insight into why no completely Eurasian genomes have ever been detected in Alaska. Such information will be useful in forecasting the movement of foreign-origin avian influenza strains should they be introduced to North America.
Collapse
Affiliation(s)
- Andrew B Reeves
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
| | | | | | | | | |
Collapse
|
40
|
Wille M, Robertson GJ, Whitney H, Bishop MA, Runstadler JA, Lang AS. Extensive geographic mosaicism in avian influenza viruses from gulls in the northern hemisphere. PLoS One 2011; 6:e20664. [PMID: 21697989 PMCID: PMC3115932 DOI: 10.1371/journal.pone.0020664] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 05/08/2011] [Indexed: 12/27/2022] Open
Abstract
Due to limited interaction of migratory birds between Eurasia and America, two independent avian influenza virus (AIV) gene pools have evolved. There is evidence of low frequency reassortment between these regions, which has major implications in global AIV dynamics. Indeed, all currently circulating lineages of the PB1 and PA segments in North America are of Eurasian origin. Large-scale analyses of intercontinental reassortment have shown that viruses isolated from Charadriiformes (gulls, terns, and shorebirds) are the major contributor of these outsider events. To clarify the role of gulls in AIV dynamics, specifically in movement of genes between geographic regions, we have sequenced six gull AIV isolated in Alaska and analyzed these along with 142 other available gull virus sequences. Basic investigations of host species and the locations and times of isolation reveal biases in the available sequence information. Despite these biases, our analyses reveal a high frequency of geographic reassortment in gull viruses isolated in America. This intercontinental gene mixing is not found in the viruses isolated from gulls in Eurasia. This study demonstrates that gulls are important as vectors for geographically reassorted viruses, particularly in America, and that more surveillance effort should be placed on this group of birds.
Collapse
Affiliation(s)
- Michelle Wille
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Gregory J. Robertson
- Wildlife Research Division, Environment Canada, Mount Pearl, Newfoundland, Canada
| | - Hugh Whitney
- Animal Health Division, Department of Natural Resources, St. John's, Newfoundland, Canada
| | - Mary Anne Bishop
- Prince William Sound Science Centre, Cordova, Alaska, United States of America
| | - Jonathan A. Runstadler
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| |
Collapse
|
41
|
Pearce JM, Reeves AB, Ramey AM, Hupp JW, Ip HS, Bertram M, Petrula MJ, Scotton BD, Trust KA, Meixell BW, Runstadler JA. Interspecific exchange of avian influenza virus genes in Alaska: the influence of trans-hemispheric migratory tendency and breeding ground sympatry. Mol Ecol 2011; 20:1015-25. [PMID: 21073586 PMCID: PMC3041836 DOI: 10.1111/j.1365-294x.2010.04908.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The movement and transmission of avian influenza viral strains via wild migratory birds may vary by host species as a result of migratory tendency and sympatry with other infected individuals. To examine the roles of host migratory tendency and species sympatry on the movement of Eurasian low-pathogenic avian influenza (LPAI) genes into North America, we characterized migratory patterns and LPAI viral genomic variation in mallards (Anas platyrhynchos) of Alaska in comparison with LPAI diversity of northern pintails (Anas acuta). A 50-year band-recovery data set suggests that unlike northern pintails, mallards rarely make trans-hemispheric migrations between Alaska and Eurasia. Concordantly, fewer (14.5%) of 62 LPAI isolates from mallards contained Eurasian gene segments compared to those from 97 northern pintails (35%), a species with greater inter-continental migratory tendency. Aerial survey and banding data suggest that mallards and northern pintails are largely sympatric throughout Alaska during the breeding season, promoting opportunities for interspecific transmission. Comparisons of full-genome isolates confirmed near-complete genetic homology (>99.5%) of seven viruses between mallards and northern pintails. This study found viral segments of Eurasian lineage at a higher frequency in mallards than previous studies, suggesting transmission from other avian species migrating inter-hemispherically or the common occurrence of endemic Alaskan viruses containing segments of Eurasian origin. We conclude that mallards are unlikely to transfer Asian-origin viruses directly to North America via Alaska but that they are likely infected with Asian-origin viruses via interspecific transfer from species with regular migrations to the Eastern Hemisphere.
Collapse
Affiliation(s)
- John M Pearce
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Bui VN, OGAWA H, KARIBE K, MATSUO K, NGUYEN TH, AWAD SSA, Minoungou GL, Xininigen, SAITO K, WATANABE Y, Runstadler JA, HAPP GM, IMAI K. Surveillance of Avian Influenza Virus in Migratory Water Birds in Eastern Hokkaido, Japan. J Vet Med Sci 2011; 73:209-15. [DOI: 10.1292/jvms.10-0356] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Vuong N. Bui
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
- National Institute of Veterinary Research
| | - Haruko OGAWA
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
| | - Kazuji KARIBE
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
| | - Kengo MATSUO
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
| | - Tung H. NGUYEN
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
| | - Sanaa S. A. AWAD
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
- Faculty of Veterinary Medicine, Mansoura University
| | - Germaine L. Minoungou
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
| | - Xininigen
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
| | | | | | | | - George M. HAPP
- Institute of Arctic Biology, University of Alaska Fairbanks
| | - Kunitoshi IMAI
- Research Center for Animal Hygiene and Food Safety, Obihiro University of Agriculture and Veterinary Medicine
| |
Collapse
|
43
|
Abstract
Little is known about the ecology and evolution of avian influenza in the natural environment, despite how these affect the potential for transmission. Most work has focused on characterizing viruses isolated from hosts such as waterfowl, and there have also been several instances of isolation and detection from abiotic sources such as water and ice. We used RT-PCR to amplify and characterize the influenza virus sequences present in sediments of ponds that are used heavily by waterfowl. The detection rate of influenza virus was high (>50%). Characterization of the viruses present by sequencing part of the haemagglutinin (HA) gene showed that there is a diverse collection of viruses in these sediments. We sequenced 117 partial HA gene clones from 11 samples and detected four different HA subtypes (H3, H8, H11 and H12), with approximately 65% of clone sequences being unique. This culture-independent approach was also able to detect a virus subtype that was not found by sampling of birds in the same geographical region in the same year. Viruses were detected readily in the winter when the ponds were frozen, indicating that these sediments could be a year-to-year reservoir of viruses to infect birds using the ponds, although we have not shown that these viruses are viable. We demonstrate that this approach is a feasible and valuable way to assess the prevalence and diversity of viruses present in the environment, and can be a valuable complement to more difficult viral culturing in attempting to understand the ecology of influenza viruses.
Collapse
Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Anke Kelly
- Institute of Arctic Biology, PO Box 757000, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Jonathan A Runstadler
- Institute of Arctic Biology, PO Box 757000, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| |
Collapse
|
44
|
Runstadler JA, Happ GM, Slemons RD, Sheng ZM, Gundlach N, Petrula M, Senne D, Nolting J, Evers DL, Modrell A, Huson H, Hills S, Rothe T, Marr T, Taubenberger JK. Using RRT-PCR analysis and virus isolation to determine the prevalence of avian influenza virus infections in ducks at Minto Flats State Game Refuge, Alaska, during August 2005. Arch Virol 2007; 152:1901-10. [PMID: 17541700 PMCID: PMC2538573 DOI: 10.1007/s00705-007-0994-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 04/26/2007] [Indexed: 10/23/2022]
Abstract
This study describes surveillance for avian influenza viruses (AIV) in the Minto Flats State Game Refuge, high-density waterfowl breeding grounds in Alaska. Five hundred paired cloacal samples from dabbling ducks (Northern Pintail, Mallard, Green Wing Teal, and Widgeon) were placed into ethanol and viral transport medium (VTM). Additional ethanol-preserved samples were taken. Of the ethanol-preserved samples, 25.6% were AIV RNA-positive by real-time RT-PCR. The hemagglutinin (HA) and neuraminidase (NA) subtypes were determined for 38 of the first-passage isolates, and four first-passage isolates could not be definitively subtyped. Five influenza A virus HA-NA combinations were identified: H3N6, H3N8, H4N6, H8N4, and H12N5. Differences in the prevalence of AIV infections by sex and by age classes of Northern Pintail and Mallard ducks were detected, but the significance of these differences is undefined. In the 500 paired samples, molecular screening detected positive birds at a higher rate than viral isolation (chi(2) = 8.35, p = 0.0035, df = 1); however, 20 AIV isolates were recovered from PCR-negative ducks. Further research is warranted to compare the two screening protocols' potential for estimating true prevalence in wild birds. Our success during 2005 indicates Minto Flats will be a valuable study site for a longitudinal research project designed to gain further insight into the natural history, evolution, and ecology of AIV in wild birds.
Collapse
Affiliation(s)
- J A Runstadler
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Runstadler JA, Angles JM, Pedersen NC. Dog leucocyte antigen class II diversity and relationships among indigenous dogs of the island nations of Indonesia (Bali), Australia and New Guinea. ACTA ACUST UNITED AC 2006; 68:418-26. [PMID: 17092255 DOI: 10.1111/j.1399-0039.2006.00696.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The genetic polymorphism at the dog leucocyte antigen (DLA) class II loci DQA1, DQB1 and DRB1 was studied in a large genetically diverse population of feral and wild-type dogs from the large island nations of Indonesia (Bali), Australia and New Guinea (Bali street dog, dingo and New Guinea singing dog, respectively). Sequence-based typing (SBT) of the hypervariable region of DLA-DRB1, -DQA1 and -DQB1 alleles was used to determine genetic diversity. No new DQA1 alleles were recognized among the three dog populations, but five novel DLA-DRB1 and 2 novel DLA-DQB1 allele sequences were detected. Additional unknown alleles were postulated to exist in Bali street dogs, as indicated by the large percentage of individuals (15%-33%) that had indeterminate DRB1, DQA1 and DQB1 alleles by SBT. All three groups of dogs possessed alleles that were relatively uncommon in conventional purebreds. The New Guinea singing dog and dingo shared alleles that were not present in the Bali street dogs. These findings suggested that the dingo was more closely related to indigenous dogs from New Guinea. Feral dog populations, in particular large ones such as that of Bali, show genetic diversity that existed prior to phenotypic selection for breeds originating from their respective regions. This diversity needs to be identified and maintained in the face of progressive Westernization. These populations deserve further study as potential model populations for the evolution of major histocompatibility complex alleles, for the study of canine genetic diversity, for the development of dog breeds and for studies on the comigration of ancestral human and dog populations.
Collapse
Affiliation(s)
- J A Runstadler
- Center for Veterinary Genetics, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | | | | |
Collapse
|
46
|
Runstadler JA, Säilä H, Savolainen A, Leirisalo-Repo M, Aho K, Tuomilehto-Wolf E, Tuomilehto J, Seldin MF. HLA-DRB1, TAP2/TAP1, and HLA-DPB1 haplotypes in Finnish juvenile idiopathic arthritis: more complexity within the MHC. Genes Immun 2005; 5:562-71. [PMID: 15343265 DOI: 10.1038/sj.gene.6364129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This study further defines genetic susceptibility to JIA in the region centromeric to HLA-DRB1. DNA from 234 Finnish JIA nuclear families and 639 elderly Finnish control individuals was genotyped for five functional SNPs within the TAP2 and TAP1 loci ( approximately 200 kb centromeric of HLA-DRB1). Subsets of the controls (186) and patients (145) that had been previously typed for HLA-DRB1 were also genotyped by sequence for the HLA-DPB1 locus. Case/control and transmission disequilibrium test (TDT) methods revealed an association with the DPB1(*)030101 allele for JIA (OR 2.3, 95% CI 1.5-3.5). Notably, a detailed haplotypic analysis of the TAP2/TAP1 loci and their interaction with the HLA-DPB1(*)030101 and DRB1(*)08 and (*)11 alleles showed a variety of over-represented and under-represented TAP2/TAP1 haplotypes not evident in the single marker analysis. The strongest effect was observed in the polyarticular RF negative JIA subgroup for the 2-2-1-2-1 TAP2/TAP1 haplotype (TAP2B and TAP1A alleles) which showed an independent effect from both DRB1(*)08 and (*)11 (P<0.000003) and DPB1(*)030101 (P=0.02). We have provided evidence that the extended haplotypes (including HLA-DRB1, TAP2/TAP1, and HLA-DPB1) of pauciarticular and polyarticular RF negative disease are distinct. This observation may have implications for functional etiological differences between the pauciarticular and polyarticular JIA patients.
Collapse
Affiliation(s)
- J A Runstadler
- Rowe Program in Human Genetics and Molecular Medicine, Department of Biological Chemistry, University of California, Davis 95616, USA.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Runstadler JA, Säilä H, Savolainen A, Leirisalo-Repo M, Aho K, Tuomilehto-Wolf E, Tuomilehto J, Seldin MF. Association of SLC11A1 (NRAMP1) with persistent oligoarticular and polyarticular rheumatoid factor-negative juvenile idiopathic arthritis in Finnish patients: haplotype analysis in Finnish families. ACTA ACUST UNITED AC 2005; 52:247-56. [PMID: 15641099 DOI: 10.1002/art.20772] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE The SLC11A1 (formerly called NRAMP1) gene is important in natural resistance to a variety of intracellular infections mediated by macrophages and has been proposed as a candidate gene for autoimmune disease susceptibility. The aim of this study was to examine susceptibility in Finnish patients with persistent oligoarticular and polyarticular rheumatoid factor (RF)-negative juvenile idiopathic arthritis (JIA) due to the presence of the SLC11A1 locus on chromosome 2. METHODS A total of 234 Finnish JIA nuclear families and 639 elderly Finnish controls without a history of JIA were evaluated for association with JIA at 3 intragenic single-nucleotide polymorphisms: an intragenic insertion/deletion, a promoter microsatellite (NRAMP1), and a 3' microsatellite (D2S1471). RESULTS Analysis of marker haplotypes demonstrated a strong association of Finnish JIA with 6-marker, 4-marker, and 2-marker haplotypes. Most impressively, 1 of the 6-marker haplotypes showed an odds ratio (OR) of 4.0 (95% confidence interval [95% CI] 2.6-6.2) in all JIA patients, 3.5 (95% CI 1.9-6.5) in those with persistent oligoarticular JIA, and 4.1 (95% CI 2.5-6.7) in those with polyarticular RF-negative JIA. Stratification of the haplotype data suggested that susceptibility to JIA in the haplotype spanning the SLC11A1 locus is independent (P < 0.01) of an association with a DRB1 JIA shared epitope (DRB1*JIASE) that includes well-characterized strong susceptibility to DRB1*08 and *11 alleles. This SLC11A1 haplotype also had an additive effect with DRB1*JIASE in those with polyarticular, but not those with persistent oligoarticular, disease (P = 0.06, OR 2.9 [95% CI 0.9-9.2] versus P = 0.5, OR 1.6 [95% CI 0.4-6.0]). CONCLUSION Taken together, these data provide support for the existence of a locus at or near SLC11A1 that is a strong susceptibility factor for JIA in Finnish patients.
Collapse
Affiliation(s)
- Jonathan A Runstadler
- Davis Rowe Program in Human Genetics, University of California-Davis, One Shields Avenue, Davis, CA 95616, USA
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Runstadler JA, Säilä H, Savolainen A, Leirisalo-Repo M, Aho K, Tuomilehto-Wolf E, Tuomilehto J, Seldin MF. Analysis of MHC region genetics in Finnish patients with juvenile idiopathic arthritis: evidence for different locus-specific effects in polyarticular vs pauciarticular subsets and a shared DRB1 epitope. Genes Immun 2003; 4:326-35. [PMID: 12847547 DOI: 10.1038/sj.gene.6364002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This study used Finnish juvenile idiopathic arthritis (JIA) probands with pauciarticular and rheumatoid factor (RF) negative polyarticular subtypes of JIA to further define the genetic susceptibility to JIA. We examined 16 markers spanning an 18 cM region of chromosome 6 encompassing the MHC and surrounding genomic region in a set of 235 Finnish JIA nuclear families and 639 Finnish control individuals. Analysis by case/control association and transmission disequilibrium test (TDT) methods each demonstrated strong evidence for a susceptibility locus near the D6S2447 microsatellite (P<10(-6) for both methods) that is flanked by DQB1 and DRB1. Analysis of the DRB1 locus suggested that DRB1*0801 and DRB1*1101 rather than DQA1 or other HLA alleles may be responsible for conferring susceptibility to disease. These findings are consistent with the most compelling results of previous reports on HLA associations and suggest a JIA DRB1 shared epitope encompassing critical amino-acid residues in the third hypervariable region of this molecule. Most importantly, in pauciarticular patients, the strong association does not extend to proximal markers as it does in polyarticular patients (P<0.00001). Analysis strongly suggests that the difference is because of additional JIA susceptibility loci within the MHC being present in polyarticular RF negative patients.
Collapse
Affiliation(s)
- J A Runstadler
- Rowe Program in Human Genetics and Molecular Medicine, Department of Biological Chemistry, University of California, Davis, USA.
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Oberbauer AM, Runstadler JA, Murray JD, Havel PJ. Obesity and elevated plasma leptin concentration in oMT1A-o growth hormone transgenic mice. Obes Res 2001; 9:51-8. [PMID: 11346667 DOI: 10.1038/oby.2001.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE This study was undertaken to evaluate plasma leptin concentration in the regulatable ovine metallothionein-ovine growth hormone (oMT1a-oGH) transgenic (TG) mouse model of obesity. RESEARCH METHODS AND PROCEDURES Transgene stimulus (zinc) was provided at 21 days of age to male and female wild-type (WT) and TG mice. Plasma leptin concentrations were measured by radioimmunoassay at 42, 63, 84, and 105 days of age and from inactivated TG mice at 84 and 105 days. RESULTS WT and TG mice did not differ significantly in plasma leptin concentration at any of the ages examined (42, 63, 84, and 105 days), although females showed consistently higher plasma leptin concentrations than males regardless of genotype throughout the duration of the study. Male and female TG mice in which the transgene was inactivated at 63 days had a 1.5-fold to 3.5-fold increase in plasma leptin concentration over WT mice and continuously activated TG mice at 84 and 105 days of age. The elevated plasma leptin concentration seen in the inactivated TG mice at 84 and 105 days of age reflects the >300% increase in white adipose tissue seen in this model and correlated with all adipose depot weights and overall body lipid at these later ages. When plasma leptin was expressed per gram of total body fat, the leptin adjusted for body lipid was significantly higher in WT mice than either continuously activated TG or activated and then inactivated TG groups. DISCUSSION The inactivated TG mice in this study had higher plasma leptin levels with increasing total body adiposity, but the relative proportion of circulating leptin, on a total body lipid basis, was reduced when compared with the WT mice. This reduction was also observed in activated TG mice at the older ages. Although the absolute levels of circulating leptin were elevated in the inactivated TG animals, the amount of leptin produced per gram of fat was lowered. With the inactivation of the transgene, the leptin remained depressed after the removal of the elevated growth hormone. This represents a potential explanation for the ensuing hypertrophy of the fat depots and the abnormal phenotypic response of inactivated TG mice to elevated plasma leptin concentrations resulting in the development of obesity.
Collapse
Affiliation(s)
- A M Oberbauer
- Department Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California 95616, USA.
| | | | | | | |
Collapse
|
50
|
|