Lucy G Thorne
Lucy G Thorne
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,#,
Mehdi Bouhaddou
Mehdi Bouhaddou
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,#,
Ann-Kathrin Reuschl
Ann-Kathrin Reuschl
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,#,
Lorena Zuliani-Alvarez
Lorena Zuliani-Alvarez
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,#,
Ben Polacco
Ben Polacco
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Adrian Pelin
Adrian Pelin
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Jyoti Batra
Jyoti Batra
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Matthew V X Whelan
Matthew V X Whelan
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,
Myra Hosmillo
Myra Hosmillo
6Division of Virology, Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
6,
Andrea Fossati
Andrea Fossati
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Roberta Ragazzini
Roberta Ragazzini
7Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
7,
Irwin Jungreis
Irwin Jungreis
8MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA USA
9Broad Institute of MIT and Harvard, Cambridge, MA USA
8,9,
Manisha Ummadi
Manisha Ummadi
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Ajda Rojc
Ajda Rojc
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Jane Turner
Jane Turner
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,
Marie L Bischof
Marie L Bischof
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,
Kirsten Obernier
Kirsten Obernier
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Hannes Braberg
Hannes Braberg
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Margaret Soucheray
Margaret Soucheray
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Alicia Richards
Alicia Richards
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Kuei-Ho Chen
Kuei-Ho Chen
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Bhavya Harjai
Bhavya Harjai
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Danish Memon
Danish Memon
10European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
10,
Joseph Hiatt
Joseph Hiatt
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Romel Rosales
Romel Rosales
11Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
12Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
11,12,
Briana L McGovern
Briana L McGovern
11Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
12Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
11,12,
Aminu Jahun
Aminu Jahun
6Division of Virology, Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
6,
Jacqueline M Fabius
Jacqueline M Fabius
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Kris White
Kris White
11Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
12Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
11,12,
Ian G Goodfellow
Ian G Goodfellow
6Division of Virology, Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
6,
Yasu Takeuchi
Yasu Takeuchi
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,
Paola Bonfanti
Paola Bonfanti
7Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
7,
Kevan Shokat
Kevan Shokat
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
13Howard Hughes Medical Institute, San Francisco, CA USA
2,3,4,5,13,
Natalia Jura
Natalia Jura
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
14Division of Advanced Therapies, National Institute for Biological Standards and Control, South Mimms, UK
15Present Address: Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA USA
2,3,5,14,15,
Klim Verba
Klim Verba
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,5,
Mahdad Noursadeghi
Mahdad Noursadeghi
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,
Pedro Beltrao
Pedro Beltrao
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
10European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
2,10,
Manolis Kellis
Manolis Kellis
8MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA USA
9Broad Institute of MIT and Harvard, Cambridge, MA USA
8,9,
Danielle L Swaney
Danielle L Swaney
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,
Adolfo García-Sastre
Adolfo García-Sastre
11Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
12Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
16The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
17Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY USA
18Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
11,12,16,17,18,
Clare Jolly
Clare Jolly
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,✉,
Greg J Towers
Greg J Towers
1Present Address: Division of Infection and Immunity, University College London, London, UK
1,✉,
Nevan J Krogan
Nevan J Krogan
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
2,3,4,5,✉
1Present Address: Division of Infection and Immunity, University College London, London, UK
2QBI Coronavirus Research Group (QCRG), University of California San Francisco, San Francisco, CA USA
3Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA USA
4J. David Gladstone Institutes, San Francisco, CA USA
5Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA USA
6Division of Virology, Department of Pathology, Addenbrooke’s Hospital, University of Cambridge, Cambridge, UK
7Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
8MIT Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA USA
9Broad Institute of MIT and Harvard, Cambridge, MA USA
10European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
11Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
12Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
13Howard Hughes Medical Institute, San Francisco, CA USA
14Division of Advanced Therapies, National Institute for Biological Standards and Control, South Mimms, UK
15Present Address: Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA USA
16The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
17Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY USA
18Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
Subject terms: SARS-CoV-2, Systems biology
© The Author(s) 2022
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
