ArticleCell2023
A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike.
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Article in Cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 142 papers.
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142citing papers in PubMed
42.9field-weighted citation impact, top 1% of its field
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142 citing papers in PubMed, 203 citations in OpenAlex.
- Deep mutational scanning reveals the antibody escape and infectivity landscape of SARS-CoV-2 Omicron JN.1 and XEC receptor-binding domains.Emerging microbes & infections · 2026Article
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- Computational design of potent, broadly neutralizing anti-Nipah virus and Hendra virus miniproteins.bioRxiv : the preprint server for biology · 2026Article
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- A predictive model for rapid assessment of protective efficacy against emerging SARS-CoV-2 variants.Infectious Disease Modelling · 2026Article
- Serum Escape Landscape of SARS-CoV-2 Omicron JN.1 and XEC RBD Under COVID-19 Vaccine Breakthrough Immunity in China.Microorganisms · 2026Article
- Concepts of RNA virus evolution for the design of better antiviral countermeasures.Nature reviews. Microbiology · 2026Review
- Scanning the horizon: deep mutational scanning approaches in virology.Journal of virology · 2026Review
- A deep mutational scanning-informed protein language model predicts SARS-CoV-2 evolution dynamics with spatiotemporal resolution.Nature microbiology · 2026Article
- Deep mutational scanning of recent SARS-CoV-2 variants highlights changing amino acid preferences within epistatic hotspot residues.PLoS pathogens · 2026Article
- TMPRSS2-mediated coronavirus spike activation and inhibition.Nature structural & molecular biology · 2026Article
- Stringent selection drives convergence toward omicron-like SARS-CoV-2 receptor-binding motifs.Nature communications · 2026Article
- Structural mimics of SARS-CoV-2.Infection · 2026Review
- Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures.bioRxiv : the preprint server for biology · 2026Article
- Stabilization of the H5 clade 2.3.4.4b hemagglutinin improves vaccine-elicited neutralizing antibody responses in mice.Science translational medicine · 2026Article
- Evaluation of an H5 influenza virus mRNA-lipid nanoparticle (LNP) vaccine in lactating dairy cows.bioRxiv : the preprint server for biology · 2026Article
- Pleiotropic mutational effects on function and stability constrain the antigenic evolution of influenza haemagglutinin.Nature ecology & evolution · 2026Article
- Learning a viral protein's vocabulary.Nature ecology & evolution · 2026Article
- Comparative analysis of deep mutational scanning datasets in enteroviruses A and B identifies functional divergence and therapeutic targets.Nature ecology & evolution · 2026Article
- Transition from infectivity and immune escape to pure escape as an evolutionary strategy during the COVID-19 pandemic.bioRxiv : the preprint server for biology · 2026Article
82 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 6 institutions in 2 countries.
Bernadeta DadonaiteBasic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Katharine H D CrawfordBasic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Genome Sciences & Medical Scientist Training Program, University of Washington, Seattle, WA 98109, USA.
Caelan E RadfordBasic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA.
Ariana G FarrellBasic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
Timothy C YuBasic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA.
William W HannonBasic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98109, USA.
Panpan ZhouDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
Raiees AndrabiDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA.
Dennis R BurtonDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, MIT & Harvard, Cambridge, MA 02139, USA.
Lihong LiuAaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
David D HoAaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA.
Helen Y ChuUniversity of Washington, Department of Medicine, Division of Allergy and Infectious Diseases, Seattle, WA, USA.
Richard A NeherBiozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Jesse D BloomBasic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address: jbloom@fredhutch.org.
University of Washington · USScripps Research Institute · USAaron Diamond AIDS Research Center · USFred Hutch Cancer Center · USHoward Hughes Medical Institute · USSIB Swiss Institute of Bioinformatics · CH
Funding
Identification of neutralizing epitopes on SARS-CoV-2 spike for design of vaccines and small-molecule antiviralsUM1AI144462 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI BURTON, DENNIS R. · 2019 to 2025
$201.6MNIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00015 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HENSLEY, SCOTT · 2021 to 2025
$50.7MTRAINING IN MOLECULAR AND CELLULAR BIOLOGYT32GM007270 · NIGMS · UNIVERSITY OF WASHINGTON · PI RAIBLE, DAVID W · 1985 to 2020
$21.0MStructure-based design of broadly protective coronavirus vaccinesP01AI167966 · NIAID · UNIVERSITY OF WASHINGTON · PI BALI PULENDRAN · 2022 to 2026
$15.3MTraining in Cellular & Molecular BiologyT32GM136534 · NIGMS · UNIVERSITY OF WASHINGTON · PI Andrew Atwell Oberst, LARRY S ZWEIFEL · 2021 to 2026
$5.8MViral Pathogenesis Training ProgramT32AI083203 · NIAID · UNIVERSITY OF WASHINGTON · PI BLOOM, JESSE D, LAGUNOFF, MICHAEL · 2009 to 2023
$2.7MComplete mapping of immune selection from antibodies to HIVR01AI140891 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BLOOM, JESSE D · 2019 to 2024
$2.4MProspectively characterizing the functional and antigenic effects of mutations to viral entry proteinsR01AI141707 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BLOOM, JESSE D · 2018 to 2022
$2.1MComplete mapping of the functional and antigenic effects of mutations to Lassa virus glycoproteinF30AI149928 · NIAID · UNIVERSITY OF WASHINGTON · PI CRAWFORD, KATHARINE HOLT DUSENBURY · 2020 to 2021
$91kNIAID NIH HHS 75N93021C00015NIAID NIH HHS F30 AI149928NIAID NIH HHS P01 AI167966NIAID NIH HHS R01 AI140891NIAID NIH HHS R01 AI141707NIAID NIH HHS T32 AI083203NIAID NIH HHS UM1 AI144462NIGMS NIH HHS T32 GM007270NIGMS NIH HHS T32 GM136534
Abstract
A major challenge in understanding SARS-CoV-2 evolution is interpreting the antigenic and functional effects of emerging mutations in the viral spike protein. Here, we describe a deep mutational scanning platform based on non-replicative pseudotyped lentiviruses that directly quantifies how large numbers of spike mutations impact antibody neutralization and pseudovirus infection. We apply this platform to produce libraries of the Omicron BA.1 and Delta spikes. These libraries each contain ∼7,000 distinct amino acid mutations in the context of up to ∼135,000 unique mutation combinations. We use these libraries to map escape mutations from neutralizing antibodies targeting the receptor-binding domain, N-terminal domain, and S2 subunit of spike. Overall, this work establishes a high-throughput and safe approach to measure how ∼10
Indexed as
COVID-19RNA VirusesAntibodies, NeutralizingAntibodies, ViralHumansMutationSARS-CoV-2Antibodies, NeutralizingAntibodies, Viralantibody escapeantibody neutralizationBA.1deep mutational scanningDeltaOmicronpseudovirusSARS-CoV-2spike
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.