Cited by 461SARS-CoV-2 and COVID-19 Researchvaccines and immunoinformatics approachesAnimal Virus Infections Studies

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Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

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Abstract

SARS-CoV-2 has caused over 2 million deaths in little over a year. Vaccines are being deployed at scale, aiming to generate responses against the virus spike. The scale of the pandemic and error-prone virus replication is leading to the appearance of mutant viruses and potentially escape from antibody responses. Variant B.1.1.7, now dominant in the UK, with increased transmission, harbors 9 amino acid changes in the spike, including N501Y in the ACE2 interacting surface. We examine the ability of B.1.1.7 to evade antibody responses elicited by natural SARS-CoV-2 infection or vaccination. We map the impact of N501Y by structure/function analysis of a large panel of well-characterized monoclonal antibodies. B.1.1.7 is harder to neutralize than parental virus, compromising neutralization by some members of a major class of public antibodies through light-chain contacts with residue 501. However, widespread escape from monoclonal antibodies or antibody responses generated by natural infection or vaccination was not observed.

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Overview

AI snapshot

Written from the paper’s full text.

TL;DR

The SARS-CoV-2 B.1.1.7 variant is harder to neutralize than the early Victoria strain by convalescent and vaccine sera, with reduced potency partly attributable to the N501Y spike mutation. However, the paper finds no widespread escape from monoclonal antibodies or from natural infection- or vaccine-induced antibody responses.

Key findings

  • B.1.1.7 required higher serum concentrations for neutralization: convalescent plasma FRNT50 titers were 2.9-fold lower against B.1.1.7 than Victoria (geometric mean, n = 34, p < 0.0001); AstraZeneca AZD1222 vaccine sera showed 2.5-fold (n = 15, p < 0.0001) and 2.1-fold (n = 10, p < 0.002) reductions at 14 and 28 days after the second dose; Pfizer-BioNTech BNT162b2 sera showed a 3.3-fold reduction (n = 25, p < 0.0001).
  • N501Y increased RBD binding affinity for ACE2 approximately 7-fold by biolayer interferometry: WT RBD(501N)-ACE2 KD 75.1 nM versus RBD(501Y)-ACE2 KD 10.7 nM, due to a slower off rate.
  • Some public IGHV3-53 antibodies were affected: mAbs 150, 158, and 175 showed roughly 3-fold reduced affinity, mAb 269 was hypersensitive with a 30-fold affinity effect and almost complete loss of neutralization, and mAb 278 failed to reach 100% neutralization with a maximum of 78%. Regeneron and AstraZeneca antibodies showed only modest or no reduction.
  • Plasma from 13 patients infected with B.1.1.7 showed no significant difference in neutralization titers between B.1.1.7 and Victoria strains.

Methods

  • The study analyzed 377 spike-targeting mAbs from first-wave SARS-CoV-2 cases, focusing on 20 potent neutralizing antibodies (19 anti-RBD, 1 anti-NTD), using BLI binding assays, crystallography of Fab 269 with WT and N501Y RBD, and focus reduction neutralization tests (FRNT) against Victoria and B.1.1.7.
  • Neutralization was tested with 34 convalescent plasma samples, AstraZeneca AZD1222 vaccine sera at 14 days (n = 15) and 28 days (n = 10) after the second dose, Pfizer-BioNTech BNT162b2 vaccine sera (n = 25) 7–17 days after the second dose, and plasma from 13 B.1.1.7-infected patients.
  • COG-UK sequence analysis examined 180,000 sequences; statistical comparisons used the Wilcoxon matched-pairs signed-rank test with two-tailed p values and geometric means.

Limitations

  • Stated: correlates of protection from SARS-CoV-2 are not established; in vitro neutralization assays do not capture contributions from T cells, Fcγ receptor interactions, or complement activation; convalescent plasma and vaccine serum were taken relatively soon after infection or vaccination, so titers may drop over time.
  • Stated: further work is needed to understand antibody responses to B.1.1.7, including adaptation to N501Y and NTD deletions, and to test neutralization of other variants such as B.1.351 and P.1.
  • Evident from the text: some groups were small (e.g., n = 10, n = 13, n = 15, n = 25), and the study reports in vitro neutralization only, without in vivo protection or durability data.

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Integrity signals

Registry

Crossref · 10.1016/j.cell.2021.02.033

Cites

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Statistics

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Figures

Graphical abstract
Graphical abstract CC BY · PubMed Central
Figure 1 The B.1.1.7 variant spike protein and effect on ACE binding of the N501Y mutation (A) The SARS-CoV-2 spike trimer is depicted as a gray surface with mutations highlighted in yellow-green or with symbols. The RBD N501Y and the NTD 144 and 69–70 deletions are highlighted with green stars and red triangles, respectively. On the right, a protomer is highlighted as a colored ribbon within the transparent gray spike surface, illustrating its topology and marking key domains. (B) The RBD “torso” analogy. The RBD is represented as a gray surface with the ACE2 receptor binding site in dark green. Binding sites for the panel of antibodies (Dejnirattisai et al., 2021) on which this study draws are represented by spheres. The spheres represent the point at which placing spherical antibodies would optimally predict the BLI competition data and are colored according to their neutralization, from red (potent) to blue (non-neutralizing). The position of the B.1.1.7 N501Y mutation in the RBD is highlighted in light green toward the right shoulder. (C) Proximity of ACE2 to N501Y. The RBD is depicted as in (B) with ACE2 bound (in yellow cartoon format) with glycosylation drawn as sticks. (D) Left panel: interactions of N501 of WT RBD with residues Y41 and K353. The structure shown is the complex of N501 RBD with ACE2 determined by X-ray crystallography (PDB ID 6M0J, Lan et al., 2020). When the 501 is mutated to a tyrosine with the conformation seen in the N501Y RBD-269 Fab complex (right panel), Y501 makes T-shaped ring stacking interactions with Y41 and more hydrophobic contacts with K353 of ACE2 (note there are minor clashes of the side chain of Y501 to the end of the K353 side chain, which has ample room to adjust to optimize interactions). (E) BLI plots for WT (left) and N501Y (right) RBDs binding to ACE2. A titration series is shown for each (see STAR Methods). Note the much slower off rate for the mutant.
Figure 1 The B.1.1.7 variant spike protein and effect on ACE binding of the N501Y mutation (A) The SARS-CoV-2 spike trimer is depicted as a gray surface with mutations highlighted in yellow-green or with symbols. The RBD N501Y and the NTD 144 and 69–70 deletions are highlighted with green stars and red triangles, respectively. On the right, a protomer is highlighted as a colored ribbon within the transparent gray spike surface, illustrating its topology and marking key domains. (B) The RBD “torso” analogy. The RBD is represented as a gray surface with the ACE2 receptor binding site in dark green. Binding sites for the panel of antibodies (Dejnirattisai et al., 2021) on which this study draws are represented by spheres. The spheres represent the point at which placing spherical antibodies would optimally predict the BLI competition data and are colored according to their neutralization, from red (potent) to blue (non-neutralizing). The position of the B.1.1.7 N501Y mutation in the RBD is highlighted in light green toward the right shoulder. (C) Proximity of ACE2 to N501Y. The RBD is depicted as in (B) with ACE2 bound (in yellow cartoon format) with glycosylation drawn as sticks. (D) Left panel: interactions of N501 of WT RBD with residues Y41 and K353. The structure shown is the complex of N501 RBD with ACE2 determined by X-ray crystallography (PDB ID 6M0J, Lan et al., 2020). When the 501 is mutated to a tyrosine with the conformation seen in the N501Y RBD-269 Fab complex (right panel), Y501 makes T-shaped ring stacking interactions with Y41 and more hydrophobic contacts with K353 of ACE2 (note there are minor clashes of the side chain of Y501 to the end of the K353 side chain, which has ample room to adjust to optimize interactions). (E) BLI plots for WT (left) and N501Y (right) RBDs binding to ACE2. A titration series is shown for each (see STAR Methods). Note the much slower off rate for the mutant.CC BY · PubMed Central
Figure S1 N5-1Y-containing sequences in the UK, related to STAR Methods (A) proportion of three subgroups of B.1.1.7 expressed as percentage of total 501Y-containing identifiable sequences. Black line shows dominant form with 501Y and Δ69-70. Blue, orange lines both lack 69-70 and have either wild-type or S982A mutation respectively. (B) associated mutations for blue (left), orange (middle) and black (right) plotted on Spike protein structure where modeled, with extended modeled N terminus (PDB: 6ZWV). Red circles show point mutations (circle size proportional to the log of the 100% occurrence), gray circles show deletions.
Figure S1 N5-1Y-containing sequences in the UK, related to STAR Methods (A) proportion of three subgroups of B.1.1.7 expressed as percentage of total 501Y-containing identifiable sequences. Black line shows dominant form with 501Y and Δ69-70. Blue, orange lines both lack 69-70 and have either wild-type or S982A mutation respectively. (B) associated mutations for blue (left), orange (middle) and black (right) plotted on Spike protein structure where modeled, with extended modeled N terminus (PDB: 6ZWV). Red circles show point mutations (circle size proportional to the log of the 100% occurrence), gray circles show deletions.CC BY · PubMed Central
Figure 2 mAb binding to WT and N501Y RBD (A) Structural overlay of RBD-Fab complexes in which Fabs have direct contact with N501. The overlay was done by superimposing the RBD. Structures of 38 antibody Fabs in complex with RBD were analyzed. 18 have direct contact with N501 (left), which includes 14 IGHV3-53, 2 IGHV3-66 and two others. 20 Fabs do not have direct contact with N501 of the RBD (right), these include 3 IGHV3-53 or IGHV3-66 Fabs (Table S3). The RBD is shown as a gray surface with the ACE2 binding surface dark green and residue N501 highlighted in yellow-green. The Fabs are shown as spheres positioned at the tips of the CDR-H3s. (B) Examples of optimized binding to the asparagine 501 side chain for antibodies B38 (PDB ID 7BZ5) and 158 (PDB ID 7BEJ). (C) BLI results for potent binders selected from a panel of antibodies (Dejnirattisai et al., 2021) comparing 501Y RBD with 501N RBD. Error bars are derived from curve fitting and may underestimate experimental error. (D) Left pair: BLI data mapped onto the RBD using mabscape (https://github.com/helenginn/mabscape) and the method described in Dejnirattisai et al., 2021. The spheres represent the point at which placing spherical antibodies would optimally predict the BLI competition data. Front and back views of the RBD are depicted as in (A) but with the spheres representing the antibody binding sites colored according to the log of the ratio (KD501Y/KD501N). For white, the ratio is 1; for red, it is <0.1 (i.e., at least 10-fold reduction). Note the strong concordance between the two effects, with 269 being the most strongly affected. The nearby pink antibodies are mainly the IGHV3-53 and IGHV3-66 antibodies. See also Table S2.
Figure 2 mAb binding to WT and N501Y RBD (A) Structural overlay of RBD-Fab complexes in which Fabs have direct contact with N501. The overlay was done by superimposing the RBD. Structures of 38 antibody Fabs in complex with RBD were analyzed. 18 have direct contact with N501 (left), which includes 14 IGHV3-53, 2 IGHV3-66 and two others. 20 Fabs do not have direct contact with N501 of the RBD (right), these include 3 IGHV3-53 or IGHV3-66 Fabs (Table S3). The RBD is shown as a gray surface with the ACE2 binding surface dark green and residue N501 highlighted in yellow-green. The Fabs are shown as spheres positioned at the tips of the CDR-H3s. (B) Examples of optimized binding to the asparagine 501 side chain for antibodies B38 (PDB ID 7BZ5) and 158 (PDB ID 7BEJ). (C) BLI results for potent binders selected from a panel of antibodies (Dejnirattisai et al., 2021) comparing 501Y RBD with 501N RBD. Error bars are derived from curve fitting and may underestimate experimental error. (D) Left pair: BLI data mapped onto the RBD using mabscape (https://github.com/helenginn/mabscape) and the method described in Dejnirattisai et al., 2021. The spheres represent the point at which placing spherical antibodies would optimally predict the BLI competition data. Front and back views of the RBD are depicted as in (A) but with the spheres representing the antibody binding sites colored according to the log of the ratio (KD501Y/KD501N). For white, the ratio is 1; for red, it is <0.1 (i.e., at least 10-fold reduction). Note the strong concordance between the two effects, with 269 being the most strongly affected. The nearby pink antibodies are mainly the IGHV3-53 and IGHV3-66 antibodies. See also Table S2.CC BY · PubMed Central
Figure 3 Molecular mechanisms of escape and comparison of N501Y RBD/269 Fab and RBD/scFv269 complexes (A) CDR-L1 (thin sticks) positions of a panel of V3-53 Fabs relative to N501 on the RBD (surface, with N501 highlighted in green). (B) The side chain of N501 makes extensive contacts with residues from CDR-L1 in the RBD-158 Fab complex (left, PDB: 7BEJ). In the right panel, N501 does not make any contact with p2c-2f11 Fab (PDB: 7CDI) whose LC is most similar in sequence and has the same CDR-L1, L2, and L3 lengths to mAb 222 shown by a blast of the LC of 222 against the PDB. The orientation and position of Y501 in the N501Y RBD/269 Fab complex is shown by overlapping the RBDs in both panels. (C) Crystallographic structures of RBD/Fab 269, N501Y RBD/Fab 269, and RBD/scFv269. Overlay of Cαs of N501Y RBD/Fab 269 (blue) with RBD/Fab 269 (cyan) and RBD/scFv269 (salmon) by superimposing the RBDs of the three complexes (PDB: 7NEG, 7NEH, 7BEM, respectively). (D) Structure changes in the 496–501 loop of the RBD and the CDR-L1 loop that contacts the mutation site. (E) Structural differences of the CDR-L3 loops between the three complexes. See also Tables S1 and S3.
Figure 3 Molecular mechanisms of escape and comparison of N501Y RBD/269 Fab and RBD/scFv269 complexes (A) CDR-L1 (thin sticks) positions of a panel of V3-53 Fabs relative to N501 on the RBD (surface, with N501 highlighted in green). (B) The side chain of N501 makes extensive contacts with residues from CDR-L1 in the RBD-158 Fab complex (left, PDB: 7BEJ). In the right panel, N501 does not make any contact with p2c-2f11 Fab (PDB: 7CDI) whose LC is most similar in sequence and has the same CDR-L1, L2, and L3 lengths to mAb 222 shown by a blast of the LC of 222 against the PDB. The orientation and position of Y501 in the N501Y RBD/269 Fab complex is shown by overlapping the RBDs in both panels. (C) Crystallographic structures of RBD/Fab 269, N501Y RBD/Fab 269, and RBD/scFv269. Overlay of Cαs of N501Y RBD/Fab 269 (blue) with RBD/Fab 269 (cyan) and RBD/scFv269 (salmon) by superimposing the RBDs of the three complexes (PDB: 7NEG, 7NEH, 7BEM, respectively). (D) Structure changes in the 496–501 loop of the RBD and the CDR-L1 loop that contacts the mutation site. (E) Structural differences of the CDR-L3 loops between the three complexes. See also Tables S1 and S3.CC BY · PubMed Central
Figure S2 Electron density maps for residue 501, related to Figure 3 Electron density maps for RBDN501Y/Fab269 with residue 501 refined as a tyrosine in (A) and as an asparagine in (B). 2Fo-Fc maps are contoured at 1.2 σ and colored in blue in both panels. The negative density (red) in (A) is contoured at −3 σ, and the positive density (green) in (B) at 3 σ.
Figure S2 Electron density maps for residue 501, related to Figure 3 Electron density maps for RBDN501Y/Fab269 with residue 501 refined as a tyrosine in (A) and as an asparagine in (B). 2Fo-Fc maps are contoured at 1.2 σ and colored in blue in both panels. The negative density (red) in (A) is contoured at −3 σ, and the positive density (green) in (B) at 3 σ.CC BY · PubMed Central
Figure 4 Neutralization of SARS-CoV-2 strains Victoria and B.1.1.7 by mAb (A) Neutralization curves of potent (FRNT50 <100 ng/mL) anti-RBD antibodies including those expressing the public heavy chain VH3-53 (150, 158, 175, 222, 269). (B) Regeneron antibodies, REGN10933 and REGN10987, and AstraZeneca antibodies, AZD8895 and AZD1061, are included for comparison. Neutralization of SARS-CoV-2 was measured using a focus reduction neutralization test (FRNT). Data are shown as mean ± SEM. See also Table S2.
Figure 4 Neutralization of SARS-CoV-2 strains Victoria and B.1.1.7 by mAb (A) Neutralization curves of potent (FRNT50 <100 ng/mL) anti-RBD antibodies including those expressing the public heavy chain VH3-53 (150, 158, 175, 222, 269). (B) Regeneron antibodies, REGN10933 and REGN10987, and AstraZeneca antibodies, AZD8895 and AZD1061, are included for comparison. Neutralization of SARS-CoV-2 was measured using a focus reduction neutralization test (FRNT). Data are shown as mean ± SEM. See also Table S2.CC BY · PubMed Central
Figure 5 Neutralization activity of convalescent plasma and vaccine sera (A) Neutralization titers of 34 convalescent plasma samples collected 4–9 weeks following infection are shown with the WHONIBSC 20/130 reference serum (B) Neutralization titers of serum from volunteers vaccinated with the AstraZeneca vaccine ADZ1222, samples were taken at (1) 14 days following the second dose (n = 15) and (2) 28 days following the second dose (n = 10). (C) Neutralization titers of serum taken from volunteer healthcare workers recruited following vaccination with Pfizer-BioNTech BNT162b2 (n = 25). Neutralization was measured by FRNT, the Wilcoxon matched-pairs signed-rank test was used for the analysis, and two-tailed p values were calculated; geometric mean values are indicated above each column.
Figure 5 Neutralization activity of convalescent plasma and vaccine sera (A) Neutralization titers of 34 convalescent plasma samples collected 4–9 weeks following infection are shown with the WHONIBSC 20/130 reference serum (B) Neutralization titers of serum from volunteers vaccinated with the AstraZeneca vaccine ADZ1222, samples were taken at (1) 14 days following the second dose (n = 15) and (2) 28 days following the second dose (n = 10). (C) Neutralization titers of serum taken from volunteer healthcare workers recruited following vaccination with Pfizer-BioNTech BNT162b2 (n = 25). Neutralization was measured by FRNT, the Wilcoxon matched-pairs signed-rank test was used for the analysis, and two-tailed p values were calculated; geometric mean values are indicated above each column.CC BY · PubMed Central
Figure 6 Neutralization activity of serum taken from patients suffering infection with B.1.1.7 (A) Neutralization titers of plasma from 13 patients infected with B.1.1.7 at various time points following infection. The days since infection are indicated in each panel. Neutralization was measured by FRNT. (B) Comparison of FRNT50 titers of individual sera against Victoria and B.1.1.7 strains, the number above each column is the geometric mean, the Wilcoxon matched-pairs signed-rank test was used for the analysis, and two-tailed p values were calculated.
Figure 6 Neutralization activity of serum taken from patients suffering infection with B.1.1.7 (A) Neutralization titers of plasma from 13 patients infected with B.1.1.7 at various time points following infection. The days since infection are indicated in each panel. Neutralization was measured by FRNT. (B) Comparison of FRNT50 titers of individual sera against Victoria and B.1.1.7 strains, the number above each column is the geometric mean, the Wilcoxon matched-pairs signed-rank test was used for the analysis, and two-tailed p values were calculated.CC BY · PubMed Central

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  • Probably not a substantial claim. 24
  • It may state two separate claims as one. 24
38 of 38
  • The authors state this as an assumption.

    A further increase in ACE2 affinity will increase the likelihood that stochastic virus attachment events lead to localization for sufficient time to trigger internalization.

    “It is reasonable to assume that a further increase in affinity will increase the likelihood of the stochastic events of virus attachment resulting in localization for sufficient time to trigger, perhaps by the recruitment of additional receptors, internalization of the virus.”
  • The paper relies on this without support.

    The higher affinity of SARS-CoV-2 for ACE2 underlies its greater transmission.

    “the higher affinity for ACE2 of SARS-CoV-2 has been imputed to underlie its greater transmission.”
  • The paper relies on this without support.

    The Pfizer vaccinees had no prior SARS-CoV-2 infection at entry.

    “participants were to the best of their knowledge seronegative at entry”
    “Vaccinees were Health Care Workers, based at Oxford University Hospitals NHS Foundation Trust, not known to have prior infection with SARS-C0V-2.”
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Citations

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Research works printed but not linked: 2

  1. Nelson, 2021, bioRxiv
  2. Zhu, 2021, Cryo-EM Structure of the N501Y SARS-CoV-2 Spike Protein in Complex with a Potent Neutralizing Antibody, bioRxiv

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Metadata

Authors
Supasa, P., Zhou, D., Dejnirattisai, W., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Nutalai, R., Tuekprakhon, A., Wang, B., Paesen, G. C., Slon-Campos, J., López-Camacho, C., Hallis, B., Coombes, N., Bewley, K. R., Charlton, S., Walter, T. S., Barnes, E., Dunachie, S. J., Skelly, D., Lumley, S. F., Baker, N., Shaik, I., Humphries, H. E., Godwin, K., Gent, N., Sienkiewicz, A., Dold, C., Levin, R., Dong, T., Pollard, A. J., Knight, J. C., Klenerman, P., Crook, D., Lambe, T., Clutterbuck, E., Bibi, S., Flaxman, A., Bittaye, M., Belij-Rammerstorfer, S., Gilbert, S., Hall, D. R., Williams, M. A., Paterson, N. G., James, W., Carroll, M. W., Fry, E. E., Mongkolsapaya, J., Ren, J., Stuart, D. I., & Screaton, G. R.
Affiliations
  • Centre for Human Genetics (GB)
  • Diamond Light Source (GB)
  • Public Health England (GB)
  • University of Oxford (GB)
  • Worthing Hospital (GB)
  • Siriraj Hospital (TH)
Corresponding author
  • Mongkolsapaya, Juthathip
  • Ren, Jingshan
  • Stuart, David I.
  • Screaton, Gavin R.
Venue
Cell
Publisher
Elsevier BV
Published
2021-04
Volume
184
Issue
8
Pages
2201-2211.e7
ISSN
0092-8674 (ISSN-L)
OpenAlex
W3129558828
Cited by
460
References
60
Citations by year
2025: 15 · 2024: 24 · 2023: 60 · 2022: 171 · 2021: 188
FWCI
35.16
Type
journal article
Language
en
Open access
Locations
  • Cell (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Greater South Information System
Funders
  • UK Research and Innovation
  • MRC (MR/N00065X/1)
  • China Academy of Chinese Medical Sciences (2018-I2M-2-002)
  • National Institute for Health Research (203141/Z/16/Z, 095541/A/11/Z, 090532/Z/09/Z)
  • Coalition for Epidemic Preparedness Innovations
  • Department of Health and Social Care
  • NIHR Oxford Biomedical Research Centre
  • National Institutes of Health (U19 I082360, WT204969/Z/16/Z)
  • Wellcome Trust (101122/Z/13/Z)
  • Cancer Research UK (C375/A17721)
  • Chinese Academy of Medical Sciences
  • Public Health England
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, B.1.1.7 variant, N501Y mutation, spike protein, antibody neutralization, antibody escape, monoclonal antibodies, convalescent sera, ACE2 binding
MeSH terms
COVID-19, SARS-CoV-2, Animals, Antibodies, Monoclonal, Antibodies, Viral, Chlorocebus aethiops, Cricetulus, Humans, Protein Binding, Structure-Activity Relationship, Vero Cells, CHO Cells, Antibodies, Neutralizing, HEK293 Cells, Pandemics, Spike Glycoprotein, Coronavirus

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