ArticleCell2023
SARS-CoV-2 variants evolve convergent strategies to remodel the host response.
Abstract read
In one paragraph
Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
0numbers the graph read from it
0cells of the map it votes in
71citing papers in PubMed
–field-weighted citation impact
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
71 citing papers in PubMed.
- A Phase III Randomized Controlled Trial of Plitidepsin, a Marine-Derived Compound, in Hospitalized Adults With Moderate COVID-19.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2024Trial
- Epitope Tagging and Coimmunoprecipitation to Identify Viral Protein Interactors.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Circulating cholesterol fuels SARS-CoV-2 replication via ORF3a.EMBO reports · 2026Article
- SARS-CoV-2 defective viral genomes from distinct genomic regions drive divergent interferon responses.PLoS pathogens · 2026Article
- Paracrine signals from HIV-1-infected immune cells reprogram cervical cancer pathways.iScience · 2026Article
- Evolution of a truncated nucleocapsid protein enhances SARS-CoV-2 fitness by suppressing antiviral responses.PLoS biology · 2026Article
- Prospective multicentre study of upper respiratory mucosal transcriptomics reveals two major endotypes of critically ill COVID-19 patients.Communications medicine · 2026Article
- Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections.Cell reports. Medicine · 2026Article
- Stealth replication of SARS-CoV-2 Omicron in the nasal epithelium at physiological temperature.Journal of virology · 2026Article
- Intramolecular loops control SARS-CoV-2 nucleocapsid protein self-association and nucleic acid binding dependent on phosphorylation.bioRxiv : the preprint server for biology · 2026Article
- Age-dependent immune profiles and variant-driven humoral alterations across two SARS-CoV-2 epidemic phases.Frontiers in immunology · 2026Article
- Distinct characteristics on mixed infection of SARS-CoV-2 variants and other respiratory pathogens among patients with acute COVID-19 in central China.Frontiers in cellular and infection microbiology · 2026Article
- Article
- Integrative multi-omics analysisiScience · 2025Article
- Evolution of a fuzzy ribonucleoprotein complex in viral assembly.bioRxiv : the preprint server for biology · 2025Article
- Review
- Article
- SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.The Lancet. Microbe · 2025Observational
- SARS-CoV-2 nucleocapsid protein directly prevents cGAS-DNA recognition through competitive binding.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Inference of differential kinase interaction networks with KINference.Bioinformatics (Oxford, England) · 2025Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
80 authors.
Mehdi BouhaddouQuantitative 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 ReuschlQBI 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 PolaccoQuantitative 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 ThorneQBI 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 UmmadiQuantitative 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 YeQBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA.
Romel RosalesQBI 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 PelinQuantitative 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 BatraQuantitative 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 JangQuantitative 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 XuQuantitative 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 MoenQuantitative 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 RichardsQuantitative 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 ZhouQuantitative 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 HarjaiQuantitative 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 StevensonQuantitative 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 RojcQuantitative 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 RagazziniDivision 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 WhelanDivision of Infection and Immunity, University College London, London, UK.
Wilhelm FurnonMRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
Giuditta De LorenzoMRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
Vanessa CowtonMRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
Abdullah M SyedQBI 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 CilingQBI 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 DeutschSchool of Computer Science, Tel Aviv University, Tel Aviv, Israel.
Daniel PirakSchool of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel.
Giulia DowgierCOVID Surveillance Unit, The Francis Crick Institute, London, UK.
Dejan MesnerDivision of Infection and Immunity, University College London, London, UK.
Jane L TurnerDivision of Infection and Immunity, University College London, London, UK.
Briana L McGovernQBI 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 RodriguezQBI 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-RebolloQBI 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 DunhamEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden, UK.
Xiaofang ZhongQuantitative 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 EckhardtQuantitative 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 FossatiQuantitative 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 LiottaQBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA.
Thomas KehrerQBI 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 CupicQBI 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 RutkowskaQBI 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 MenaQBI 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 AslamQBI 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 HoffertQuantitative 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 FoussardQuantitative 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' OlwalQBI 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 HuangHuffington 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 ZwakaHuffington 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 PhamSynthego Corporation, Redwood City, CA, USA.
Molly LyonsSynthego Corporation, Redwood City, CA, USA.
Laura DonohueSynthego Corporation, Redwood City, CA, USA.
Aliesha GriffinSynthego Corporation, Redwood City, CA, USA.
Rebecca NugentSynthego Corporation, Redwood City, CA, USA.
Kevin HoldenSynthego Corporation, Redwood City, CA, USA.
Robert DeansSynthego Corporation, Redwood City, CA, USA.
Pablo AvilesPharma Mar S.A, Madrid, Spain.
Jose A Lopez-MartinPharma Mar S.A, Madrid, Spain.
Jose M JimenoPharma Mar S.A, Madrid, Spain.
Kirsten ObernierQuantitative 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 FabiusQuantitative 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 SoucherayQuantitative 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 HüttenhainQuantitative 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 JungreisMIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Manolis KellisMIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Ignacia EcheverriaQuantitative 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 VerbaQuantitative 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 BonfantiDivision of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK.
Pedro BeltraoQBI 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 SharanSchool of Computer Science, Tel Aviv University, Tel Aviv, Israel.
Jennifer A DoudnaQBI 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-SobridoQBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA.
Arvind H PatelMRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
Massimo PalmariniMRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
Lisa MiorinQBI 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 WhiteQBI 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 SwaneyQuantitative 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-SastreQBI 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. Electronic address: adolfo.garcia-sastre@mssm.edu.
Clare JollyQBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK. Electronic address: c.jolly@ucl.ac.uk.
Lorena Zuliani-AlvarezQuantitative 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. Electronic address: lzulianialvarez@gmail.com.
Greg J TowersQBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK. Electronic address: g.towers@ucl.ac.uk.
Nevan J KroganQuantitative 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. Electronic address: nevan.krogan@ucsf.edu.
Funding
Targeting Viroporins and Coronavirus M ProteinU19AI171110 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Nevan J Krogan · 2022 to 2026
$103.4MNIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00014 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI GARCIA-SASTRE, ADOLFO · 2021 to 2025
$62.6MSARS-CoV adaptations through a Systems Biology Lens (SYBIL)U19AI135972 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Adolfo Garcia-Sastre · 2018 to 2026
$27.2MTechnology Development Project - Increasing the complexity of ex vivo human airway models for studying immune response to viral infectionU19AI142733 · NIAID · JACKSON LABORATORY · PI Damien Chaussabel · 2019 to 2026
$23.1MRESEARCH PROJECT 2U19AI135990 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Melanie Maria Ott · 2018 to 2026
$21.4MTRAINING PROGRAM: MECHANISMS OF VIRUS-HOST INTERACTIONST32AI007647 · NIAID · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI Domenico Tortorella · 2000 to 2026
$11.5MVulnerability of SARS- CoV-2 Infection in Lung Cancer Based on Serological Antibody AnalysesU54CA260560 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI SHYR, YU · 2020 to 2024
$10.0MMechanism-based Targeting of the RNA Processing Machinery of SARS-CoV-2R01AI161363 · NIAID · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI GUPTA, YOGESH K · 2021 to 2025
$3.2MThe origin and future protective activity of SARS-CoV-2 RBD specific neutralizing antibodiesR01AI161175 · NIAID · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI KOBIE, JAMES J, MARTINEZ-SOBRIDO, LUIS · 2021 to 2024
$2.5MDeveloping a Thermostable SARS-CoV-2 RBD-particle VaccineR43AI165089 · NIAID · POP BIOTECHNOLOGIES, INC · PI HUANG, WEI-CHIAO · 2021 to 2022
$600kIdentifying and inhibiting the SARS-CoV-2 packaging mechanismR21AI159666 · NIAID · J. DAVID GLADSTONE INSTITUTES · PI DOUDNA, JENNIFER A · 2021 to 2021
$520kDecoding Viral Control of Host Kinase Signaling to Design Combination TherapyK99AI163868 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BOUHADDOU, MEHDI · 2022 to 2022
$125kDepartment of HealthMedical Research Council MC_PC_19026Medical Research Council MC_UU_00034/3Medical Research Council MC_UU_00034/8Medical Research Council MC_UU_12014/2Medical Research Council MR/S023380/1Medical Research Council MR/W005611/1NCI NIH HHS U54 CA260560NIAID NIH HHS 75N93021C00014NIAID NIH HHS K99 AI163868NIAID NIH HHS R01 AI161175NIAID NIH HHS R01 AI161363NIAID NIH HHS R21 AI159666NIAID NIH HHS R43 AI165089NIAID NIH HHS T32 AI007647NIAID NIH HHS U19 AI135972NIAID NIH HHS U19 AI135990NIAID NIH HHS U19 AI142733NIAID NIH HHS U19 AI171110Wellcome TrustWellcome Trust 206369/Z/17/ZWellcome Trust 214344Wellcome Trust 220863Wellcome Trust 223065
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.
Indexed as
COVID-19SARS-CoV-2HumansImmunity, InnatePandemicsinnate immunityprotein-protein interactionsproteomicsSARS-CoV-2systems biologytranscriptomicsvariantsvirus-host interactions
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