SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor
Open accessPreprint — published as 10.1038/s41564-021-00954-4
Abstract
SARS-CoV-2 is continually evolving, with more contagious mutations spreading rapidly. Using in vitro evolution to affinity maturate the receptor-binding domain (RBD) of the spike protein towards ACE2 resulted in the more contagious mutations, S477N, E484K, and N501Y, to be among the first selected, explaining the convergent evolution of the “European” (20E-EU1), “British” (501.V1),”South African” (501.V2), and ‘‘Brazilian” variants (501.V3). Plotting the binding affinity to ACE2 of all RBD mutations against their incidence in the population shows a strong correlation between the two. Further in vitro evolution enhancing binding by 600-fold provides guidelines towards potentially new evolving mutations with even higher infectivity. For example, Q498R epistatic to N501Y. Nevertheless, the high-affinity RBD is also an efficient drug, inhibiting SARS-CoV-2 infection. The 2.9Å Cryo-EM structure of the high-affinity complex, including all rapidly spreading mutations, provides a structural basis for future drug and vaccine development and for in silico evaluation of known antibodies.
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The RBD mutation N501Y increases affinity to ACE2 and is present in B.1.1.7 and B.1.351, but does not impair post-vaccine serum neutralization on its own.
“The RBD mutation N501Y, which increases affinity to ACE2 and is present in B.1.1.7 and B.1.351(ref.20 ), does not impair on its own post-vaccine serum neutralization 21 .”
From Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies (2021) · cites this paper as [20]
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“351 and P.1 variants [reviewed in (Plante et al., 2021)] as well as the Y453F mutation (Bayarri-Olmos et al., 2021; Zahradník et al., 2021b) significantly increased the binding affinity to human ACE2 (Figures 2B and 2C; RBD parental KD = 2.05 ± 0.26 nM; RBD N501Y KD = 0.59 ± 0.03 nM; and RBD Y453F…”
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“This viral evolution is a well-characterized phenomenon observed in seasonal coronaviruses (78–80) and has been recently replicated in vitro (81).”
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Waning antibody responses in COVID-19: what can we learn from the analysis of other coronaviruses?
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Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants
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The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants
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Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic
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Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2
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COVID-19, the first pandemic in the post-genomic era
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SARS-CoV-2 neutralizing antibodies: Longevity, breadth, and evasion by emerging viral variants
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“To address viral neutralization in the presence of ACE2 and TMPRSS2, a portfolio of Hek293T expressing clonal cell lines with ACE2 and TMPRSS2 (HekAT) was generated.”
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“Despite the ability of 1–57 and 2–7 to still potently neutralize emerging strains that carry N501Y, K417N, and E484Kmutations, we observed that individual mutations at 452, 494, 477, and 439 (Figure 4B)—which may affect 1–57 and 2–7 recognition—do not or only weakly enhance ACE2 binding (Bayarri-Olmos et al., 2021; Lo…”
The localized rise of a B.1.526 SARS-CoV-2 variant containing an E484K mutation in New York StatePreprint
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“3 | Sample selection criteria/strategy for whole genome sequencing Previously, we had used the SGTF as a proxy for the detection of alpha variant in Pakistan using theTaqPathTM kit (Thermo Fisher Scientific).(13) This detection method can also be used the other way around for surveillance of other lineages.”
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“Whether it also enhances the exposure of the S2′ site is not clear, but our results clearly show that Furin cleavage at the S2′ site is enhanced in the presence of ACE2 [74].”
BackgroundInfluentialMutational dynamics of SARS-CoV-2: Impact on future COVID-19 vaccine strategies
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“This may be explained by the presence of the N501Y mutation in the receptor binding domain (RBD) of the spike protein, which enhances viral particle binding to the ACE2 receptor (18).”
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A tale of three SARS-CoV-2 variants with independently acquired P681H mutations in New York StatePreprint
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“The L452R and T478K enhance S protein’s binding affinity with human angiotensin-converting enzyme 2 (ACE2) receptor [21,22].”
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“In B.1.1.7 lineage, there is one critical mutation in the RBM namely-N501Y, which has been re-ported previously to enhance the interaction with the hACE2 (Zahradnik et al., 2021; Zhu et al., 2021).”
InfluentialDecomposing the sources of SARS-CoV-2 fitness variation in the United States
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“Most of these mutations are previously described variants that either increase cellular binding avidity (D614G), escape neutralizing antibodies (L452R and E484K) or both (N501Y/T) (Deng et al., 2021; Greaney et al., 2021; Zahradnik et al., 2021).”
BackgroundMeta-Analysis and Structural Dynamics of the Emergence of Genetic Variants of SARS-CoV-2
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“, neutralization by 14 of 17 of 96 the most potent mRNA vaccine-elicited monoclonal antibodies (mAbs) was either decreased or 97 abolished variants E484K, N501Y or the K417N:E484K:N501Y combination (6, 30).”
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“To assess the potential to resist future mutations, highly neutralizing Nbs were also evaluated for their binding to a potential future RBD variant (RBD62 with 9 point mutations), which was identified by in vitro evolution for ultrahigh-affinity ACE2 binding 27 .”
Science's Response to CoVID‐19
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“Vero E6 cells, a common cell line for the SARS-CoV-2 study, have high ACE2 expression levels but with low TMPRSS2 expression.”
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“3] In combination with N501Y increases affinity to ACE2 [43].”
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Immunogenic amino acid motifs and linear epitopes of COVID-19 mRNA vaccines
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“Nonetheless, the RBD is an important target of neutralizing antibodies that develop in vivo during natural infection [33], and possibly a driver for the evolution of mutations given its critical role in the virus life cycle [34, 35].”
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“7 was predicted to be more transmissible [4].”
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B-Cell Memory Responses to Variant Viral Antigens
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The limits of SARS-CoV-2 predictability
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On the Evolutionary Trajectory of SARS-CoV-2: Host Immunity as a Driver of Adaptation in RNA Viruses
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“K356 participates in the formation of a hydrophobic pocket in the RBD (38) that may explain its functional importance and evolutionary conservation.”
BackgroundImmune response variables and viral mutations impact on COVID-19 reinfection and relapse
Sanaie, S., Golipour, E., Shamekh, A., Sadaie, M. R., Mahmoodpoor, A., & Yousefi, M. (2021) · International Immunopharmacology · doi:10.1016/j.intimp.2021.108108 · Cited by 12 · see citing works
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“The RBD mutations enhance infectivity due to presence of L452R and T478K by increasing the spike protein's affinity for the human ACE2 receptor [11, 12].”
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“7 variant was shown to have higher affinity for hACE2 along with a lower dissociation rate constant [30].”
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“K417 is a unique ACE2-interacting residue outside of the RBM. Amino acid changes N501Y and E484K enhance the binding affinity of the S protein to ACE2 which might be correlated to the epidemiologically observed higher infectivity and transmission (Zahradnik et al. 2021).”
BackgroundFive Challenges in the Field of Viral Diversity and Evolution
Sanjuán, R., Illingworth, C. J. R., Geoghegan, J. L., Iranzo, J., Zwart, M. P., Ciota, A. T., Moratorio, G., Gago‐Zachert, S., Duffy, S., & Vijaykrishna, D. (2021) · Frontiers in Virology · doi:10.3389/fviro.2021.684949 · Cited by 24 · see citing works
“For instance, the recurrent emergence of certain variants both in laboratory evolution experiments and in nature can help us predict the evolution of some viral features (8, 9).”
BackgroundReplicative fitness SARS-CoV-2 20I/501Y.V1 variant in a human reconstituted bronchial epithelium
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“This may be explained by the presence of the 85 N501Y mutation in the receptor binding domain (RBD) of the spike protein which enhances 86 viral particle binding to the ACE2 receptor (9).”
BackgroundShrivastava, S., Mhaske, S. T., Modak, M. S., Virkar, R., Pisal, S. S., Mishra, A. C., & Arankalle, V. A. (2022) · Archives of Virology · doi:10.1007/s00705-021-05320-7 · Cited by 7 · see citing works
“In in-vitro experiments, an increased binding affinity of the T478K mutant for the ACE2 receptor has been shown [27].”
BackgroundSARS-CoV-2 convergent evolution as a guide to explore adaptive advantagePreprint
Zahradník, J., Nunvář, J., & Schreiber, G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.24.445534 · Cited by 6 · see citing works
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“…Rambaut et al., 2020), suggesting that they confer a selective advantage, rather than emerged by chance, such as through a founder effect. were the main mutations that appeared following random RBD mutagenesis and in vitro selection of mutants with enhanced ACE2 binding (Zahradník et al., 2021).”
BackgroundInfluential2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic?
Goldhill, D. H., & Barclay, W. (2021) · Evolution · doi:10.1111/evo.14317 · Cited by 6 · see citing works
A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules
Folescu, D., & Onufriev, A. (2021) · ACS Omega · doi:10.1021/acsomega.2c01484 · Cited by 6
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Zahradník, J., & Schreiber, G. (2021) · Biochemistry · doi:10.1021/acs.biochem.1c00356 · Cited by 4 · see citing works
Self-citationUltrafast topological data analysis reveals pandemic-scale dynamics of convergent evolutionPreprint
Bleher, M., Hahn, L., Neumann, M., Ardern, Z., Patiño-Galindo, J. Á., Carrière, M., Bauer, U., Rabadán, R., & Ott, A. (2021) · medRxiv · doi:10.1101/2021.06.10.21258550 · Cited by 3 · see citing works
“One approach to identify potential adaptive mutations is by experimentally mutating many positions and testing the effect of these mutations in certain phenotypes, like binding to the human receptor or immune escape [9, 35, 45].”
BackgroundEnsovibep, a novel trispecific DARPin candidate that protects against SARS-CoV-2 variantsPreprint
Rothenberger, S., Hurdiss, D. L., Walser, M., Malvezzi, F., Mayor, J., Ryter, S., Moreno, H., Liechti, N., Bosshart, A., Iss, C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.03.429164 · Cited by 17 · see citing works
May Vaccines Select SARS-Cov-2 Variants More Readily Escaping Immunity - An Analysis of Public Data
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Potential differentiation of successive SARS-CoV-2 mutations by RNA: DNA hybrid analyses
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Worldwide SARS-CoV-2 haplotype distribution in early pandemic
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IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome
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“V1) emerging in the UK [15], B.1.351 (clade 20H/501Y.V2) in South Africa [16], and P.1 (clade 20J/501Y.V3) in Brazil [17] that were found to harbour a total of 32, 25 and 25 median mutations across 13, 82 and 13 samples, respectively, for each lineage (Additional file 1: Tables S3 and S4).”
BackgroundInfluentialThe Development of Epitope-Based Recombinant Protein Vaccines against SARS-CoV-2
Khalid, K., Lim, H. X., Hwang, J. S., & Poh, C. L. (2024) · The AAPS Journal · doi:10.1208/s12248-024-00963-1 · Cited by 2 · see citing works
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CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillancePreprint
Wittig, A., Miranda, F. M., Hölzer, M., Altenburg, T., Bartoszewicz, J. M., Beyvers, S., Dieckmann, M. A., Genske, U., Giese, S. H., Nowicka, M., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.03.429146 · Cited by 2 · see citing works
The basis of a more contagious 501Y.V1 variant of SARS-COV-2
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Immunoediting in SARS-CoV-2: Mutual relationship between the virus and the host
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Nikitin, P. A., DiMuzio, J. M., Dowling, J. P., Patel, N. B., Bingaman, J. L., Heimbach, B. C., Henriquez, N., Nicolescu, C., Polley, A. M., Sikorski, E. L., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.18.464900 · Cited by 1 · see citing works
- Authors
- Zahradník, J., Marciano, S., Shemesh, M., Zoler, E., Chiaravalli, J., Meyer, B., Rudich, Y., Dym, O., Elad, N., & Schreiber, G.
- Affiliations
- Weizmann Institute of Science (IL)
- Institut Pasteur (FR)
- Corresponding author
- Schreiber, Gideon
- ORCID
- Venue
- Nature Microbiology
- Publisher
- openRxiv
- Published
- 2021-01-06
- Volume
- 6
- Issue
- 9
- Pages
- 1188-1198
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W3193682077
- Cited by
- 458
- References
- 0
- Citations by year
- 2026: 14 · 2025: 27 · 2024: 42 · 2023: 82 · 2022: 177 · 2021: 103 · 2020: 1 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1 · 2012: 1
- FWCI
- 32.05
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature Microbiology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (acceptedVersion, cc-by)
- HAL (submittedVersion)
- Funders
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases
- Weizmann Institute of Science
- Israel Science Foundation (3814/19)
- Nature
- National Institutes of Health
- 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
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, spike protein receptor-binding domain, ACE2 binding affinity, in vitro evolution, affinity maturation, SARS-CoV-2 variants, E484K, N501Y, antiviral drug design, hamster challenge model, COVID-19 pandemic, vaccine development
- MeSH terms
- Protein Domains, Angiotensin-Converting Enzyme 2, COVID-19, SARS-CoV-2, COVID-19 Drug Treatment, Animals, Antiviral Agents, Female, Cricetinae, Humans, Male, Mesocricetus, Mutation, Protein Binding, Receptors, Virus, Drug Design, Evolution, Molecular, Virus Internalization, Molecular Dynamics Simulation, Spike Glycoprotein, Coronavirus
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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