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Rasmussen AL, Gronvall G, Lowen AC, Goodrum F. Reply to Lipsitch et al., "Public role in research oversight". J Virol 2024; 98:e0008424. [PMID: 38477585 PMCID: PMC11019829 DOI: 10.1128/jvi.00084-24] [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: 03/14/2024] Open
Affiliation(s)
- Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Gigi 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 School of Medicine, Atlanta, Georgia, USA
| | - Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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2
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Rasmussen AL, Gronvall G, Lowen AC, Goodrum F. Reply to Ebright et al., "Implementing governmental oversight of enhanced potential pandemic pathogen research". J Virol 2024; 98:e0025624. [PMID: 38477587 PMCID: PMC11019956 DOI: 10.1128/jvi.00256-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Affiliation(s)
- Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Gigi 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 School of Medicine, Atlanta, Georgia, USA
| | - Felicia Goodrum
- Department of Immunobiology, BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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3
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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
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4
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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.
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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
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5
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Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic. bioRxiv 2023:2023.09.13.557637. [PMID: 37745602 PMCID: PMC10515900 DOI: 10.1101/2023.09.13.557637] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.
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Affiliation(s)
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan E. Pekar
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Reema Singh
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal
| | - Karthik Gangavarapu
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Matthew B. Rogers
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Niema Moshiri
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA
| | - Robert F. Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marion P. G. Koopmans
- Department of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Saskia Popescu
- University of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK
| | - Marc A. Suchard
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Florence Débarre
- Institut d’Écologie et des Sciences de l’Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France
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6
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Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. The coronavirus recombination pathway. Cell Host Microbe 2023; 31:874-889. [PMID: 37321171 PMCID: PMC10265781 DOI: 10.1016/j.chom.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.
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Affiliation(s)
- Heather L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA; Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
| | - Cassandra M Bonavita
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Isamara Navarrete-Macias
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Blake Vilchez
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
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7
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Cross RW, Prasad AN, Woolsey CB, Agans KN, Borisevich V, Dobias NS, Comer JE, Deer DJ, Geisbert JB, Rasmussen AL, Lipkin WI, Fenton KA, Geisbert TW. Natural history of nonhuman primates after conjunctival exposure to Ebola virus. Sci Rep 2023; 13:4175. [PMID: 36914721 PMCID: PMC10011569 DOI: 10.1038/s41598-023-31027-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Transmission of Ebola virus (EBOV) primarily occurs via contact exposure of mucosal surfaces with infected body fluids. Historically, nonhuman primate (NHP) challenge studies have employed intramuscular (i.m.) or small particle aerosol exposure, which are largely lethal routes of infection, but mimic worst-case scenarios such as a needlestick or intentional release, respectively. When exposed by more likely routes of natural infection, limited NHP studies have shown delayed onset of disease and reduced mortality. Here, we performed a series of systematic natural history studies in cynomolgus macaques with a range of conjunctival exposure doses. Challenge with 10,000 plaque forming units (PFU) of EBOV was uniformly lethal, whereas 5/6 subjects survived lower dose challenges (100 or 500 PFU). Conjunctival challenge resulted in a protracted time-to death compared to i.m. Asymptomatic infection was observed in survivors with limited detection of EBOV replication. Inconsistent seropositivity in survivors may suggest physical or natural immunological barriers are sufficient to prevent widespread viral dissemination.
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Affiliation(s)
- Robert W Cross
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Abhishek N Prasad
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Courtney B Woolsey
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Krystle N Agans
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Viktoriya Borisevich
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Natalie S Dobias
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Jason E Comer
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Daniel J Deer
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Joan B Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY, 10032, USA.,Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Walter Ian Lipkin
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY, 10032, USA
| | - Karla A Fenton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA.,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA
| | - Thomas W Geisbert
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77550, USA. .,Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX, 77550, USA.
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8
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Worobey M, Levy JI, Serrano LM, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, Suchard MA, Wertheim JO, Lemey P, Robertson DL, Garry RF, Holmes EC, Rambaut A, Andersen KG. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 2022; 377:951-959. [PMID: 35881010 PMCID: PMC9348750 DOI: 10.1126/science.abp8715] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [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: 03/02/2022] [Accepted: 07/18/2022] [Indexed: 12/25/2022]
Abstract
Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.
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Affiliation(s)
- Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Joshua I. Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lorena Malpica Serrano
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jonathan E. Pekar
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Informatics, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon SK S7N 5E3, Canada
- Center for Global Health Science and Security, Georgetown University, Washington, DC 20057, USA
| | | | - Chris Newman
- Wildlife Conservation Research Unit, Department of Zoology, The Recanati-Kaplan Centre, University of Oxford, Oxford OX13 5QL, UK
| | - Marion P. G. Koopmans
- Pandemic and Disaster Preparedness Centre, Erasmus University Medical Center, 3015 CE Rotterdam, Netherlands
- Department of Viroscience, Erasmus University Medical Center, 3015 CE Rotterdam, Netherlands
| | - Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
- Global Virus Network (GVN), Baltimore, MD 21201, USA
| | - David L. Robertson
- MRC-University of Glasgow Center for Virus Research, Glasgow G61 1QH, UK
| | - Robert F. Garry
- Global Virus Network (GVN), Baltimore, MD 21201, USA
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA
- Zalgen Labs, Frederick, MD 21703, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
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9
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Brosseau LM, Escandón K, Ulrich AK, Rasmussen AL, Roy CJ, Bix GJ, Popescu SV, Moore KA, Osterholm MT. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Dose, Infection, and Disease Outcomes for Coronavirus Disease 2019 (COVID-19): A Review. Clin Infect Dis 2022; 75:e1195-e1201. [PMID: 34651164 PMCID: PMC8524637 DOI: 10.1093/cid/ciab903] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 07/21/2021] [Indexed: 01/19/2023] Open
Abstract
The relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) dose, infection, and coronavirus disease 2019 (COVID-19) outcomes remains poorly understood. This review summarizes the existing literature regarding this issue, identifies gaps in current knowledge, and suggests opportunities for future research. In humans, host characteristics, including age, sex, comorbidities, smoking, and pregnancy, are associated with severe COVID-19. Similarly, in animals, host factors are strong determinants of disease severity, although most animal infection models manifest clinically with mild to moderate respiratory disease. The influence of variants of concern as it relates to infectious dose, consequence of overall pathogenicity, and disease outcome in dose-response remains unknown. Epidemiologic data suggest a dose-response relationship for infection contrasting with limited and inconsistent surrogate-based evidence between dose and disease severity. Recommendations include the design of future infection studies in animal models to investigate inoculating dose on outcomes and the use of better proxies for dose in human epidemiology studies.
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Affiliation(s)
- Lisa M Brosseau
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Kevin Escandón
- School of Medicine, Universidad del Valle, Cali, Colombia
- Grupo de Investigación en Virus Emergentes y Enfermedad (VIREM), Department of Microbiology, Universidad del Valle, Cali, Colombia
| | - Angela K Ulrich
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Georgetown Center for Global Health Science and Security, Washington, D.C., USA
| | - Chad J Roy
- Tulane National Primate Research Center, Division of Microbiology, Covington, Louisiana, USA
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Gregory J Bix
- Clinical Neuroscience Research Center, Departments of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, Louisiana, USA
- Tulane Brain Institute, Tulane University, New Orleans, Louisiana, USA
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, USAand
| | - Saskia V Popescu
- Georgetown Center for Global Health Science and Security, Washington, D.C., USA
- Biodefense Program, Schar School of Policy and Government, George Mason University, Arlington, Virginia, USA
| | - Kristine A Moore
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael T Osterholm
- Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, Minnesota, USA
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
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10
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Affiliation(s)
- Muge Cevik
- Division of Infection and Global Health Research, School of Medicine, University of St Andrews, St Andrews, UK
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Isaac I Bogoch
- Division of Infectious Diseases, University of Toronto, Toronto General Hospital, Toronto, Canada
| | - Jason Kindrachuk
- Laboratory of Emerging and Re-emerging Viruses, Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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11
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Broeckel RM, Feldmann F, McNally KL, Chiramel AI, Sturdevant GL, Leung JM, Hanley PW, Lovaglio J, Rosenke R, Scott DP, Saturday G, Bouamr F, Rasmussen AL, Robertson SJ, Best SM. A pigtailed macaque model of Kyasanur Forest disease virus and Alkhurma hemorrhagic disease virus pathogenesis. PLoS Pathog 2021; 17:e1009678. [PMID: 34855915 PMCID: PMC8638978 DOI: 10.1371/journal.ppat.1009678] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
Kyasanur Forest disease virus (KFDV) and the closely related Alkhurma hemorrhagic disease virus (AHFV) are emerging flaviviruses that cause severe viral hemorrhagic fevers in humans. Increasing geographical expansion and case numbers, particularly of KFDV in southwest India, class these viruses as a public health threat. Viral pathogenesis is not well understood and additional vaccines and antivirals are needed to effectively counter the impact of these viruses. However, current animal models of KFDV pathogenesis do not accurately reproduce viral tissue tropism or clinical outcomes observed in humans. Here, we show that pigtailed macaques (Macaca nemestrina) infected with KFDV or AHFV develop viremia that peaks 2 to 4 days following inoculation. Over the course of infection, animals developed lymphocytopenia, thrombocytopenia, and elevated liver enzymes. Infected animals exhibited hallmark signs of human disease characterized by a flushed appearance, piloerection, dehydration, loss of appetite, weakness, and hemorrhagic signs including epistaxis. Virus was commonly present in the gastrointestinal tract, consistent with human disease caused by KFDV and AHFV where gastrointestinal symptoms (hemorrhage, vomiting, diarrhea) are common. Importantly, RNAseq of whole blood revealed that KFDV downregulated gene expression of key clotting factors that was not observed during AHFV infection, consistent with increased severity of KFDV disease observed in this model. This work characterizes a nonhuman primate model for KFDV and AHFV that closely resembles human disease for further utilization in understanding host immunity and development of antiviral countermeasures.
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MESH Headings
- Animals
- Chlorocebus aethiops
- Cytokines/blood
- Disease Models, Animal
- Encephalitis Viruses, Tick-Borne/genetics
- Encephalitis Viruses, Tick-Borne/immunology
- Encephalitis Viruses, Tick-Borne/pathogenicity
- Encephalitis, Tick-Borne/immunology
- Encephalitis, Tick-Borne/pathology
- Encephalitis, Tick-Borne/virology
- Female
- HEK293 Cells
- Hemorrhagic Fevers, Viral/immunology
- Hemorrhagic Fevers, Viral/pathology
- Hemorrhagic Fevers, Viral/virology
- Humans
- Lymph Nodes/virology
- Macaca nemestrina
- Vero Cells
- Viremia
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Affiliation(s)
- Rebecca M. Broeckel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kristin L. McNally
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Abhilash I. Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Gail L. Sturdevant
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Jacqueline M. Leung
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Patrick W. Hanley
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Rebecca Rosenke
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Dana P. Scott
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Fadila Bouamr
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Center for Global Health Science and Security, Georgetown University, Washington, District of Columbia, United States of America
| | - Shelly J. Robertson
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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12
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Albery GF, Becker DJ, Brierley L, Brook CE, Christofferson RC, Cohen LE, Dallas TA, Eskew EA, Fagre A, Farrell MJ, Glennon E, Guth S, Joseph MB, Mollentze N, Neely BA, Poisot T, Rasmussen AL, Ryan SJ, Seifert S, Sjodin AR, Sorrell EM, Carlson CJ. The science of the host-virus network. Nat Microbiol 2021; 6:1483-1492. [PMID: 34819645 DOI: 10.1038/s41564-021-00999-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/18/2021] [Indexed: 01/21/2023]
Abstract
Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral infections. Related approaches have so far helped to identify basic biological rules that govern cross-species transmission and structure the global virome. We highlight ways to make modelling both accurate and actionable, and discuss the barriers that prevent researchers from translating viral ecology into public health policies that could prevent future pandemics.
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Affiliation(s)
- Gregory F Albery
- Department of Biology, Georgetown University, Washington DC, USA.
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Liam Brierley
- Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Cara E Brook
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Lily E Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad A Dallas
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA
| | - Evan A Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna Fagre
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maxwell J Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Emma Glennon
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarah Guth
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Maxwell B Joseph
- Earth Lab, Cooperative Institute for Research in Environmental Science, University of Colorado Boulder, Boulder, CO, USA
| | - Nardus Mollentze
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,MRC - University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Benjamin A Neely
- National Institute of Standards and Technology, Charleston, SC, USA
| | - Timothée Poisot
- Québec Centre for Biodiversity Sciences, Montréal, Québec, Canada.,Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sadie J Ryan
- Department of Geography, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Stephanie Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Anna R Sjodin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Erin M Sorrell
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA.,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA
| | - Colin J Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA. .,Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, USA.
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13
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Carlson CJ, Farrell MJ, Grange Z, Han BA, Mollentze N, Phelan AL, Rasmussen AL, Albery GF, Bett B, Brett-Major DM, Cohen LE, Dallas T, Eskew EA, Fagre AC, Forbes KM, Gibb R, Halabi S, Hammer CC, Katz R, Kindrachuk J, Muylaert RL, Nutter FB, Ogola J, Olival KJ, Rourke M, Ryan SJ, Ross N, Seifert SN, Sironen T, Standley CJ, Taylor K, Venter M, Webala PW. The future of zoonotic risk prediction. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200358. [PMID: 34538140 PMCID: PMC8450624 DOI: 10.1098/rstb.2020.0358] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [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] [Accepted: 07/15/2021] [Indexed: 01/26/2023] Open
Abstract
In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges? This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Colin J. Carlson
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Zoe Grange
- Public Health Scotland, Glasgow G2 6QE, UK
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Millbrook, NY 12545, USA
| | - Nardus Mollentze
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Alexandra L. Phelan
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Angela L. Rasmussen
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Gregory F. Albery
- Department of Biology, Georgetown University, Washington, DC 20007, USA
| | - Bernard Bett
- Animal and Human Health Program, International Livestock Research Institute, PO Box 30709-00100, Nairobi, Kenya
| | - David M. Brett-Major
- Department of Epidemiology, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lily E. Cohen
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70806, USA
| | - Evan A. Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, WA, USA
| | - Anna C. Fagre
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kristian M. Forbes
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Rory Gibb
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Sam Halabi
- O'Neill Institute for National and Global Health Law, Georgetown University Law Center, Washington, DC 20001, USA
| | - Charlotte C. Hammer
- Centre for the Study of Existential Risk, University of Cambridge, Cambridge, UK
| | - Rebecca Katz
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Jason Kindrachuk
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
| | - Renata L. Muylaert
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Felicia B. Nutter
- 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, School of Medicine, Tufts University, Boston, MA 02111, USA
| | | | | | - Michelle Rourke
- Law Futures Centre, Griffith Law School, Griffith University, Nathan, Queensland 4111, Australia
| | - Sadie J. Ryan
- Department of Geography and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Noam Ross
- EcoHealth Alliance, New York, NY 10018, USA
| | - Stephanie N. Seifert
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, USA
| | - Tarja Sironen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Claire J. Standley
- Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC 20007, USA
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Kishana Taylor
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Paul W. Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok 20500, Kenya
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14
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Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A. The origins of SARS-CoV-2: A critical review. Cell 2021; 184:4848-4856. [PMID: 34480864 PMCID: PMC8373617 DOI: 10.1016/j.cell.2021.08.017] [Citation(s) in RCA: 256] [Impact Index Per Article: 85.3] [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: 07/10/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 01/11/2023]
Abstract
Since the first reports of a novel severe acute respiratory syndrome (SARS)-like coronavirus in December 2019 in Wuhan, China, there has been intense interest in understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in the human population. Recent debate has coalesced around two competing ideas: a "laboratory escape" scenario and zoonotic emergence. Here, we critically review the current scientific evidence that may help clarify the origin of SARS-CoV-2.
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Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Stephen A Goldstein
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alexander Crits-Christoph
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94704, USA
| | - Joel O Wertheim
- Department of Medicine, University of California-San Diego, La Jolla, CA 92093, USA
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California-Davis School of Veterinary Medicine, Davis, CA 95616, USA
| | - Wendy S Barclay
- Department of Infectious Disease, Imperial College, London W2 1PG, UK
| | - Maciej F Boni
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Peter C Doherty
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute, 792 Elizabeth Street, Melbourne, VIC 3000, Australia
| | | | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, New Zealand; Institute of Environmental Science and Research, Wellington 5022, New Zealand
| | - Xiaowei Jiang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University (XJTLU), Suzhou, China
| | - Julian L Leibowitz
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX 77807, USA
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Tim Skern
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria
| | - Susan R Weiss
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Zalgen Labs, Germantown, MD 20876, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK.
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15
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Gibb R, Albery GF, Becker DJ, Brierley L, Connor R, Dallas TA, Eskew EA, Farrell MJ, Rasmussen AL, Ryan SJ, Sweeny A, Carlson CJ, Poisot T. Data Proliferation, Reconciliation, and Synthesis in Viral Ecology. Bioscience 2021. [DOI: 10.1093/biosci/biab080] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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
Abstract
The fields of viral ecology and evolution are rapidly expanding, motivated in part by concerns around emerging zoonoses. One consequence is the proliferation of host–virus association data, which underpin viral macroecology and zoonotic risk prediction but remain fragmented across numerous data portals. In the present article, we propose that synthesis of host–virus data is a central challenge to characterize the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open database of mammal host–virus associations that reconciles four published data sets. We show that this offers a substantially richer view of the known virome than any individual source data set but also that databases such as these risk becoming out of date as viral discovery accelerates. We argue for a shift in practice toward the development, incremental updating, and use of synthetic data sets in viral ecology, to improve replicability and facilitate work to predict the structure and dynamics of the global virome.
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Affiliation(s)
- Rory Gibb
- Centre on Climate Change and Planetary Health, London School of Hygiene and Tropical Medicine, London, England, United Kingdom
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, United States
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman Oklahoma, United States
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, England, United Kingdom
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Ryan Connor
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Tad A Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Evan A Eskew
- Department of Biology, Pacific Lutheran University, Tacoma, Washington, United States
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Maxwell J Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Angela L Rasmussen
- Vaccine Infectious Disease Organization and International Vaccine Centre, University of Saskatchewan, Saskatchewan, Saskatoon, Canada
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Sadie J Ryan
- Quantitative Disease Ecology and Conservation Lab, Department of Geography and with the Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States, and with the College of Life Sciences, University of KwaZulu Natal, Durban, South Africa
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Amy Sweeny
- Institute of Evolutionary Biology, University of Edinburgh, in Edinburgh, Scotland, United Kingdom
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Colin J Carlson
- Global Health Science and Security, Georgetown University Medical Center, Georgetown University, Washington, DC, United States
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
| | - Timothée Poisot
- Département de Sciences Biologiques, Université de Montréal, and with the Québec Centre for Biodiversity Sciences, both in Montréal, Québec, Canada
- Viral Emergence Research Initiative consortium, a global scientific collaboration to predict which viruses could infect humans, which animals host them, and where they could emerge
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16
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Aminian M, Ghosh T, Peterson A, Rasmussen AL, Stiverson S, Sharma K, Kirby M. Early prognosis of respiratory virus shedding in humans. Sci Rep 2021; 11:17193. [PMID: 34433834 PMCID: PMC8387366 DOI: 10.1038/s41598-021-95293-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 07/23/2021] [Indexed: 11/24/2022] Open
Abstract
This paper addresses the development of predictive models for distinguishing pre-symptomatic infections from uninfected individuals. Our machine learning experiments are conducted on publicly available challenge studies that collected whole-blood transcriptomics data from individuals infected with HRV, RSV, H1N1, and H3N2. We address the problem of identifying discriminatory biomarkers between controls and eventual shedders in the first 32 h post-infection. Our exploratory analysis shows that the most discriminatory biomarkers exhibit a strong dependence on time over the course of the human response to infection. We visualize the feature sets to provide evidence of the rapid evolution of the gene expression profiles. To quantify this observation, we partition the data in the first 32 h into four equal time windows of 8 h each and identify all discriminatory biomarkers using sparsity-promoting classifiers and Iterated Feature Removal. We then perform a comparative machine learning classification analysis using linear support vector machines, artificial neural networks and Centroid-Encoder. We present a range of experiments on different groupings of the diseases to demonstrate the robustness of the resulting models.
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Affiliation(s)
- M Aminian
- Department of Mathematics and Statistics, California State Polytechnic University, Pomona, CA, USA
| | - T Ghosh
- Department of Computer Science, Colorado State University, Fort Collins, CO, 80524, USA
| | - A Peterson
- Department of Mathematics, Colorado State University, Fort Collins, CO, 80524, USA
| | - A L Rasmussen
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,Center for Global Health Science and Security, Georgetown University Medical Center, Washington, DC, USA
| | - S Stiverson
- Department of Mathematics, Colorado State University, Fort Collins, CO, 80524, USA
| | - K Sharma
- Department of Computer Science, Colorado State University, Fort Collins, CO, 80524, USA
| | - M Kirby
- Department of Mathematics, Colorado State University, Fort Collins, CO, 80524, USA. .,Department of Computer Science, Colorado State University, Fort Collins, CO, 80524, USA.
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17
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Escandón K, Rasmussen AL, Bogoch II, Murray EJ, Escandón K, Popescu SV, Kindrachuk J. COVID-19 false dichotomies and a comprehensive review of the evidence regarding public health, COVID-19 symptomatology, SARS-CoV-2 transmission, mask wearing, and reinfection. BMC Infect Dis 2021; 21:710. [PMID: 34315427 PMCID: PMC8314268 DOI: 10.1186/s12879-021-06357-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Scientists across disciplines, policymakers, and journalists have voiced frustration at the unprecedented polarization and misinformation around coronavirus disease 2019 (COVID-19) pandemic. Several false dichotomies have been used to polarize debates while oversimplifying complex issues. In this comprehensive narrative review, we deconstruct six common COVID-19 false dichotomies, address the evidence on these topics, identify insights relevant to effective pandemic responses, and highlight knowledge gaps and uncertainties. The topics of this review are: 1) Health and lives vs. economy and livelihoods, 2) Indefinite lockdown vs. unlimited reopening, 3) Symptomatic vs. asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, 4) Droplet vs. aerosol transmission of SARS-CoV-2, 5) Masks for all vs. no masking, and 6) SARS-CoV-2 reinfection vs. no reinfection. We discuss the importance of multidisciplinary integration (health, social, and physical sciences), multilayered approaches to reducing risk ("Emmentaler cheese model"), harm reduction, smart masking, relaxation of interventions, and context-sensitive policymaking for COVID-19 response plans. We also address the challenges in understanding the broad clinical presentation of COVID-19, SARS-CoV-2 transmission, and SARS-CoV-2 reinfection. These key issues of science and public health policy have been presented as false dichotomies during the pandemic. However, they are hardly binary, simple, or uniform, and therefore should not be framed as polar extremes. We urge a nuanced understanding of the science and caution against black-or-white messaging, all-or-nothing guidance, and one-size-fits-all approaches. There is a need for meaningful public health communication and science-informed policies that recognize shades of gray, uncertainties, local context, and social determinants of health.
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Affiliation(s)
- Kevin Escandón
- School of Medicine, Universidad del Valle, Cali, Colombia.
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
| | - Isaac I Bogoch
- Division of Infectious Diseases, University of Toronto, Toronto General Hospital, Toronto, Canada
| | - Eleanor J Murray
- Department of Epidemiology, Boston University School of Public Health, Boston, USA
| | - Karina Escandón
- Department of Anthropology, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Saskia V Popescu
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA
- Schar School of Policy and Government, George Mason University, Fairfax, VA, USA
| | - Jason Kindrachuk
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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18
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Affiliation(s)
- Angela L Rasmussen
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA.
| | - Saskia V Popescu
- Georgetown Center for Global Health Science and Security, Georgetown University, Washington, DC, USA. .,Schar School of Policy and Government, George Mason University, Fairfax, VA, USA
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19
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Forbes KM, Anzala O, Carlson CJ, Kelvin AA, Kuppalli K, Leroy EM, Maganga GD, Masika MM, Mombo IM, Mwaengo DM, Niama RF, Nziza J, Ogola J, Pickering BS, Rasmussen AL, Sironen T, Vapalahti O, Webala PW, Kindrachuk J. Towards a coordinated strategy for intercepting human disease emergence in Africa. The Lancet Microbe 2021; 2:e51-e52. [DOI: 10.1016/s2666-5247(20)30220-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/06/2023] Open
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20
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Gurdasani D, Bear L, Bogaert D, Burgess RA, Busse R, Cacciola R, Charpak Y, Colbourn T, Drury J, Friston K, Gallo V, Goldman LR, Greenhalgh T, Hyde Z, Kuppalli K, Majumder MS, Martin-Moreno JM, McKee M, Michie S, Mossialos E, Nouri A, Pagel C, Pimenta D, Popescu S, Priesemann V, Rasmussen AL, Reicher S, Ricciardi W, Rice K, Silver J, Smith TC, Wenham C, West R, Yamey G, Yates C, Ziauddeen H. The UK needs a sustainable strategy for COVID-19. Lancet 2020; 396:1800-1801. [PMID: 33181080 PMCID: PMC7834725 DOI: 10.1016/s0140-6736(20)32350-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 11/16/2022]
Affiliation(s)
| | - Laura Bear
- London School of Economics and Political Science, London, UK
| | | | | | | | - Roberto Cacciola
- Department of Surgical Sciences, Università Di Tor Vergata, Rome, Italy
| | - Yves Charpak
- Fondation Charpak, L'esprit des Sciences, Paris, France
| | | | | | | | - Valentina Gallo
- University of Groningen, Campus Fryslân, Leeuwarden, Netherlands
| | - Lynn R Goldman
- George Washington University Milken Institute School of Public Health, Washington, DC, USA
| | | | - Zoë Hyde
- University of Western Australia, Perth, WA, Australia
| | | | | | | | - Martin McKee
- London School of Hygiene & Tropical Medicine, London, UK
| | | | - Elias Mossialos
- London School of Economics and Political Science, London, UK
| | - Ali Nouri
- Federation of American Scientists, Washington, DC, USA
| | | | | | | | - Viola Priesemann
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | | | | | | | - Ken Rice
- University of Edinburgh, Edinburgh, UK
| | | | | | - Clare Wenham
- London School of Economics and Political Science, London, UK
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21
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Abstract
Population-level herd immunity is critical for long-term control of SARS-CoV-2. However, proposals to reach the herd immunity threshold through naturally acquired infection, rather than vaccination, have complicated public health efforts and popularized policies that will lead to widespread transmission and mortality. Vaccination is the only viable path to herd immunity.
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Affiliation(s)
- Angela L Rasmussen
- Center for Global Health Science and Security, Georgetown University, Washington, DC 20057, USA
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22
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Muñoz-Fontela C, Dowling WE, Funnell SGP, Gsell PS, Riveros-Balta AX, Albrecht RA, Andersen H, Baric RS, Carroll MW, Cavaleri M, Qin C, Crozier I, Dallmeier K, de Waal L, de Wit E, Delang L, Dohm E, Duprex WP, Falzarano D, Finch CL, Frieman MB, Graham BS, Gralinski LE, Guilfoyle K, Haagmans BL, Hamilton GA, Hartman AL, Herfst S, Kaptein SJF, Klimstra WB, Knezevic I, Krause PR, Kuhn JH, Le Grand R, Lewis MG, Liu WC, Maisonnasse P, McElroy AK, Munster V, Oreshkova N, Rasmussen AL, Rocha-Pereira J, Rockx B, Rodríguez E, Rogers TF, Salguero FJ, Schotsaert M, Stittelaar KJ, Thibaut HJ, Tseng CT, Vergara-Alert J, Beer M, Brasel T, Chan JFW, García-Sastre A, Neyts J, Perlman S, Reed DS, Richt JA, Roy CJ, Segalés J, Vasan SS, Henao-Restrepo AM, Barouch DH. Animal models for COVID-19. Nature 2020; 586:509-515. [PMID: 32967005 PMCID: PMC8136862 DOI: 10.1038/s41586-020-2787-6] [Citation(s) in RCA: 572] [Impact Index Per Article: 143.0] [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] [Received: 06/22/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the aetiological agent of coronavirus disease 2019 (COVID-19), an emerging respiratory infection caused by the introduction of a novel coronavirus into humans late in 2019 (first detected in Hubei province, China). As of 18 September 2020, SARS-CoV-2 has spread to 215 countries, has infected more than 30 million people and has caused more than 950,000 deaths. As humans do not have pre-existing immunity to SARS-CoV-2, there is an urgent need to develop therapeutic agents and vaccines to mitigate the current pandemic and to prevent the re-emergence of COVID-19. In February 2020, the World Health Organization (WHO) assembled an international panel to develop animal models for COVID-19 to accelerate the testing of vaccines and therapeutic agents. Here we summarize the findings to date and provides relevant information for preclinical testing of vaccine candidates and therapeutic agents for COVID-19.
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Affiliation(s)
- César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - William E Dowling
- Centre for Epidemic Preparedness Innovations (CEPI), Washington, DC, USA
| | | | | | | | - Randy A Albrecht
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miles W Carroll
- National Infection Service, Public Health England, Salisbury, UK
| | | | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Peking, China
| | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kai Dallmeier
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | | | - Emmie de Wit
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Erik Dohm
- Animal Resources Program, University of Alabama at Birmingham, Birmingham, AL, USA
| | - W Paul Duprex
- Department of Microbiology and Molecular Genetics, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Darryl Falzarano
- VIDO-Intervac, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Courtney L Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Bart L Haagmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Amy L Hartman
- Department of Microbiology and Molecular Genetics, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sander Herfst
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Suzanne J F Kaptein
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - William B Klimstra
- Department of Immunology, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Philip R Krause
- Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Roger Le Grand
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Inserm, CEA, Université Paris-Saclay, Paris, France
| | | | - Wen-Chun Liu
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pauline Maisonnasse
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Inserm, CEA, Université Paris-Saclay, Paris, France
| | - Anita K McElroy
- Division of Pediatric Infectious Diseases, Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vincent Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Nadia Oreshkova
- Wageningen Bioveterinary Research (WBVR), Wageningen University and Research, Lelystad, The Netherlands
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia Mailman |School of Public Health, New York, NY, USA
| | - Joana Rocha-Pereira
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Barry Rockx
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Estefanía Rodríguez
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Thomas F Rogers
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | | | - Michael Schotsaert
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Hendrik Jan Thibaut
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Chien-Te Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Júlia Vergara-Alert
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Trevor Brasel
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jasper F W Chan
- Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Adolfo García-Sastre
- Department of Microbiology, Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Douglas S Reed
- Department of Immunology, Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juergen A Richt
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Chad J Roy
- Tulane National Primate Research Center, Covington, LA, USA
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Seshadri S Vasan
- Australian Centre for Disease Preparedness, CSIRO, Geelong, Victoria, Australia
- Department of Health Sciences, University of York, York, UK
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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23
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Abstract
In this issue of Cell, Korber et al. found that a SARS-CoV-2 variant in the spike protein D614G rapidly became dominant around the world. Although clinical and in vitro data suggest that D614G changes the virus phenotype, the impact of the mutation on transmission, disease, and vaccine and therapeutic development are largely unknown.
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Affiliation(s)
- Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia Mailman School of Public Health, New York, NY 10032, USA
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24
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Affiliation(s)
- Krutika Kuppalli
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, United States; Center for Innovation in Global Health, Stanford University School of Medicine, United States
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia Mailman School of Public Health, United States.
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25
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Goodman AG, Rasmussen AL. Editorial: Host-Pathogen Interactions During Arboviral Infections. Front Cell Infect Microbiol 2019; 9:77. [PMID: 30972308 PMCID: PMC6443840 DOI: 10.3389/fcimb.2019.00077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/05/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alan G Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, United States.,Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Angela L Rasmussen
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, United States
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26
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Dutta M, Robertson SJ, Okumura A, Scott DP, Chang J, Weiss JM, Sturdevant GL, Feldmann F, Haddock E, Chiramel AI, Ponia SS, Dougherty JD, Katze MG, Rasmussen AL, Best SM. A Systems Approach Reveals MAVS Signaling in Myeloid Cells as Critical for Resistance to Ebola Virus in Murine Models of Infection. Cell Rep 2017; 18:816-829. [PMID: 28099857 DOI: 10.1016/j.celrep.2016.12.069] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [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: 07/14/2016] [Revised: 11/11/2016] [Accepted: 12/20/2016] [Indexed: 01/08/2023] Open
Abstract
The unprecedented 2013-2016 outbreak of Ebola virus (EBOV) resulted in over 11,300 human deaths. Host resistance to RNA viruses requires RIG-I-like receptor (RLR) signaling through the adaptor protein, mitochondrial antiviral signaling protein (MAVS), but the role of RLR-MAVS in orchestrating anti-EBOV responses in vivo is not known. Here we apply a systems approach to MAVS-/- mice infected with either wild-type or mouse-adapted EBOV. MAVS controlled EBOV replication through the expression of IFNα, regulation of inflammatory responses in the spleen, and prevention of cell death in the liver, with macrophages implicated as a major cell type influencing host resistance. A dominant role for RLR signaling in macrophages was confirmed following conditional MAVS deletion in LysM+ myeloid cells. These findings reveal tissue-specific MAVS-dependent transcriptional pathways associated with resistance to EBOV, and they demonstrate that EBOV adaptation to cause disease in mice involves changes in two distinct events, RLR-MAVS antagonism and suppression of RLR-independent IFN-I responses.
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Affiliation(s)
- Mukta Dutta
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 59105, USA
| | - Shelly J Robertson
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Atsushi Okumura
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 59105, USA; Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Dana P Scott
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Jean Chang
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 59105, USA
| | - Jeffrey M Weiss
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 59105, USA
| | - Gail L Sturdevant
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Friederike Feldmann
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Elaine Haddock
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Abhilash I Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Sanket S Ponia
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Jonathan D Dougherty
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA
| | - Michael G Katze
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 59105, USA
| | - Angela L Rasmussen
- Department of Microbiology, School of Medicine, University of Washington, Seattle, WA 59105, USA; Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, Hamilton, MT 59840, USA.
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27
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Affiliation(s)
- Angela L. Rasmussen
- Department of Microbiology, University of Washington, Seattle, Washington 98109;
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28
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Abstract
Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehensive studies of population-level responses to infection and provides novel methods for predicting clinical outcomes. As genomic technologies become more accessible, these methods will redefine how emerging viruses are studied and outbreaks are contained. Here we review the existing and emerging genomic technologies that are enabling systems epidemiology and systems virology and making it possible to respond rapidly to emerging viruses such as Zika.
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Affiliation(s)
- Angela L Rasmussen
- Department of Microbiology, University of Washington, 960 Republican Street, Seattle, WA 98109, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, 960 Republican Street, Seattle, WA 98109, USA.
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Lubick KJ, Robertson SJ, McNally KL, Freedman BA, Rasmussen AL, Taylor RT, Walts AD, Tsuruda S, Sakai M, Ishizuka M, Boer EF, Foster EC, Chiramel AI, Addison CB, Green R, Kastner DL, Katze MG, Holland SM, Forlino A, Freeman AF, Boehm M, Yoshii K, Best SM. Flavivirus Antagonism of Type I Interferon Signaling Reveals Prolidase as a Regulator of IFNAR1 Surface Expression. Cell Host Microbe 2016; 18:61-74. [PMID: 26159719 DOI: 10.1016/j.chom.2015.06.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 04/08/2015] [Accepted: 06/16/2015] [Indexed: 11/25/2022]
Abstract
Type I interferon (IFN-α/β or IFN-I) signals through two receptor subunits, IFNAR1 and IFNAR2, to orchestrate sterile and infectious immunity. Cellular pathways that regulate IFNAR1 are often targeted by viruses to suppress the antiviral effects of IFN-I. Here we report that encephalitic flaviviruses, including tick-borne encephalitis virus and West Nile virus, antagonize IFN-I signaling by inhibiting IFNAR1 surface expression. Loss of IFNAR1 was associated with binding of the viral IFN-I antagonist, NS5, to prolidase (PEPD), a cellular dipeptidase implicated in primary immune deficiencies in humans. Prolidase was required for IFNAR1 maturation and accumulation, activation of IFNβ-stimulated gene induction, and IFN-I-dependent viral control. Human fibroblasts derived from patients with genetic prolidase deficiency exhibited decreased IFNAR1 surface expression and reduced IFNβ-stimulated signaling. Thus, by understanding flavivirus IFN-I antagonism, prolidase is revealed as a central regulator of IFN-I responses.
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Affiliation(s)
- Kirk J Lubick
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Shelly J Robertson
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Kristin L McNally
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Brett A Freedman
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Angela L Rasmussen
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - R Travis Taylor
- Department of Medical Microbiology and Immunology, College of Medicine, University of Toledo Health Science Campus, Toledo, OH 43614, USA
| | - Avram D Walts
- Translational Medicine Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Seitaro Tsuruda
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0818, Japan
| | - Mizuki Sakai
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0818, Japan
| | - Mariko Ishizuka
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0818, Japan
| | - Elena F Boer
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Erin C Foster
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Abhilash I Chiramel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Conrad B Addison
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA
| | - Richard Green
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Daniel L Kastner
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, WA 98109, USA
| | - Steven M Holland
- Immunopathogenesis Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20814, USA
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
| | - Alexandra F Freeman
- Immunopathogenesis Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20814, USA
| | - Manfred Boehm
- Translational Medicine Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Kentaro Yoshii
- Laboratory of Public Health, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0818, Japan
| | - Sonja M Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, NIH, Hamilton, MT 59840, USA.
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Green CR, Cowan P, Elk R, O'Neil KM, Rasmussen AL. National Institutes of Health Pathways to Prevention Workshop: Advancing the Research on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Ann Intern Med 2015; 162:860-5. [PMID: 26075757 DOI: 10.7326/m15-0338] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The National Institutes of Health (NIH) Pathways to Prevention Workshop: Advancing the Research on Myalgic Encephalomyelitis/Chronic Fatigue Syndrome was cosponsored by the NIH Office of Disease Prevention and the Trans-NIH Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Research Working Group. A multidisciplinary working group developed the agenda, and an Evidence-based Practice Center prepared an evidence report through a contract with the Agency for Healthcare Research and Quality to facilitate the discussion. During the 1.5-day workshop, invited experts discussed the body of evidence and attendees had the opportunity to comment during open discussions. After weighing evidence from the evidence report, expert presentations, and public comments, an unbiased, independent panel prepared a draft report that identified research gaps and future research priorities. The report was posted on the NIH Office of Disease Prevention Web site for 4 weeks for public comment.
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Affiliation(s)
- Carmen R. Green
- From University of Michigan Health System, Ann Arbor, Michigan; American Chronic Pain Association, Rocklin, California; College of Nursing, University of South Carolina, Columbia, South Carolina; Indiana University School of Medicine and Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana; and Katze Lab, University of Washington, Seattle, Washington
| | - Penney Cowan
- From University of Michigan Health System, Ann Arbor, Michigan; American Chronic Pain Association, Rocklin, California; College of Nursing, University of South Carolina, Columbia, South Carolina; Indiana University School of Medicine and Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana; and Katze Lab, University of Washington, Seattle, Washington
| | - Ronit Elk
- From University of Michigan Health System, Ann Arbor, Michigan; American Chronic Pain Association, Rocklin, California; College of Nursing, University of South Carolina, Columbia, South Carolina; Indiana University School of Medicine and Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana; and Katze Lab, University of Washington, Seattle, Washington
| | - Kathleen M. O'Neil
- From University of Michigan Health System, Ann Arbor, Michigan; American Chronic Pain Association, Rocklin, California; College of Nursing, University of South Carolina, Columbia, South Carolina; Indiana University School of Medicine and Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana; and Katze Lab, University of Washington, Seattle, Washington
| | - Angela L. Rasmussen
- From University of Michigan Health System, Ann Arbor, Michigan; American Chronic Pain Association, Rocklin, California; College of Nursing, University of South Carolina, Columbia, South Carolina; Indiana University School of Medicine and Riley Hospital for Children at Indiana University Health, Indianapolis, Indiana; and Katze Lab, University of Washington, Seattle, Washington
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31
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Tchitchek N, Safronetz D, Rasmussen AL, Martens C, Virtaneva K, Porcella SF, Feldmann H, Ebihara H, Katze MG. Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. PLoS One 2014; 9:e112617. [PMID: 25398096 PMCID: PMC4232415 DOI: 10.1371/journal.pone.0112617] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022] Open
Abstract
Background The Syrian hamster (golden hamster, Mesocricetus auratus) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species. Results A cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our Mesocricetus auratus Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species. Conclusions This Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species. Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.
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Affiliation(s)
- Nicolas Tchitchek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - David Safronetz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Angela L Rasmussen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Craig Martens
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Kimmo Virtaneva
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Hideki Ebihara
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America; Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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Rasmussen AL, Okumura A, Ferris MT, Green R, Feldmann F, Kelly SM, Scott DP, Safronetz D, Haddock E, LaCasse R, Thomas MJ, Sova P, Carter VS, Weiss JM, Miller DR, Shaw GD, Korth MJ, Heise MT, Baric RS, de Villena FPM, Feldmann H, Katze MG. Host genetic diversity enables Ebola hemorrhagic fever pathogenesis and resistance. Science 2014; 346:987-91. [PMID: 25359852 DOI: 10.1126/science.1259595] [Citation(s) in RCA: 208] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Existing mouse models of lethal Ebola virus infection do not reproduce hallmark symptoms of Ebola hemorrhagic fever, neither delayed blood coagulation and disseminated intravascular coagulation nor death from shock, thus restricting pathogenesis studies to nonhuman primates. Here we show that mice from the Collaborative Cross panel of recombinant inbred mice exhibit distinct disease phenotypes after mouse-adapted Ebola virus infection. Phenotypes range from complete resistance to lethal disease to severe hemorrhagic fever characterized by prolonged coagulation times and 100% mortality. Inflammatory signaling was associated with vascular permeability and endothelial activation, and resistance to lethal infection arose by induction of lymphocyte differentiation and cellular adhesion, probably mediated by the susceptibility allele Tek. These data indicate that genetic background determines susceptibility to Ebola hemorrhagic fever.
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Affiliation(s)
| | - Atsushi Okumura
- Department of Microbiology, University of Washington, Seattle, WA, USA. Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Martin T Ferris
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Richard Green
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Sara M Kelly
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Dana P Scott
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - David Safronetz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Elaine Haddock
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Rachel LaCasse
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Matthew J Thomas
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Pavel Sova
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Victoria S Carter
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Jeffrey M Weiss
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Darla R Miller
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Marcus J Korth
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Mark T Heise
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA. Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Heinz Feldmann
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT, USA
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, WA, USA. Washington National Primate Research Center, Seattle, WA, USA.
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Falzarano D, de Wit E, Feldmann F, Rasmussen AL, Okumura A, Peng X, Thomas MJ, van Doremalen N, Haddock E, Nagy L, LaCasse R, Liu T, Zhu J, McLellan JS, Scott DP, Katze MG, Feldmann H, Munster VJ. Infection with MERS-CoV causes lethal pneumonia in the common marmoset. PLoS Pathog 2014; 10:e1004250. [PMID: 25144235 PMCID: PMC4140844 DOI: 10.1371/journal.ppat.1004250] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 06/30/2014] [Indexed: 12/03/2022] Open
Abstract
The availability of a robust disease model is essential for the development of countermeasures for Middle East respiratory syndrome coronavirus (MERS-CoV). While a rhesus macaque model of MERS-CoV has been established, the lack of uniform, severe disease in this model complicates the analysis of countermeasure studies. Modeling of the interaction between the MERS-CoV spike glycoprotein and its receptor dipeptidyl peptidase 4 predicted comparable interaction energies in common marmosets and humans. The suitability of the marmoset as a MERS-CoV model was tested by inoculation via combined intratracheal, intranasal, oral and ocular routes. Most of the marmosets developed a progressive severe pneumonia leading to euthanasia of some animals. Extensive lesions were evident in the lungs of all animals necropsied at different time points post inoculation. Some animals were also viremic; high viral loads were detected in the lungs of all infected animals, and total RNAseq demonstrated the induction of immune and inflammatory pathways. This is the first description of a severe, partially lethal, disease model of MERS-CoV, and as such will have a major impact on the ability to assess the efficacy of vaccines and treatment strategies as well as allowing more detailed pathogenesis studies. The development of vaccines and treatment strategies is aided by robust animal disease models that accurately depict the illness that is observed in humans. Here we describe a new, improved model for MERS-CoV using the common marmoset, whereby the severe, and even lethal, illness that has been observed in many human cases is recapitulated. Prior to the development of this model, the only available animal models for MERS-CoV infection were the rhesus macaque and a mouse model that requires adenovirus-transduced expression of the human version of the protein required for virus entry. The rhesus macaque model more closely mimics the mild to moderate disease observed in some patients—mainly those without significant comorbidities. The increased severity of illness in the common marmoset model is an important advance in the ability to evaluate potential therapeutic agents against MERS-CoV, as discrimination between successfully treated and control animals should be more apparent. In addition, the closer models recapitulate the disease observed in humans, the more likely findings can be eventually translated into use in humans.
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Affiliation(s)
- Darryl Falzarano
- Disease Modeling and Transmission, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Emmie de Wit
- Disease Modeling and Transmission, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Angela L. Rasmussen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Atsushi Okumura
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Xinxia Peng
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Matthew J. Thomas
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Neeltje van Doremalen
- Virus Ecology Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Elaine Haddock
- Disease Modeling and Transmission, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Lee Nagy
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Rachel LaCasse
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Tingting Liu
- Department of Immunology and Microbial Science, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jiang Zhu
- Department of Immunology and Microbial Science, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jason S. McLellan
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Dana P. Scott
- Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Michael G. Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Heinz Feldmann
- Disease Modeling and Transmission, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail: (HF); (VJM)
| | - Vincent J. Munster
- Virus Ecology Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
- * E-mail: (HF); (VJM)
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Diamond DL, Krasnoselsky AL, Burnum KE, Monroe ME, Webb-Robertson BJ, McDermott JE, Yeh MM, Dzib JFG, Susnow N, Strom S, Proll SC, Belisle SE, Purdy DE, Rasmussen AL, Walters KA, Jacobs JM, Gritsenko MA, Camp DG, Bhattacharya R, Perkins JD, Carithers RL, Liou IW, Larson AM, Benecke A, Waters KM, Smith RD, Katze MG. Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation. Hepatology 2012; 56:28-38. [PMID: 22331615 PMCID: PMC3387320 DOI: 10.1002/hep.25649] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/25/2012] [Indexed: 12/23/2022]
Abstract
UNLABELLED Liver transplant tissues offer the unique opportunity to model the longitudinal protein abundance changes occurring during hepatitis C virus (HCV)-associated liver disease progression in vivo. In this study, our goal was to identify molecular signatures, and potential key regulatory proteins, representative of the processes influencing early progression to fibrosis. We performed global protein profiling analyses on 24 liver biopsy specimens obtained from 15 HCV(+) liver transplant recipients at 6 and/or 12 months posttransplantation. Differentially regulated proteins associated with early progression to fibrosis were identified by analysis of the area under the receiver operating characteristic curve. Analysis of serum metabolites was performed on samples obtained from an independent cohort of 60 HCV(+) liver transplant patients. Computational modeling approaches were applied to identify potential key regulatory proteins of liver fibrogenesis. Among 4,324 proteins identified, 250 exhibited significant differential regulation in patients with rapidly progressive fibrosis. Patients with rapid fibrosis progression exhibited enrichment in differentially regulated proteins associated with various immune, hepatoprotective, and fibrogenic processes. The observed increase in proinflammatory activity and impairment in antioxidant defenses suggests that patients who develop significant liver injury experience elevated oxidative stresses. This was supported by an independent study demonstrating the altered abundance of oxidative stress-associated serum metabolites in patients who develop severe liver injury. Computational modeling approaches further highlight a potentially important link between HCV-associated oxidative stress and epigenetic regulatory mechanisms impacting on liver fibrogenesis. CONCLUSION Our proteome and metabolome analyses provide new insights into the role for increased oxidative stress in the rapid fibrosis progression observed in HCV(+) liver transplant recipients. These findings may prove useful in prognostic applications for predicting early progression to fibrosis.
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Affiliation(s)
- Deborah L. Diamond
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | | | - Kristin E. Burnum
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew E. Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | | | - Jason E. McDermott
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Matthew M. Yeh
- Dept. of Pathology, University of Washington School of Medicine, Seattle, WA
| | | | - Nathan Susnow
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Susan Strom
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Sean C. Proll
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Sarah E. Belisle
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - David E. Purdy
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Angela L. Rasmussen
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Kathie-Anne Walters
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Jon M. Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Marina A. Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Renuka Bhattacharya
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - James D. Perkins
- Dept. of Surgery, University of Washington School of Medicine, Seattle, WA
| | - Robert L. Carithers
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Iris W. Liou
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Anne M. Larson
- Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA
| | - Arndt Benecke
- Institut des Hautes Etudes Scientifiques, CNRS, Bures-sur-Yvette, France
| | - Katrina M. Waters
- Computational Biology & Bioinformatics, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Michael G. Katze
- Dept. of Microbiology, University of Washington School of Medicine, Seattle, WA,Washington National Primate Research Center, University of Washington, Seattle, WA
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35
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Rasmussen AL, Tchitchek N, Susnow NJ, Krasnoselsky AL, Diamond DL, Yeh MM, Proll SC, Korth MJ, Walters KA, Lederer S, Larson AM, Carithers RL, Benecke A, Katze MG. Early transcriptional programming links progression to hepatitis C virus-induced severe liver disease in transplant patients. Hepatology 2012; 56:17-27. [PMID: 22278598 PMCID: PMC3349763 DOI: 10.1002/hep.25612] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/15/2012] [Indexed: 12/13/2022]
Abstract
UNLABELLED Liver failure resulting from chronic hepatitis C virus (HCV) infection is a major cause for liver transplantation worldwide. Recurrent infection of the graft is universal in HCV patients after transplant and results in a rapid progression to severe fibrosis and end-stage liver disease in one third of all patients. No single clinical variable, or combination thereof, has, so far, proven accurate in identifying patients at risk of hepatic decompensation in the transplant setting. A combination of longitudinal, dimensionality reduction and categorical analysis of the transcriptome from 111 liver biopsy specimens taken from 57 HCV-infected patients over time identified a molecular signature of gene expression of patients at risk of developing severe fibrosis. Significantly, alterations in gene expression occur before histologic evidence of liver disease progression, suggesting that events that occur during the acute phase of infection influence patient outcome. Additionally, a common precursor state for different severe clinical outcomes was identified. CONCLUSION Based on this patient cohort, incidence of severe liver disease is a process initiated early during HCV infection of the donor organ. The probable cellular network at the basis of the initial transition to severe liver disease was identified and characterized.
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Affiliation(s)
- Angela L. Rasmussen
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA
| | - Nicolas Tchitchek
- Institut des Hautes Études Scientifiques & Centre National de la Recherche Scientifique, Bures-sur-Yvette, France
| | - Nathan J. Susnow
- University of Washington Medical Center, Hepatology Section, Seattle, WA,Meriter Medical Group, Madison, WI
| | | | - Deborah L. Diamond
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA
| | - Matthew M. Yeh
- University of Washington School of Medicine, Department of Pathology, Seattle, WA
| | - Sean C. Proll
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA
| | - Marcus J. Korth
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA
| | - Kathie-Anne Walters
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA,Institute for Systems Biology, Seattle, WA
| | - Sharon Lederer
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA
| | - Anne M. Larson
- University of Washington Medical Center, Hepatology Section, Seattle, WA,The Liver Center, Swedish Medical Center, Seattle, WA
| | | | - Arndt Benecke
- Institut des Hautes Études Scientifiques & Centre National de la Recherche Scientifique, Bures-sur-Yvette, France
| | - Michael G. Katze
- University of Washington School of Medicine, Department of Microbiology, Seattle, WA
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Rasmussen AL, Wang IM, Shuhart MC, Proll SC, He Y, Cristescu R, Roberts C, Carter VS, Williams CM, Diamond DL, Bryan JT, Ulrich R, Korth MJ, Thomassen LV, Katze MG. Chronic immune activation is a distinguishing feature of liver and PBMC gene signatures from HCV/HIV coinfected patients and may contribute to hepatic fibrogenesis. Virology 2012; 430:43-52. [PMID: 22608059 DOI: 10.1016/j.virol.2012.04.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 04/06/2012] [Accepted: 04/17/2012] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus/human immunodeficiency virus (HCV/HIV) coinfected patients demonstrate accelerated progression to severe liver injury in comparison to HCV monoinfected patients, although the underlying mechanisms are unclear owing to infection of separate tissue compartments with two distinct viral pathogens. Microarray analysis of paired liver biopsy and peripheral blood mononuclear cell (PBMC) specimens from HCV/HIV coinfected and HCV monoinfected patients identified a gene expression signature associated with increased inflammation and immune activation that was present only in liver and PBMC samples from coinfected patients. We also identified in these samples liver- and PBMC-specific signatures enriched with fibrogenic/hepatic stellate activation and proinflammatory genes, respectively. Finally, Bayesian networks were constructed by assimilating these data with existing data from liver and PBMC samples from other cohorts, augmenting enrichment of biologically important pathways and further indicating that chronic immune activation in HCV/HIV coinfection may exacerbate liver disease progression in coinfected patients.
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Affiliation(s)
- Angela L Rasmussen
- Department of Microbiology, University of Washington, Box 358070, Seattle, WA 98195, USA
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Rasmussen AL, Racaniello VR. Selection of rhinovirus 1A variants adapted for growth in mouse lung epithelial cells. Virology 2011; 420:82-8. [PMID: 21943827 DOI: 10.1016/j.virol.2011.08.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/11/2011] [Accepted: 08/27/2011] [Indexed: 11/26/2022]
Abstract
Rhinoviruses (RVs) are picornaviruses that are causative agents of the majority of upper respiratory tract infections, or "common colds," in humans. RVs infect both the upper and lower respiratory tract, and in addition to the common cold may also cause pneumonia, complications in patients with chronic lung diseases such as cystic fibrosis, and asthma exacerbations. Convenient animal models are not available to study the pathogenesis of rhinovirus-induced illness. Rhinovirus RV1A replicates poorly in mouse cells; variants with improved replication were selected by serial passage through mouse embryonic fibroblasts and mouse lung epithelial cells. Adaptation for improved growth in mouse cells was mediated by amino acid changes in the RV1a non-structural protein 3A. Mouse cell-adapted RV1A was capable of productively infecting mice in which the airway was subjected to chemical permeabilization. A mouse model for RV infection will permit studies of RV pathogenesis and may identify targets for therapeutic intervention.
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Affiliation(s)
- Angela L Rasmussen
- Department of Microbiology, University of Washington, Seattle, WA 98114, USA.
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Schmidt KL, Rasmussen AL, Thomsen PH. [Refugee and immigrant children referred to a department of pediatric psychiatry during the years 1991-1994]. Ugeskr Laeger 2000; 162:2318-23. [PMID: 10827561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The purpose of this study was to describe a group of 42 refugee- and immigrant children up to 14 years old compared to Danish controls in order to identify groups at risk and describe course, examination, treatment and contact. The investigation was based on case records. The only statistically significant results were higher frequencies of referral than expected regarding children from Lebanon and Somalia. However, the data indicate differences between the foreign and Danish groups as to greater problems of speech and language and less behavioural and emotional problems among the foreigners. No foreign children were offered foster homes. The attitudes of the parents towards referral, examination and treatment are more negative in the foreign group. The need for more research is emphasized.
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Affiliation(s)
- K L Schmidt
- Arhus Universitetshospital, Børne- og Ungdomspsykiatrisk Hospital
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Abstract
The effect of feed withdrawal or total withdrawal (simultaneous feed and water withdrawal) on the composition and quality of broiler meat was evaluated. Feed or water or both were withdrawn 0, 6, 12, or 18 h before slaughter. A gradual and significant (P less than .05) increase in weight loss was seen as hours of withdrawal increased. Overall, birds subjected to feed withdrawal treatments experienced a 3.8% shrinkage; birds on total withdrawal treatments lost 4.4% in body weight. Percentage of water uptake during chilling increased gradually as feed withdrawal time increased. Birds on total withdrawal absorbed water in this fashion until 18 h of chilling, when there was a sharp and significant drop in water uptake. No significant differences were found among treatments for precook and cooked weights, cooking loss, total loss, proximate analysis, and shear. Withdrawal times for feed or feed and water did not influence the tenderness or flavor of breast or thigh meat.
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Affiliation(s)
- A L Rasmussen
- Department of Food Science, Pennsylvania State University, University Park 16802
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Abstract
Principles and detailed procedures are described for measuring laser energy and power in terms of electrical energy based on voltage, resistance, and frequency standards. The construction of a small isoperibol calorimeter used for the measurements is described. The calorimeter will accommodate 0.01 to 20 J and 4 × 10-5 to 1 W cw and is limited to a maximum pulse intensity of 0.1 J/cm2. The standard deviation of comparison measurements using two calorimeters and a beam splitter is 0.08 percent when the smaller energy input is not less than 0.3 J. The estimated limits of systematic error for one calorimeter are ± 1.0 percent of the laser energy measured by the calorimeter.
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Affiliation(s)
- E D West
- Institute for Basic Standards, National Bureau of Standards, Boulder, Colorado 80302
| | - W E Case
- Institute for Basic Standards, National Bureau of Standards, Boulder, Colorado 80302
| | - A L Rasmussen
- Institute for Basic Standards, National Bureau of Standards, Boulder, Colorado 80302
| | - L B Schmidt
- Institute for Basic Standards, National Bureau of Standards, Boulder, Colorado 80302
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