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Lewis SC, Jourdain AA, Schulman BA, Vousden KH, Fabius JM, Liu H. Recovering from the stress of the COVID-19 pandemic. Mol Cell 2024; 84:8-11. [PMID: 38181764 DOI: 10.1016/j.molcel.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
For our special issue on stress, we asked scientists about recovering from the stress of the pandemic, including some who shared insights with us in mid-2020. They discuss the importance of teamwork, reassessing priorities, and the added stresses of the cost-of-living crisis, funding cuts, and retaining scientists in academia.
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Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell 2023; 186:4597-4614.e26. [PMID: 37738970 PMCID: PMC10604369 DOI: 10.1016/j.cell.2023.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/22/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately converged to suppress interferon-stimulated genes (ISGs), Omicron BA.1 did not. ISG suppression correlated with the expression of viral innate immune antagonist proteins, including Orf6, N, and Orf9b, which we mapped to specific mutations. Later Omicron subvariants BA.4 and BA.5 more potently suppressed innate immunity than early subvariant BA.1, which correlated with Orf6 levels, although muted in BA.4 by a mutation that disrupts the Orf6-nuclear pore interaction. Our findings suggest that SARS-CoV-2 convergent evolution overcame human adaptive and innate immune barriers, laying the groundwork to tackle future pandemics.
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Affiliation(s)
- Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ann-Kathrin Reuschl
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Lucy G Thorne
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Manisha R Ummadi
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Chengjin Ye
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Romel Rosales
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Gwendolyn M Jang
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Bhavya Harjai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Abdullah M Syed
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noa Deutsch
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Pirak
- School of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Giulia Dowgier
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Briana L McGovern
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rocio Leiva-Rebollo
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alistair S Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden, UK
| | - Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nicholas F Liotta
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA
| | - Thomas Kehrer
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Rutkowska
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ignacio Mena
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sadaf Aslam
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alyssa Hoffert
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Charles Ochieng' Olwal
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Weiqing Huang
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Pham
- Synthego Corporation, Redwood City, CA, USA
| | | | | | | | | | | | | | | | | | | | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ignacia Echeverria
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Kliment Verba
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zurich, Switzerland
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Jennifer A Doudna
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Luis Martinez-Sobrido
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lisa Miorin
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris White
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo Garcia-Sastre
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Clare Jolly
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
| | - Greg J Towers
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
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Kehrer T, Cupic A, Ye C, Yildiz S, Bouhaddou M, Crossland NA, Barrall EA, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena I, Aslam S, Saqi A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Ak B, Marin A, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. Cell Host Microbe 2023; 31:1668-1684.e12. [PMID: 37738983 PMCID: PMC10750313 DOI: 10.1016/j.chom.2023.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 01/10/2023] [Revised: 07/01/2023] [Accepted: 08/07/2023] [Indexed: 09/24/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes several proteins that inhibit host interferon responses. Among these, ORF6 antagonizes interferon signaling by disrupting nucleocytoplasmic trafficking through interactions with the nuclear pore complex components Nup98-Rae1. However, the roles and contributions of ORF6 during physiological infection remain unexplored. We assessed the role of ORF6 during infection using recombinant viruses carrying a deletion or loss-of-function (LoF) mutation in ORF6. ORF6 plays key roles in interferon antagonism and viral pathogenesis by interfering with nuclear import and specifically the translocation of IRF and STAT transcription factors. Additionally, ORF6 inhibits cellular mRNA export, resulting in the remodeling of the host cell proteome, and regulates viral protein expression. Interestingly, the ORF6:D61L mutation that emerged in the Omicron BA.2 and BA.4 variants exhibits reduced interactions with Nup98-Rae1 and consequently impairs immune evasion. Our findings highlight the role of ORF6 in antagonizing innate immunity and emphasize the importance of studying the immune evasion strategies of SARS-CoV-2.
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Affiliation(s)
- Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anastasija Cupic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA 90024, USA; Institute for Quantitative and Computational Biosciences (OCBio), University of California, Los Angeles, Los Angeles, CA 90024, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Nicholas A Crossland
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02215, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Erika A Barrall
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Phillip Cohen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Tseng
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02215, USA; Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Tolga Çağatay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Flores
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Fahmida Alam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ignacio Mena
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sadaf Aslam
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Magdalena Rutkowska
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manisha R Ummadi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Giuseppe Pisanelli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Veterinary Medicine and Animal Production, University of Naples Federico II, 80137 Naples, Italy
| | - R Blake Richardson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ethan C Veit
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Baran Ak
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arturo Marin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew J Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Harm van Bakel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lorena Zuliani-Alvarez
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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4
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Olwal CO, Fabius JM, Zuliani-Alvarez L, Eckhardt M, Kyei GB, Quashie PK, Krogan NJ, Bouhaddou M, Bediako Y. Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer. Mol Omics 2023; 19:538-551. [PMID: 37204043 PMCID: PMC10524288 DOI: 10.1039/d3mo00025g] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Women coinfected with human immunodeficiency virus type 1 (HIV-1) and human papillomavirus (HPV) are six times as likely to develop invasive cervical carcinoma compared to those without HIV. Unlike other HIV-associated cancers, the risk of cervical cancer development does not change when HPV/HIV coinfected women begin antiretroviral therapy, suggesting HIV-associated immune suppression is not a key driver of cervical cancer development in coinfected women. Here, we investigated whether the persistent secretion of inflammatory factors in HIV-positive patients on antiretroviral therapy could enhance cancer signaling in HPV-infected cervical cells via endocrine mechanisms. We integrated previously reported HIV-induced secreted inflammatory factors (Hi-SIFs), HIV and HPV virus-human protein interactions, and cervical cancer patient genomic data using network propagation to understand the pathways underlying disease development in HPV/HIV coinfection. Our results pinpointed the PI3K-AKT signaling pathway to be enriched at the interface between Hi-SIFs and HPV-host molecular networks, in alignment with PI3K pathway mutations being prominent drivers of HPV-associated, but HIV independent, cervical cancer development. Furthermore, we experimentally stimulated cervical cells with 14 Hi-SIFs to assess their ability to activate PI3K-AKT signaling. Strikingly, we found 8 factors (CD14, CXCL11, CXCL9, CXCL13, CXCL17, AHSG, CCL18, and MMP-1) to significantly upregulate AKT phosphorylation (pAKT-S473) relative to a phosphate buffered saline control. Our findings suggest that Hi-SIFs cooperate with HPV infection in cervical cells to over-activate PI3K-AKT signaling, effectively phenocopying PI3K-AKT pathway mutations, resulting in enhanced cervical cancer development in coinfected women. Our insights could support the design of therapeutic interventions targeting the PI3K-AKT pathway or neutralizing Hi-SIFs in HPV/HIV coinfected cervical cancer patients.
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Affiliation(s)
- Charles Ochieng' Olwal
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Jacqueline M Fabius
- The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Lorena Zuliani-Alvarez
- The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Manon Eckhardt
- The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - George Boateng Kyei
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- University of Ghana Medical Centre, University of Ghana, Accra, Ghana
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
| | - Nevan J Krogan
- The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
- The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
- Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, LA, USA
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, LA, USA.
- Molecular Biology Institute, University of California, Los Angeles, LA, USA
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.
- Yemaachi Biotech, Accra, Ghana
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5
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Fabius JM, Krogan NJ. Lessons learned for pandemic preparedness: A collaborative network is imperative. Cell Host Microbe 2023; 31:843-846. [PMID: 37321167 PMCID: PMC10265763 DOI: 10.1016/j.chom.2023.05.008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023]
Abstract
The scientific community improvised to respond quickly to the SARS-CoV-2 pandemic without a template on how to work together on a global scale to understand and combat the virus. Here, we describe how we tackled impediments to success and the valuable lessons learned that prepare us for a future pandemic.
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Affiliation(s)
- Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA; QBI COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA; QBI COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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6
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Perier C, Nasinghe E, Charles I, Ssetaba LJ, Ahyong V, Bangs D, Beatty PR, Czudnochowski N, Diallo A, Dugan E, Fabius JM, Fong Baker H, Gardner J, Isaacs S, Joanah B, Kalantar K, Kateete D, Knight M, Krasilnikov M, Krogan NJ, Langelier C, Lee E, Li LM, Licht D, Lien K, Lyons Z, Mboowa G, Mwebaza I, Mwesigwa S, Nalwadda G, Nichols R, Penaranda ME, Petnic S, Phelps M, Popper SJ, Rape M, Reingold A, Robbins R, Rosenberg OS, Savage DF, Schildhauer S, Settles ML, Sserwadda I, Stanley S, Tato CM, Tsitsiklis A, Van Dis E, Vanaerschot M, Vinden J, Cox JS, Joloba ML, Schaletzky J. Workshop-based learning and networking: a scalable model for research capacity strengthening in low- and middle-income countries. Glob Health Action 2022; 15:2062175. [PMID: 35730550 PMCID: PMC9225690 DOI: 10.1080/16549716.2022.2062175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Science education and research have the potential to drive profound change in low- and middle-income countries (LMICs) through encouraging innovation, attracting industry, and creating job opportunities. However, in LMICs, research capacity is often limited, and acquisition of funding and access to state-of-the-art technologies is challenging. The Alliance for Global Health and Science (the Alliance) was founded as a partnership between the University of California, Berkeley (USA) and Makerere University (Uganda), with the goal of strengthening Makerere University’s capacity for bioscience research. The flagship program of the Alliance partnership is the MU/UCB Biosciences Training Program, an in-country, hands-on workshop model that trains a large number of students from Makerere University in infectious disease and molecular biology research. This approach nucleates training of larger and more diverse groups of students, development of mentoring and bi-directional research partnerships, and support of the local economy. Here, we describe the project, its conception, implementation, challenges, and outcomes of bioscience research workshops. We aim to provide a blueprint for workshop implementation, and create a valuable resource for bioscience research capacity strengthening in LMICs.
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Affiliation(s)
- Celine Perier
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Isabelle Charles
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Derek Bangs
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - P Robert Beatty
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Amy Diallo
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Eli Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Hildy Fong Baker
- School of Public Health, Center for Global Public Health (CGPH), University of California, Berkeley, CA, USA
| | - Jackson Gardner
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Birungi Joanah
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | - David Kateete
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Matt Knight
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Maria Krasilnikov
- Department of Molecular Biology and Microbiology, Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA.,Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | | | - Eric Lee
- Graduate Group in Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Lucy M Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Daniel Licht
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Katie Lien
- Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Zilose Lyons
- California China Climate Institute, University of California, Berkeley, CA, USA
| | - Gerald Mboowa
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Ivan Mwebaza
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | | | | | - Robert Nichols
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Sarah Petnic
- Quality and Clinical Excellence Department, Providence Queen of the Valley Medical Center, Napa, CA, USA
| | | | - Stephen J Popper
- Sustainable Sciences Institute, San Francisco, CA, USA.,School of Public Health, Department of Infectious Disease and Vaccinology, University of California, Berkeley, CA, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Arthur Reingold
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | | | - Oren S Rosenberg
- Department of Medicine, University of California, San Francisco, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | | | - Ivan Sserwadda
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Sarah Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | | | | | - Erik Van Dis
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Joanna Vinden
- Division of Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, CA, USA
| | - Jeffery S Cox
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Moses L Joloba
- School of Biomedical Sciences, Makerere University, Kampala, Uganda
| | - Julia Schaletzky
- H. Wheeler Center for Emerging & Neglected Diseases (CEND), University of California, Berkeley, CA, USA
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7
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Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. bioRxiv 2022:2022.10.18.512708. [PMID: 36299428 DOI: 10.1101/2022.12.07.519389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
UNLABELLED We and others have previously shown that the SARS-CoV-2 accessory protein ORF6 is a powerful antagonist of the interferon (IFN) signaling pathway by directly interacting with Nup98-Rae1 at the nuclear pore complex (NPC) and disrupting bidirectional nucleo-cytoplasmic trafficking. In this study, we further assessed the role of ORF6 during infection using recombinant SARS-CoV-2 viruses carrying either a deletion or a well characterized M58R loss-of-function mutation in ORF6. We show that ORF6 plays a key role in the antagonism of IFN signaling and in viral pathogenesis by interfering with karyopherin(importin)-mediated nuclear import during SARS-CoV-2 infection both in vitro , and in the Syrian golden hamster model in vivo . In addition, we found that ORF6-Nup98 interaction also contributes to inhibition of cellular mRNA export during SARS-CoV-2 infection. As a result, ORF6 expression significantly remodels the host cell proteome upon infection. Importantly, we also unravel a previously unrecognized function of ORF6 in the modulation of viral protein expression, which is independent of its function at the nuclear pore. Lastly, we characterized the ORF6 D61L mutation that recently emerged in Omicron BA.2 and BA.4 and demonstrated that it is able to disrupt ORF6 protein functions at the NPC and to impair SARS-CoV-2 innate immune evasion strategies. Importantly, the now more abundant Omicron BA.5 lacks this loss-of-function polymorphism in ORF6. Altogether, our findings not only further highlight the key role of ORF6 in the antagonism of the antiviral innate immune response, but also emphasize the importance of studying the role of non-spike mutations to better understand the mechanisms governing differential pathogenicity and immune evasion strategies of SARS-CoV-2 and its evolving variants. ONE SENTENCE SUMMARY SARS-CoV-2 ORF6 subverts bidirectional nucleo-cytoplasmic trafficking to inhibit host gene expression and contribute to viral pathogenesis.
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8
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Kehrer T, Cupic A, Ye C, Yildiz S, Bouhhadou M, Crossland NA, Barrall E, Cohen P, Tseng A, Çağatay T, Rathnasinghe R, Flores D, Jangra S, Alam F, Mena N, Aslam S, Saqi A, Marin A, Rutkowska M, Ummadi MR, Pisanelli G, Richardson RB, Veit EC, Fabius JM, Soucheray M, Polacco BJ, Evans MJ, Swaney DL, Gonzalez-Reiche AS, Sordillo EM, van Bakel H, Simon V, Zuliani-Alvarez L, Fontoura BMA, Rosenberg BR, Krogan NJ, Martinez-Sobrido L, García-Sastre A, Miorin L. Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis. bioRxiv 2022:2022.10.18.512708. [PMID: 36299428 PMCID: PMC9603824 DOI: 10.1101/2022.10.18.512708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We and others have previously shown that the SARS-CoV-2 accessory protein ORF6 is a powerful antagonist of the interferon (IFN) signaling pathway by directly interacting with Nup98-Rae1 at the nuclear pore complex (NPC) and disrupting bidirectional nucleo-cytoplasmic trafficking. In this study, we further assessed the role of ORF6 during infection using recombinant SARS-CoV-2 viruses carrying either a deletion or a well characterized M58R loss-of-function mutation in ORF6. We show that ORF6 plays a key role in the antagonism of IFN signaling and in viral pathogenesis by interfering with karyopherin(importin)-mediated nuclear import during SARS-CoV-2 infection both in vitro , and in the Syrian golden hamster model in vivo . In addition, we found that ORF6-Nup98 interaction also contributes to inhibition of cellular mRNA export during SARS-CoV-2 infection. As a result, ORF6 expression significantly remodels the host cell proteome upon infection. Importantly, we also unravel a previously unrecognized function of ORF6 in the modulation of viral protein expression, which is independent of its function at the nuclear pore. Lastly, we characterized the ORF6 D61L mutation that recently emerged in Omicron BA.2 and BA.4 and demonstrated that it is able to disrupt ORF6 protein functions at the NPC and to impair SARS-CoV-2 innate immune evasion strategies. Importantly, the now more abundant Omicron BA.5 lacks this loss-of-function polymorphism in ORF6. Altogether, our findings not only further highlight the key role of ORF6 in the antagonism of the antiviral innate immune response, but also emphasize the importance of studying the role of non-spike mutations to better understand the mechanisms governing differential pathogenicity and immune evasion strategies of SARS-CoV-2 and its evolving variants. ONE SENTENCE SUMMARY SARS-CoV-2 ORF6 subverts bidirectional nucleo-cytoplasmic trafficking to inhibit host gene expression and contribute to viral pathogenesis.
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9
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Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. Publisher Correction: Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature 2022; 604:E14. [PMID: 35332335 PMCID: PMC8944406 DOI: 10.1038/s41586-022-04653-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - Mehdi Bouhaddou
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | | | - Lorena Zuliani-Alvarez
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ben Polacco
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adrian Pelin
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Andrea Fossati
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manisha Ummadi
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ajda Rojc
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jane Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Marie L Bischof
- Division of Infection and Immunity, University College London, London, UK
| | - Kirsten Obernier
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Richards
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kuei-Ho Chen
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bhavya Harjai
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Joseph Hiatt
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aminu Jahun
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Jacqueline M Fabius
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Yasu Takeuchi
- Division of Infection and Immunity, University College London, London, UK
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Kevan Shokat
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Natalia Jura
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Division of Advanced Therapies, National Institute for Biological Standards and Control, South Mimms, UK.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Klim Verba
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle L Swaney
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, UK.
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,J. David Gladstone Institutes, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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10
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Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MVX, Hosmillo M, Fossati A, Ragazzini R, Jungreis I, Ummadi M, Rojc A, Turner J, Bischof ML, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hiatt J, Rosales R, McGovern BL, Jahun A, Fabius JM, White K, Goodfellow IG, Takeuchi Y, Bonfanti P, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Kellis M, Swaney DL, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature 2022; 602:487-495. [PMID: 34942634 PMCID: PMC8850198 DOI: 10.1038/s41586-021-04352-y] [Citation(s) in RCA: 175] [Impact Index Per Article: 87.5] [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: 05/31/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
The emergence of SARS-CoV-2 variants of concern suggests viral adaptation to enhance human-to-human transmission1,2. Although much effort has focused on the characterization of changes in the spike protein in variants of concern, mutations outside of spike are likely to contribute to adaptation. Here, using unbiased abundance proteomics, phosphoproteomics, RNA sequencing and viral replication assays, we show that isolates of the Alpha (B.1.1.7) variant3 suppress innate immune responses in airway epithelial cells more effectively than first-wave isolates. We found that the Alpha variant has markedly increased subgenomic RNA and protein levels of the nucleocapsid protein (N), Orf9b and Orf6-all known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein that is required for activation of the RNA-sensing adaptor MAVS. Moreover, the activity of Orf9b and its association with TOM70 was regulated by phosphorylation. We propose that more effective innate immune suppression, through enhanced expression of specific viral antagonist proteins, increases the likelihood of successful transmission of the Alpha variant, and may increase in vivo replication and duration of infection4. The importance of mutations outside the spike coding region in the adaptation of SARS-CoV-2 to humans is underscored by the observation that similar mutations exist in the N and Orf9b regulatory regions of the Delta and Omicron variants.
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Affiliation(s)
- Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - Mehdi Bouhaddou
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | | | - Lorena Zuliani-Alvarez
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ben Polacco
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adrian Pelin
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Andrea Fossati
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manisha Ummadi
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Ajda Rojc
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jane Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Marie L Bischof
- Division of Infection and Immunity, University College London, London, UK
| | - Kirsten Obernier
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Richards
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kuei-Ho Chen
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bhavya Harjai
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Joseph Hiatt
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Briana L McGovern
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aminu Jahun
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Jacqueline M Fabius
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Yasu Takeuchi
- Division of Infection and Immunity, University College London, London, UK
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Kevan Shokat
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Natalia Jura
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Division of Advanced Therapies, National Institute for Biological Standards and Control, South Mimms, UK
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Klim Verba
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Danielle L Swaney
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, UK.
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
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11
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Thorne LG, Bouhaddou M, Reuschl AK, Zuliani-Alvarez L, Polacco B, Pelin A, Batra J, Whelan MV, Ummadi M, Rojc A, Turner J, Obernier K, Braberg H, Soucheray M, Richards A, Chen KH, Harjai B, Memon D, Hosmillo M, Hiatt J, Jahun A, Goodfellow IG, Fabius JM, Shokat K, Jura N, Verba K, Noursadeghi M, Beltrao P, Swaney DL, Garcia-Sastre A, Jolly C, Towers GJ, Krogan NJ. Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant. bioRxiv 2021:2021.06.06.446826. [PMID: 34127972 PMCID: PMC8202424 DOI: 10.1101/2021.06.06.446826] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Emergence of SARS-CoV-2 variants, including the globally successful B.1.1.7 lineage, suggests viral adaptations to host selective pressures resulting in more efficient transmission. Although much effort has focused on Spike adaptation for viral entry and adaptive immune escape, B.1.1.7 mutations outside Spike likely contribute to enhance transmission. Here we used unbiased abundance proteomics, phosphoproteomics, mRNA sequencing and viral replication assays to show that B.1.1.7 isolates more effectively suppress host innate immune responses in airway epithelial cells. We found that B.1.1.7 isolates have dramatically increased subgenomic RNA and protein levels of Orf9b and Orf6, both known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein required for RNA sensing adaptor MAVS activation, and Orf9b binding and activity was regulated via phosphorylation. We conclude that B.1.1.7 has evolved beyond the Spike coding region to more effectively antagonise host innate immune responses through upregulation of specific subgenomic RNA synthesis and increased protein expression of key innate immune antagonists. We propose that more effective innate immune antagonism increases the likelihood of successful B.1.1.7 transmission, and may increase in vivo replication and duration of infection.
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Affiliation(s)
- Lucy G Thorne
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ann-Kathrin Reuschl
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ben Polacco
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew V.X. Whelan
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Manisha Ummadi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jane Turner
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hannes Braberg
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alicia Richards
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kuei-Ho Chen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bhavya Harjai
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Joseph Hiatt
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Aminu Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Ian G. Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Jacqueline M. Fabius
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevan Shokat
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Natalia Jura
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA 94158, U.S.A
| | - Klim Verba
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Pedro Beltrao
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Danielle L. Swaney
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adolfo Garcia-Sastre
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Greg J. Towers
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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12
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Abstract
The scientific world rewards the individual while often discouraging collaboration. However, times of crisis show us how much more we can accomplish when we work together. Here, we describe our approach to breaking down silos and fostering global collaborations and share the lessons we have learned, especially pertaining to research on SARS-CoV-2.
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Affiliation(s)
- Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA; QBI COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA; QBI COVID-19 Research Group (QCRG), University of California, San Francisco, San Francisco, CA 94158, USA; School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, USA; David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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13
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White KM, Rosales R, Yildiz S, Kehrer T, Miorin L, Moreno E, Jangra S, Uccellini MB, Rathnasinghe R, Coughlan L, Martinez-Romero C, Batra J, Rojc A, Bouhaddou M, Fabius JM, Obernier K, Dejosez M, Guillén MJ, Losada A, Avilés P, Schotsaert M, Zwaka T, Vignuzzi M, Shokat KM, Krogan NJ, García-Sastre A. Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science 2021; 371:926-931. [PMID: 33495306 PMCID: PMC7963220 DOI: 10.1126/science.abf4058] [Citation(s) in RCA: 191] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins interact with the eukaryotic translation machinery, and inhibitors of translation have potent antiviral effects. We found that the drug plitidepsin (aplidin), which has limited clinical approval, possesses antiviral activity (90% inhibitory concentration = 0.88 nM) that is more potent than remdesivir against SARS-CoV-2 in vitro by a factor of 27.5, with limited toxicity in cell culture. Through the use of a drug-resistant mutant, we show that the antiviral activity of plitidepsin against SARS-CoV-2 is mediated through inhibition of the known target eEF1A (eukaryotic translation elongation factor 1A). We demonstrate the in vivo efficacy of plitidepsin treatment in two mouse models of SARS-CoV-2 infection with a reduction of viral replication in the lungs by two orders of magnitude using prophylactic treatment. Our results indicate that plitidepsin is a promising therapeutic candidate for COVID-19.
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Affiliation(s)
- Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Soner Yildiz
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sonia Jangra
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa B Uccellini
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raveen Rathnasinghe
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lynda Coughlan
- Department of Microbiology and Immunology and Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carles Martinez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Marion Dejosez
- Huffington Foundation Center for Cell-Based Research in Parkinson's Disease, Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - María José Guillén
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Alejandro Losada
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Pablo Avilés
- Research and Development Department, PharmaMar, 28770 Colmenar Viejo, Madrid, Spain
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Foundation Center for Cell-Based Research in Parkinson's Disease, Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris Cedex 15, France
| | - Kevan M Shokat
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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14
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Reuschl AK, Thorne LG, Zuliani-Alvarez L, Bouhaddou M, Obernier K, Hiatt J, Soucheray M, Turner J, Fabius JM, Nguyen GT, Swaney DL, Rosales R, White KM, Avilés P, Kirby IT, Melnyk JE, Shi Y, Zhang Z, Shokat KM, García-Sastre A, Jolly C, Towers GJ, Krogan NJ. Host-directed therapies against early-lineage SARS-CoV-2 retain efficacy against B.1.1.7 variant. bioRxiv 2021:2021.01.24.427991. [PMID: 33501437 PMCID: PMC7836107 DOI: 10.1101/2021.01.24.427991] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths worldwide and massive societal and economic burden. Recently, a new variant of SARS-CoV-2, known as B.1.1.7, was first detected in the United Kingdom and is spreading in several other countries, heightening public health concern and raising questions as to the resulting effectiveness of vaccines and therapeutic interventions. We and others previously identified host-directed therapies with antiviral efficacy against SARS-CoV-2 infection. Less prone to the development of therapy resistance, host-directed drugs represent promising therapeutic options to combat emerging viral variants as host genes possess a lower propensity to mutate compared to viral genes. Here, in the first study of the full-length B.1.1.7 variant virus , we find two host-directed drugs, plitidepsin (aplidin; inhibits translation elongation factor eEF1A) and ralimetinib (inhibits p38 MAP kinase cascade), as well as remdesivir, to possess similar antiviral activity against both the early-lineage SARS-CoV-2 and the B.1.1.7 variant, evaluated in both human gastrointestinal and lung epithelial cell lines. We find that plitidepsin is over an order of magnitude more potent than remdesivir against both viruses. These results highlight the importance of continued development of host-directed therapeutics to combat current and future coronavirus variant outbreaks.
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Affiliation(s)
- Ann-Kathrin Reuschl
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Lucy G. Thorne
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco,CA 94143, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jane Turner
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Jacqueline M. Fabius
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Gina T. Nguyen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
| | - Danielle L. Swaney
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pablo Avilés
- PharmaMar, Research and Development Department, 28770 Colmenar Viejo, Madrid, Spain
| | - Ilsa T. Kirby
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - James E. Melnyk
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Ying Shi
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Ziyang Zhang
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Kevan M. Shokat
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Clare Jolly
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Gregory J. Towers
- Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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15
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Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science 2020; 370:eabe9403. [PMID: 33060197 PMCID: PMC7808408 DOI: 10.1126/science.abe9403] [Citation(s) in RCA: 427] [Impact Index Per Article: 106.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/12/2020] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a grave threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and Middle East respiratory syndrome coronavirus (MERS-CoV). Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analyses for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 ORF9b, an interaction we structurally characterized using cryo-electron microscopy. Combining genetically validated host factors with both COVID-19 patient genetic data and medical billing records identified molecular mechanisms and potential drug treatments that merit further molecular and clinical study.
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Affiliation(s)
- David E Gordon
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France
| | - Svenja Ulferts
- Institute for Clinical and Experimental Pharmacology and Toxicology I, University of Freiburg, 79104 Freiburg, Germany
| | - Hannes Braberg
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Alexander S Jureka
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jeffrey Z Guo
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Robyn M Kaake
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Tristan W Owens
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Meghna Gupta
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Sergei Pourmal
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Erron W Titus
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Merve Cakir
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Michael McGregor
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zeynep Cakir
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Gwendolyn Jang
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tia A Tummino
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Ziyang Zhang
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Dmitry Kuchenov
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
| | - Manisha Ummadi
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Beril Tutuncuoglu
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Maya Modak
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Paige Haas
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kelsey M Haas
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Zun Zar Chi Naing
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ernst H Pulido
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ying Shi
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Danish Memon
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Eirini Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alistair Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Miguel Correa Marrero
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - David Burke
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France
| | - Jesus A Silvas
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA
| | - Caleigh M Azumaya
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Christian Billesbølle
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Axel F Brilot
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Melody G Campbell
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Amy Diallo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Miles Sasha Dickinson
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Devan Diwanji
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Nadia Herrera
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Nick Hoppe
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Huong T Kratochvil
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yanxin Liu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Gregory E Merz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Michelle Moritz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Henry C Nguyen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Carlos Nowotny
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Cristina Puchades
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Alexandrea N Rizo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Amber M Smith
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ming Sun
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Beam Therapeutics, Cambridge, MA 02139, USA
| | - Iris D Young
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jianhua Zhao
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Daniel Asarnow
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Justin Biel
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Alisa Bowen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Julian R Braxton
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jen Chen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Cynthia M Chio
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Un Seng Chio
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Ishan Deshpande
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Loan Doan
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Bryan Faust
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Sebastian Flores
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Mingliang Jin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kate Kim
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Victor L Lam
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fei Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Junrui Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yen-Li Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Li
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Xi Liu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Megan Lo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kyle E Lopez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Arthur A Melo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Frank R Moss
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Phuong Nguyen
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Joana Paulino
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Komal Ishwar Pawar
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Jessica K Peters
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Thomas H Pospiech
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Maliheh Safari
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Smriti Sangwan
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaitlin Schaefer
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Paul V Thomas
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Aye C Thwin
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Raphael Trenker
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Eric Tse
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Tsz Kin Martin Tsui
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Feng Wang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Natalie Whitis
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Zanlin Yu
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Kaihua Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Yang Zhang
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Fengbo Zhou
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
| | - Daniel Saltzberg
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Anthony J Hodder
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Amber S Shun-Shion
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Daniel M Williams
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Romel Rosales
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas Kehrer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Suzannah Rihn
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Mir M Khalid
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Parinaz Fozouni
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Camille R Simoneau
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Theodore L Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - David Wu
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Mohd Anisul Karim
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Maya Ghoussaini
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Francesco Berardi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari 'ALDO MORO', Via Orabona, 4 70125, Bari, Italy
| | - Sebastian Weigang
- Institute of Virology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | - Maxime Chazal
- Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Jisoo Park
- Department of Medicine, University of California, San Diego, CA 92093, USA
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robert Haupt
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Matthew Elliott
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Fiona Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Kerry A Burness
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Elaine Reid
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Mark Dorward
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Stuart G Wilkinson
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Anna Geyer
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Daniel M Giesel
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Carla Baillie
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Samantha Raggett
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Hannah Leech
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola Goodman
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Abigail L Lind
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Kafi R Hemphill
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | | | - Jennifer Oki
- Synthego Corporation, Redwood City, CA 94063, USA
| | - Kevin Holden
- Synthego Corporation, Redwood City, CA 94063, USA
| | | | - Katherine S Pollard
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Andrej Sali
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - David A Agard
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yifan Cheng
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - James S Fraser
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Adam Frost
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Natalia Jura
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Tanja Kortemme
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
- The University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA 94158, USA
| | - Aashish Manglik
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Daniel R Southworth
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Robert M Stroud
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Paul Davies
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Matthew B Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, CA 92093, USA
- Department to Bioengineering, University of California, San Diego, CA 92093, USA
| | - Carmen Abate
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari 'ALDO MORO', Via Orabona, 4 70125, Bari, Italy
| | - Nolwenn Jouvenet
- Institute of Virology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
- Département de Virologie, CNRS UMR 3569, Institut Pasteur, Paris 75015, France
| | - Georg Kochs
- Institute of Virology, Medical Center-University of Freiburg, 79104 Freiburg, Germany
| | - Brian Shoichet
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, Scotland, UK
| | - Kevan M Shokat
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert Grosse
- Institute for Clinical and Experimental Pharmacology and Toxicology I, University of Freiburg, 79104 Freiburg, Germany.
- Centre for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Oren S Rosenberg
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Kliment A Verba
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.
- QBI, University of California, San Francisco, CA 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA 30303, USA.
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724, Paris, cedex 15, France.
| | - Andrew A Peden
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA.
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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16
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Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, Hüttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, Félix E, Shi Y, Goff M, Lim JK, McBride T, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, García-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ. The Global Phosphorylation Landscape of SARS-CoV-2 Infection. Cell 2020; 182:685-712.e19. [PMID: 32645325 PMCID: PMC7321036 DOI: 10.1016/j.cell.2020.06.034] [Citation(s) in RCA: 665] [Impact Index Per Article: 166.3] [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: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
Abstract
The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected millions and killed hundreds of thousands of people worldwide, highlighting an urgent need to develop antiviral therapies. Here we present a quantitative mass spectrometry-based phosphoproteomics survey of SARS-CoV-2 infection in Vero E6 cells, revealing dramatic rewiring of phosphorylation on host and viral proteins. SARS-CoV-2 infection promoted casein kinase II (CK2) and p38 MAPK activation, production of diverse cytokines, and shutdown of mitotic kinases, resulting in cell cycle arrest. Infection also stimulated a marked induction of CK2-containing filopodial protrusions possessing budding viral particles. Eighty-seven drugs and compounds were identified by mapping global phosphorylation profiles to dysregulated kinases and pathways. We found pharmacologic inhibition of the p38, CK2, CDK, AXL, and PIKFYVE kinases to possess antiviral efficacy, representing potential COVID-19 therapies.
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Affiliation(s)
- Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Miguel Correa Marrero
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Svenja Ulferts
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erica Stevenson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ajda Rojc
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Alexandra Hardy
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | - Rémy Robinot
- Virus & Immunity Unit, Department of Virology, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France; Vaccine Research Institute, 94000 Creteil, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France
| | | | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alistair Dunham
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sebastian Weigang
- Institute of Virology, Medical Center - University of Freiburg, Freiburg 79104, Germany
| | - Julian Knerr
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Diego Quintero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Alberto Valdeolivas
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Trupti Patil
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gwendolyn Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sophia Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anna Gaulton
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Emma J Manners
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eloy Félix
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | - Marisa Goff
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jean K Lim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | | | | | | | | | | | - Emmie De Wit
- NIH/NIAID/Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Andrew R Leach
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brian Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Melanie Ott
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - R Dyche Mullins
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute
| | | | - Georg Kochs
- Institute of Virology, Medical Center - University of Freiburg, Freiburg 79104, Germany; Faculty of Medicine, University of Freiburg, Freiburg 79008, Germany
| | - Robert Grosse
- Institute for Clinical and Experimental Pharmacology and Toxicology, University of Freiburg, Freiburg 79104, Germany; Faculty of Medicine, University of Freiburg, Freiburg 79008, Germany; Centre for Integrative Biological Signalling Studies (CIBSS), Freiburg 79104, Germany.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 75724 Paris, Cedex 15, France.
| | - Jeffery R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute.
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020; 583:459-468. [PMID: 32353859 PMCID: PMC7431030 DOI: 10.1038/s41586-020-2286-9] [Citation(s) in RCA: 2844] [Impact Index Per Article: 711.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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18
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu-Ozturk D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 2020. [PMID: 32353859 DOI: 10.1038/s41586‐020‐2286‐9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein-protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kris M White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Veronica V Rezelj
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Alice Mac Kain
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Lisa Miorin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elena Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jiankun Lyu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Kala Bharath Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ramachandran Rakesh
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lorenzo Calviello
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Srivats Venkataramanan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jose Liboy-Lugo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Yizhu Lin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - YongFeng Liu
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,Biophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Markus Bohn
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Maliheh Safari
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Fatima S Ugur
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Cassandra Koh
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Nastaran Sadat Savar
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Quang Dinh Tran
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Sabrina J Fletcher
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | | | | | | | | | | | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Nicole A Wenzell
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Duygu Kuzuoglu-Ozturk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Hao-Yuan Wang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Raphael Trenker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Devin A Cavero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Theodore L Roth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.,Medical Scientist Training Program, University of California San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Robert M Stroud
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Alan D Frankel
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Oren S Rosenberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kliment A Verba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David A Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Melanie Ott
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,J. David Gladstone Institutes, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Eric Verdin
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Buck Institute for Research on Aging, Novato, CA, USA
| | - Alan Ashworth
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Matt Jacobson
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Division of Genetics, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Charles S Craik
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Stephen N Floor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - John D Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Davide Ruggero
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Pedro Beltrao
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.,European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France.
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kevan M Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA. .,Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA. .,J. David Gladstone Institutes, San Francisco, CA, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. bioRxiv 2020:2020.03.22.002386. [PMID: 32511329 PMCID: PMC7239059 DOI: 10.1101/2020.03.22.002386] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption 1,2 . There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Kala B Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Rakesh Ramachandran
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco
| | | | - Yizhu Lin
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,Biophysics Graduate Program, University of California, San Francisco
| | - Markus Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Raphael Trenker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Devin Cavero
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joe Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Theo Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Björn Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Kris M White
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Biochemistry & Biophysics and Quantitative Biosciences Institute UCSF 600 16th St San Francisco, CA 94143
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98103
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Adolfo García-Sastre
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Psychiatry, San Francisco, CA, 94158, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Christophe d'Enfert
- Direction Scientifique, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Matt Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Stephen Floor
- Department of Cell and Tissue Biology, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - John Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kevan Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
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