1
|
Alwine J, Goodrum F, Banfield B, Bloom D, Britt WJ, Broadbent AJ, Campos SK, Casadevall A, Chan GC, Cliffe AR, Dermody T, Duprex P, Enquist LW, Frueh K, Geballe AP, Gaglia M, Goldstein S, Greninger AL, Gronvall GK, Jung JU, Kamil JP, Lakdawala S, Liu SL, Luftig M, Moore JP, Moscona A, Neuman BW, Nikolich JŽ, O'Connor C, Pekosz A, Permar S, Pfeiffer J, Purdy J, Rasmussen A, Semler B, Smith GA, Stein DA, Van Doorslaer K, Weller SK, Whelan SPJ, Yurochko A. The harms of promoting the lab leak hypothesis for SARS-CoV-2 origins without evidence. J Virol 2024:e0124024. [PMID: 39087765 DOI: 10.1128/jvi.01240-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024] Open
Abstract
Science is humanity's best insurance against threats from nature, but it is a fragile enterprise that must be nourished and protected. The preponderance of scientific evidence indicates a natural origin for SARS-CoV-2. Yet, the theory that SARS-CoV-2 was engineered in and escaped from a lab dominates media attention, even in the absence of strong evidence. We discuss how the resulting anti-science movement puts the research community, scientific research, and pandemic preparedness at risk.
Collapse
Affiliation(s)
- James Alwine
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Felicia Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Bruce Banfield
- Department of Biomedical and Molecular Sciences, Queens University, Kingston, Ontario, Canada
| | - David Bloom
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - William J Britt
- Department of Pediatrics, University of Alabama, Birmingham, Birmingham, Alabama, USA
| | - Andrew J Broadbent
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
| | - Samuel K Campos
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Arturo Casadevall
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gary C Chan
- Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Anna R Cliffe
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Terence Dermody
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Paul Duprex
- University of Pittsburgh, Center for Vaccine Research, Pittsburgh, Pennsylvania, USA
| | - Lynn W Enquist
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Klaus Frueh
- Oregon Health and Science University, Vaccine and Gene Therapy Institute, Beaverton, Oregon, USA
| | - Adam P Geballe
- Department of Medicine, University of Washington, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Marta Gaglia
- Department of Medical Microbiology and Immunology, University of Wisconsin, Institute for Molecular Virology, Madison, Wisconsin, USA
| | - Stephen Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Howard Hughes Medical Institute, Salt Lake City, Utah, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Alexander L Greninger
- Department of Medicine, Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Gigi Kwick Gronvall
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jae U Jung
- Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, USA
| | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences, Shreveport, Louisiana, USA
| | - Seema Lakdawala
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Shan-Lu Liu
- The Ohio State University, Center for Retrovirus Research and Infectious Disease Institute, Columbus, Ohio, USA
| | - Micah Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - John P Moore
- Department of Microbiology and Immunology, Cornell University, Weill Cornell Medicine, New York, New York, USA
| | - Anne Moscona
- Columbia University, Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Benjamin W Neuman
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Janko Ž Nikolich
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | | | - Andrew Pekosz
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Sallie Permar
- Department of Pediatrics, Cornell University, Weill Cornell Medicine, New York, New York, USA
| | - Julie Pfeiffer
- University of Texas, Southwestern Medical Center, Dallas, Texas, USA
| | - John Purdy
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Angela Rasmussen
- University of Saskatchewan, College of Medicine, Saskatoon, Canada
| | - Bert Semler
- Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, California, USA
| | - Gregory A Smith
- Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - David A Stein
- Oregon State University, Carlson College of Veterinary Medicine, Corvallis, Oregon, USA
| | | | - Sandra K Weller
- Department of Molecular Biology and Biophysics, University of Connecticut, Farmington, Connecticut, USA
| | - Sean P J Whelan
- Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Andrew Yurochko
- Department of Microbiology and Immunology, Louisiana State University Health Sciences, Shreveport, Louisiana, USA
| |
Collapse
|
2
|
Chen X, Kalyar F, Chughtai AA, MacIntyre CR. Use of a risk assessment tool to determine the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2024; 44:1896-1906. [PMID: 38488186 DOI: 10.1111/risa.14291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/28/2023] [Indexed: 08/07/2024]
Abstract
The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is contentious. Most studies have focused on a zoonotic origin, but definitive evidence such as an intermediary animal host is lacking. We used an established risk analysis tool for differentiating natural and unnatural epidemics, the modified Grunow-Finke assessment tool (mGFT) to study the origin of SARS-COV-2. The mGFT scores 11 criteria to provide a likelihood of natural or unnatural origin. Using published literature and publicly available sources of information, we applied the mGFT to the origin of SARS-CoV-2. The mGFT scored 41/60 points (68%), with high inter-rater reliability (100%), indicating a greater likelihood of an unnatural than natural origin of SARS-CoV-2. This risk assessment cannot prove the origin of SARS-CoV-2 but shows that the possibility of a laboratory origin cannot be easily dismissed.
Collapse
Affiliation(s)
- Xin Chen
- Biosecurity Program, The Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Fatema Kalyar
- Biosecurity Program, The Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Abrar Ahmad Chughtai
- School of Population Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Chandini Raina MacIntyre
- Biosecurity Program, The Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- College of Public Service & Community Solutions, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
3
|
Segala FV, Di Gennaro F, Giannini LAA, Stroffolini G, Colpani A, De Vito A, Di Gregorio S, Frallonardo L, Guido G, Novara R, Amendolara A, Ritacco IA, Ferrante F, Masini L, Iannetti I, Mazzeo S, Marello S, Veronese N, Gobbi F, Iatta R, Saracino A. Perspectives on climate action and the changing burden of infectious diseases among young Italian doctors and students: a national survey. Front Public Health 2024; 12:1382505. [PMID: 39015393 PMCID: PMC11250467 DOI: 10.3389/fpubh.2024.1382505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/18/2024] [Indexed: 07/18/2024] Open
Abstract
Background The eco-climatic crisis has been defined by the World Health Organization as the "single biggest health threat facing humanity," influencing both the emergence of zoonoses and the spread of vector-borne and water-borne diseases. The aim of this survey was to explore knowledge, eco-anxiety and attitudes toward the ecological and climate crisis among young Italian doctors and medical students. Methods A cross-sectional, multicenter survey was conducted from November 2022 to June 2023, by administering an anonymous questionnaire to Italian doctors and students of medicine. Endpoint of the study was a Knowledge, Attitudes and Practices (KAP) score on ecological and climate crisis (0-20 points). Association between variables and KAP score was assessed by Kruskal-Wallis' or Spearman's test, as appropriate, and significant variables were included into ordinal regression model and reported as adjusted odds ratio (aOR) with their 95% confidence intervals (CI). Results Both KAP and eco-anxiety scores showed acceptable levels of consistency with Cronbach's alpha. A total of 605 medical doctors and students living in 19 Italian regions were included in the study. Median age [Q1-Q3] was 27.6 [24.1-31.3] and females were 352 (58.2%). Despite showing good attitudes toward climate action, knowledge gap were found, with 42.5% (n = 257) of the respondents not knowing the temperature limits set by the Paris Agreements and 45.5% (n = 275) believing that climate change is caused by sunspots. Fears suggestive for eco-anxiety were common. At multivariable ordinal regression, high levels of eco-anxiety (aOR 1.29, p = 0.001) and low trust in government action (aOR 1.96, p = 0.003) were associated with a higher KAP score. Only one Italian medical school offered an educational module on climate change. Conclusion Young Italian doctors and medical students are concerned about the climate crisis but show poor knowledge of these topics. The Italian academic system should urgently respond to this need.
Collapse
Affiliation(s)
- Francesco Vladimiro Segala
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
- Doctors4Future, “Chi si Cura di Te?”, Rome, Italy
| | - Francesco Di Gennaro
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | | | - Giacomo Stroffolini
- Doctors4Future, “Chi si Cura di Te?”, Rome, Italy
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital Negrar, Verona, Italy
| | - Agnese Colpani
- Unit of Infectious Diseases, Department of Medicine, Surgery, and Pharmacy, University of Sassari, Sassari, Italy
| | - Andrea De Vito
- Unit of Infectious Diseases, Department of Medicine, Surgery, and Pharmacy, University of Sassari, Sassari, Italy
- PhD School in Biomedical Science, Biomedical Science Department, University of Sassari, Sassari, Italy
| | - Stefano Di Gregorio
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Luisa Frallonardo
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Giacomo Guido
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Roberta Novara
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Angela Amendolara
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Ilenia Annunziata Ritacco
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Francesca Ferrante
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | | | | | | | | | - Nicola Veronese
- Geriatric Unit, Department of Medicine, University of Palermo, Palermo, Italy
| | - Federico Gobbi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital Negrar, Verona, Italy
| | - Roberta Iatta
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| |
Collapse
|
4
|
Yin W, Li L, Yang Y, Yang Y, Liang R, Ma L, Dai J, Mao G, Ma Y. Ultra-Sensitive Detection of the SARS-CoV-2 Nucleocapsid Protein via a Clustered Regularly Interspaced Short Palindromic Repeat/Cas12a-Mediated Immunoassay. ACS Sens 2024; 9:3150-3157. [PMID: 38717584 DOI: 10.1021/acssensors.4c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Tracking trace protein analytes in precision diagnostics is an ongoing challenge. Here, we developed an ultrasensitive detection method for the detection of SARS-CoV-2 nucleocapsid (N) protein by combining enzyme-linked immunosorbent assay (ELISA) with the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) system. First, the SARS-CoV-2 N protein bound by the capture antibody adsorbed on the well plate was sequentially coupled with the primary antibody, biotinylated secondary antibody, and streptavidin (SA), followed by biotin primer binding to SA. Subsequently, rolling circle amplification was initiated to generate ssDNA strands, which were targeted by CRISPR/Cas12a to cleave the FAM-ssDNA-BHQ1 probe in trans to generate fluorescence signals. We observed a linear relationship between fluorescence intensity and the logarithm of N protein concentration ranging from 3 fg/mL to 3 × 107 fg/mL. The limit of detection (LOD) was 1 fg/mL, with approximately nine molecules in 1 μL of the sample. This detection sensitivity was 4 orders magnitude higher than that of commercially available ELISA kits (LOD: 5.7 × 104 fg/mL). This method was highly specific and sensitive and could accurately detect SARS-CoV-2 pseudovirus and clinical samples, providing a new approach for ultrasensitive immunoassay of protein biomarkers.
Collapse
Affiliation(s)
- Wen Yin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Leyao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Yuxin Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ruijing Liang
- Guangdong Key Laboratory of Nanomedicine, CAS-HK Joint Lab of Biomaterials, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Guobin Mao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingxin Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
5
|
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] [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
| |
Collapse
|
6
|
Hu B, Guo H, Si H, Shi Z. Emergence of SARS and COVID-19 and preparedness for the next emerging disease X. Front Med 2024; 18:1-18. [PMID: 38561562 DOI: 10.1007/s11684-024-1066-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 04/04/2024]
Abstract
Severe acute respiratory syndrome (SARS) and Coronavirus disease 2019 (COVID-19) are two human Coronavirus diseases emerging in this century, posing tremendous threats to public health and causing great loss to lives and economy. In this review, we retrospect the studies tracing the molecular evolution of SARS-CoV, and we sort out current research findings about the potential ancestor of SARS-CoV-2. Updated knowledge about SARS-CoV-2-like viruses found in wildlife, the animal susceptibility to SARS-CoV-2, as well as the interspecies transmission risk of SARS-related coronaviruses (SARSr-CoVs) are gathered here. Finally, we discuss the strategies of how to be prepared against future outbreaks of emerging or re-emerging coronaviruses.
Collapse
Affiliation(s)
- Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hua Guo
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haorui Si
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| |
Collapse
|
7
|
Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
Collapse
Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| |
Collapse
|
8
|
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] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US.
Collapse
Affiliation(s)
- Angela L. Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Canada
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Gigi K. Gronvall
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Felicia Goodrum
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - James Alwine
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Simon J. Anthony
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, California, USA
| | - Joel Baines
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Canada
| | - Andrew J. Broadbent
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Samuel K. Campos
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Patrizia Caposio
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gary C. Chan
- Department of Microbiology and Immunology, SUNY Upstate Medical Center, Syracuse, New York, USA
| | - Anna R. Cliffe
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia, USA
| | | | - Nancy Connell
- Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Blossom Damania
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA
| | - Kari Debbink
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Terence S. Dermody
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - W. Paul Duprex
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Michael Emerman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Denise A. Galloway
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Robert F. Garry
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Stephen A. Goldstein
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Amy L. Hartman
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Stacy M. Horner
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Peter J. Hotez
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Jae U. Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jeremy P. Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Stephanie M. Karst
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Lou Laimins
- Department of Microbiology, Ohio State University, Wooster, Ohio, USA
| | - Seema S. Lakdawala
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
| | - Igor Landais
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale University, New Haven, USA
| | - Shan-Lu Liu
- Department of Microbiology, Ohio State University, Wooster, Ohio, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, Ohio State University, Wooster, Ohio, USA
| | - Micah Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Grant McFadden
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Juliet Morrison
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Anne Moscona
- Department of Microbiology and Immunology, Columbia University, New York, New York, USA
- Department of Physiology, Columbia University, New York, New York, USA
- Department of Biophysics, Columbia University, New York, New York, USA
| | - Elke Mühlberger
- Department of Virology, Immunology, and Microbiology, Boston University, Boston, Massachusetts, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York, USA
| | - Karl Münger
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Eain Murphy
- Department of Microbiology and Immunology, SUNY Upstate Medical Center, Syracuse, New York, USA
| | | | - Janko Z. Nikolich
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
- Aegis Consortium for a Pandemic-Free Future, University of Arizona, Tucson, Arizona, USA
| | | | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Sallie R. Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, New York, USA
| | - Julie K. Pfeiffer
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Saskia V. Popescu
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - John G. Purdy
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Vincent R. Racaniello
- Department of Microbiology and Immunology, Columbia University, New York, New York, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, USA
| | - Martin J. Sapp
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Rona S. Scott
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| | - Gregory A. Smith
- Department of Microbiology, Ohio State University, Wooster, Ohio, USA
| | - Erin M. Sorrell
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Emily Speranza
- Florida Research and Innovation Center, Cleveland Clinic Lerner Research Institute, Port St. Lucie, Florida, USA
| | - Daniel Streblow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, USA
| | - Scott A. Tibbetts
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
| | - Zsolt Toth
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | | | - Susan R. Weiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth A. White
- Department of Otorhinolaryngology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Timothy M. White
- Department of Immunobiology, University of Arizona, Tucson, Arizona, USA
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Satoko Yamaoka
- Department of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew Yurochko
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, Louisiana, USA
| |
Collapse
|
9
|
Komesaroff PA, Dwyer DE. The Question of the Origins of COVID-19 and the Ends of Science. JOURNAL OF BIOETHICAL INQUIRY 2023; 20:575-583. [PMID: 37697176 PMCID: PMC10942872 DOI: 10.1007/s11673-023-10303-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/31/2023] [Indexed: 09/13/2023]
Abstract
Intense public interest in scientific claims about COVID-19, concerning its origins, modes of spread, evolution, and preventive and therapeutic strategies, has focused attention on the values to which scientists are assumed to be committed and the relationship between science and other public discourses. A much discussed claim, which has stimulated several inquiries and generated far-reaching political and economic consequences, has been that SARS-CoV-2 was deliberately engineered at the Wuhan Institute of Virology and then, either inadvertently or otherwise, released to the public by a laboratory worker. This has been pursued despite a clear refutation, through comprehensive genomic analysis, of the hypothesis that the virus was deliberately engineered and the failure of detailed investigations to identify any evidence in support of a laboratory leak. At the same time a substantial, established body of knowledge about the many factors underlying the emergence of novel zoonotic diseases has been largely ignored-including climate change and other mechanisms of environmental destruction, tourism, patterns of trade, and cultural influences. The existence and conduct of these debates have raised questions about the vulnerability of science to manipulation for political purposes. Scientific discourses are vulnerable because: (i) claims can be made with no more than probabilistic force; (ii) alleged "facts" are always subject to interpretation, which depends on social, ethical, and epistemological assumptions; and (iii) science and scientists are not inherently committed to any single set of values and historically have served diverse, and sometimes perverse, social and political interests. In the face of this complexity, the COVID-19 experience highlights the need for processes of ethical scrutiny of the scientific enterprise and its strategic deployment. To ensure reliability of truth claims and protection from corrupting influences robust ethical discourses are required that are independent of, and at times even contrary to, those of science itself.
Collapse
Affiliation(s)
- Paul A Komesaroff
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Dominic E Dwyer
- New South Wales Health Pathology-ICPMR Westmead, University of Sydney, Westmead Hospital, Westmead, NSW, 2145, Australia
| |
Collapse
|
10
|
Kononova Y, Adamenko L, Kazachkova E, Solomatina M, Romanenko S, Proskuryakova A, Utkin Y, Gulyaeva M, Spirina A, Kazachinskaia E, Palyanova N, Mishchenko O, Chepurnov A, Shestopalov A. Features of SARS-CoV-2 Replication in Various Types of Reptilian and Fish Cell Cultures. Viruses 2023; 15:2350. [PMID: 38140591 PMCID: PMC10748073 DOI: 10.3390/v15122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND SARS-CoV-2 can enter the environment from the feces of COVID-19 patients and virus carriers through untreated sewage. The virus has shown the ability to adapt to a wide range of hosts, so the question of the possible involvement of aquafauna and animals of coastal ecosystems in maintaining its circulation remains open. METHODS the aim of this work was to study the tropism of SARS-CoV-2 for cells of freshwater fish and reptiles, including those associated with aquatic and coastal ecosystems, and the effect of ambient temperature on this process. In a continuous cell culture FHM (fathead minnow) and diploid fibroblasts CGIB (silver carp), SARS-CoV-2 replication was not maintained at either 25 °C or 29 °C. At 29 °C, the continuous cell culture TH-1 (eastern box turtle) showed high susceptibility to SARS-CoV-2, comparable to Vero E6 (development of virus-induced cytopathic effect (CPE) and an infectious titer of 7.5 ± 0.17 log10 TCID50/mL on day 3 after infection), and primary fibroblasts CNI (Nile crocodile embryo) showed moderate susceptibility (no CPE, infectious titer 4.52 ± 0.14 log10 TCID50/mL on day 5 after infection). At 25 °C, SARS-CoV-2 infection did not develop in TH-1 and CNI. CONCLUSIONS our results show the ability of SARS-CoV-2 to effectively replicate without adaptation in the cells of certain reptile species when the ambient temperature rises.
Collapse
Affiliation(s)
- Yulia Kononova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Lyubov Adamenko
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Evgeniya Kazachkova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Mariya Solomatina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Anastasia Proskuryakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Yaroslav Utkin
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; (S.R.); (A.P.); (Y.U.)
| | - Marina Gulyaeva
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
- The Department of Natural Science, Novosibirsk State University, 2, Pirogova St., Novosibirsk 630090, Russia
| | - Anastasia Spirina
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Elena Kazachinskaia
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Natalia Palyanova
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Oksana Mishchenko
- 48 Central Research Institute of the Ministry of Defense of the Russian Federation, Moscow 141306, Russia;
| | - Alexander Chepurnov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, The Federal State Budget Scientific Institution, Siberian Branch of the Russian Academy of Sciences, 2, Timakova St., Novosibirsk 630117, Russia; (Y.K.); (L.A.); (E.K.); (M.S.); (A.S.); (E.K.); (N.P.); (A.C.); (A.S.)
| |
Collapse
|
11
|
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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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.
Collapse
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
| |
Collapse
|
12
|
Bloom JD. Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market. Virus Evol 2023; 9:vead050. [PMID: 39129757 PMCID: PMC11314060 DOI: 10.1093/ve/vead050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/02/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2024] Open
Abstract
The role of the Huanan Seafood Market in the early severe acute respiratory syndrome virus 2 (SARS-CoV-2) outbreak remains unclear. Recently, the Chinese Centers for Disease Control (CDC) released data from deep sequencing of environmental samples collected from the market after it was closed on 1 January 2020. Prior to this release, Crits-Christoph et al. analyzed data from a subset of the samples. Both that study and the Chinese CDC study concurred that the samples contained genetic material from a variety of species, including some like raccoon dogs that are susceptible to SARS-CoV-2. However, neither study systematically analyzed the relationship between the amount of genetic material from SARS-CoV-2 and different animal species. Here I implement a fully reproducible computational pipeline that jointly analyzes the number of reads mapping to SARS-CoV-2 and the mitochondrial genomes of chordate species across the full set of samples. I validate the presence of genetic material from numerous species and calculate mammalian mitochondrial compositions similar to those reported by Crits-Christoph et al. However, the SARS-CoV-2 content of the environmental samples is generally very low: only 21 of 176 samples contain more than ten SARS-CoV-2 reads, despite most samples being sequenced to depths exceeding 108 total reads. None of the samples with double-digit numbers of SARS-CoV-2 reads have a substantial fraction of their mitochondrial material from any non-human susceptible species. Only one of the fourteen samples with at least a fifth of the chordate mitochondrial material from raccoon dogs contains any SARS-CoV-2 reads, and that sample only has 1 of ~200,000,000 reads mapping to SARS-CoV-2. Instead, SARS-CoV-2 reads are most correlated with reads mapping to various fish, such as catfish and largemouth bass. These results suggest that while metagenomic analysis of the environmental samples is useful for identifying animals or animal products sold at the market, co-mingling of animal and viral genetic material is unlikely to reliably indicate whether any animals were infected by SARS-CoV-2.
Collapse
Affiliation(s)
- Jesse D Bloom
- Fred Hutchinson Cancer Center, Howard Hughes
Medical Institute, 1100 Fairview Ave N, Seattle, Washington 98109,
USA
| |
Collapse
|
13
|
Looi MK. Did covid-19 come from a lab leak in China? BMJ 2023; 382:p1556. [PMID: 37429612 DOI: 10.1136/bmj.p1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
|