Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
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Abstract
SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
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Class 1 antibodies are resisted by A475V; class 2 by E484K and Q493R; class 3 by R346S, N439K, and N440K.
“A475V is resistant to class 1 antibodies (structurally defined as described29); E484K and Q493R are resistant to class 2 antibodies7,8,12,13,29,30,32,33; while R346S, N439K, and N440K are resistant to class 3 antibodies7,8,12,13,29,33.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [30]
Mutations found in emergent S variants decrease sensitivity to neutralization by mAbs, convalescent plasma, and sera from vaccinated individuals.
“Mutations found in emergent S variants decrease sensitivity to neutralization by mAbs, convalescent plasma, and sera from vaccinated individuals (27, 37, 58, 61–70).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [65]
Continued viral evolution led to the emergence and selection of SARS-CoV-2 variants with enhanced infectivity/transmissibility and ability to circumvent drug and immune control.
“Continued viral evolution led to the emergence and selection of SARS-CoV-2 variants with enhanced infectivity/transmissibility2,3 4,5 and ability to circumvent drug6 and immune control7,8.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [7]
The E484K mutation can mediate antibody escape of B.1.351 and P.1 variants.
“The E484K mutation, which can mediate antibody escape of B.1.351and P.1 variants, has been recently detected in the B.1.1.7 lineage in the United Kingdom, and thus represents a major potential threat for previously immune populations.”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [25]
Mutations in B.1.351 and P.1, including E484K and K417N/T, partly compromise neutralization generated by previous infection or vaccination.
“Mutations in the B.1.351and P.1 strains, including E484K and K417N/T, are of high concern, since they partly compromise neutralization generated by previous infection or vaccination [23][24][25] or may increase inherent viral fitness.”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [25]
S:N439K occurs in two larger clusters across Europe and arose several times independently.
“S:N439K is present in two larger clusters found across Europe 19 and arose several times independently.”
From Spread of a SARS-CoV-2 variant through Europe in the summer of 2020 (2021) · cites this paper as [19]
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Self-citationmRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection
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Self-citationEstimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
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Self-citationSpread of a SARS-CoV-2 variant through Europe in the summer of 2020
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Scalable emulation of protein equilibrium ensembles with generative deep learning
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SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2
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Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
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Self-citationKinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans
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Tackling COVID-19 with neutralizing monoclonal antibodies
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Self-citationImprinted antibody responses against SARS-CoV-2 Omicron sublineages
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Self-citationFree energy perturbation calculations of mutation effects on SARS-CoV-2 RBD::ACE2 binding affinity
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Shooting at a Moving Target—Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development
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- Authors
- Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., Lytras, S., Czudnochowski, N., Shah, R., Meury, M., Jesudason, N., De Marco, A., Li, K., Bassi, J., O’Toole, A., Pinto, D., Colquhoun, R. M., Culap, K., Jackson, B., Zatta, F., Rambaut, A., Jaconi, S., Sreenu, V. B., Nix, J., Zhang, I., Jarrett, R. F., Glass, W. G., Beltramello, M., Nomikou, K., Pizzuto, M., Tong, L., Cameroni, E., Croll, T. I., Johnson, N., Di Iulio, J., Wickenhagen, A., Ceschi, A., Harbison, A. M., Mair, D., Ferrari, P., Smollett, K., Sallusto, F., Carmichael, S., Garzoni, C., Nichols, J., Galli, M., Hughes, J., Riva, A., Ho, A., Schiuma, M., Semple, M. G., Openshaw, P. J. M., Fadda, E., Baillie, J. K., Chodera, J. D., Rihn, S. J., Lycett, S. J., Virgin, H. W., Telenti, A., Corti, D., Robertson, D. L., & Snell, G.
- Affiliations
- London School of Hygiene & Tropical Medicine (GB)
- VIR Biotechnology (United States) (US)
- MRC University of Glasgow Centre for Virus Research (GB)
- Vir Biotechnology (Switzerland) (CH)
- University of Glasgow (GB)
- University of Edinburgh (GB)
- Lawrence Berkeley National Laboratory (US)
- Memorial Sloan Kettering Cancer Center (US)
- University of Cambridge (GB)
- Ente Ospedaliero Cantonale (CH)
- National University of Ireland, Maynooth (IE)
- UNSW Sydney (AU)
- ETH Zurich (CH)
- Clinica Luganese Moncucco (CH)
- Luigi Sacco Hospital (IT)
- University of Liverpool (GB)
- Imperial College London (GB)
- Roslin Institute (GB)
- Washington University in St. Louis (US)
- Corresponding author
- Robertson, David L.
- Snell, Gyorgy
- ORCID
- Thomson, Emma C.
- Rosen, Laura E.
- Shepherd, James G.
- Spreafico, Roberto
- da Silva Filipe, Ana
- Wojcechowskyj, Jason A.
- Piccoli, Luca
- Pascall, David J.
- Dillen, Josh
- Lytras, Spyros
- Czudnochowski, Nadine
- Shah, Rajiv
- Meury, Marcel
- Jesudason, Natasha
- Li, Kathy
- Bassi, Jessica
- O’Toole, Aine
- Pinto, Dora
- Colquhoun, Rachel M.
- Culap, Katja
- Jackson, Ben
- Zatta, Fabrizia
- Rambaut, Andrew
- Jaconi, Stefano
- Sreenu, Vattipally B.
- Nix, Jay
- Zhang, Ivy
- Jarrett, Ruth F.
- Glass, William G.
- Beltramello, Martina
- Nomikou, Kyriaki
- Pizzuto, Matteo
- Tong, Lily
- Cameroni, Elisabetta
- Croll, Tristan I.
- Johnson, Natasha
- Wickenhagen, Arthur
- Ceschi, Alessandro
- Harbison, Aoife M.
- Mair, Daniel
- Ferrari, Paolo
- Smollett, Katherine
- Sallusto, Federica
- Carmichael, Stephen
- Garzoni, Christian
- Nichols, Jenna
- Galli, Massimo
- Hughes, Joseph
- Riva, Agostino
- Ho, Antonia
- Schiuma, Marco
- Semple, Malcolm G.
- Openshaw, Peter J.M.
- Fadda, Elisa
- Baillie, J. Kenneth
- Chodera, John D.
- Rihn, Suzannah J.
- Lycett, Samantha J.
- Virgin, Herbert W.
- Telenti, Amalio
- Corti, Davide
- Robertson, David L.
- Snell, Gyorgy
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2021-03
- Volume
- 184
- Issue
- 5
- Pages
- 1171-1187.e20
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7843029
- OpenAlex
- W3127277789
- Cited by
- 606
- References
- 107
- Citations by year
- 2026: 9 · 2025: 24 · 2024: 39 · 2023: 63 · 2022: 176 · 2021: 284 · 2020: 9
- FWCI
- 44.70
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion, other-oa)
- Research Explorer (The University of Manchester) (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion, cc-by-sa)
- ePrints Soton (University of Southampton) (acceptedVersion)
- Maynooth University ePrints and eTheses Archive (Maynooth University) (acceptedVersion)
- Northumbria Research Link (Northumbria University) (acceptedVersion)
- University of Birmingham Research Portal (University of Birmingham) (acceptedVersion, cc-by)
- UEA Digital Repository (University of East Anglia) (acceptedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Figshare (submittedVersion, cc-by)
- UNSWorks (University of New South Wales, Sydney, Australia) (submittedVersion, cc-by-nc-nd)
- Lenus, The Irish Health Repository (Dr Steevens Hospital Library) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by-nc-nd)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- Apollo
- ETH Zürich Research Collection (cc-by)
- Funders
- NSF
- NIHR
- Bill and Melinda Gates Foundation
- NIH
- Wellcome Trust
- MRC
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, spike protein, receptor-binding motif, immune evasion, neutralizing antibodies, viral replication fitness, vaccine efficacy, therapeutic antibodies, molecular surveillance, COVID-19 pandemic
- MeSH terms
- Angiotensin-Converting Enzyme 2, COVID-19, SARS-CoV-2, Antibodies, Viral, Humans, Mutation, Phylogeny, Virulence, Genetic Fitness, Immune Evasion, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus
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