. 2021 Apr 15;184(8):2201-2211.e7.

doi: 10.1016/j.cell.2021.02.033. Epub 2021 Feb 18.

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

Piyada Supasa¹, Daming Zhou², Wanwisa Dejnirattisai¹, Chang Liu³, Alexander J Mentzer⁴, Helen M Ginn⁵, Yuguang Zhao², Helen M E Duyvesteyn², Rungtiwa Nutalai¹, Aekkachai Tuekprakhon¹, Beibei Wang¹, Guido C Paesen², Jose Slon-Campos¹, César López-Camacho¹, Bassam Hallis⁶, Naomi Coombes⁶, Kevin R Bewley⁶, Sue Charlton⁶, Thomas S Walter², Eleanor Barnes⁷, Susanna J Dunachie⁸, Donal Skelly⁹, Sheila F Lumley¹⁰, Natalie Baker⁶, Imam Shaik⁶, Holly E Humphries⁶, Kerry Godwin⁶, Nick Gent⁶, Alex Sienkiewicz⁶, Christina Dold¹¹, Robert Levin¹², Tao Dong¹³, Andrew J Pollard¹¹, Julian C Knight¹⁴, Paul Klenerman⁷, Derrick Crook¹⁵, Teresa Lambe¹⁶, Elizabeth Clutterbuck¹¹, Sagida Bibi¹¹, Amy Flaxman¹⁶, Mustapha Bittaye¹⁶, Sandra Belij-Rammerstorfer¹⁶, Sarah Gilbert¹⁶, David R Hall⁵, Mark A Williams⁵, Neil G Paterson⁵, William James¹⁷, Miles W Carroll¹⁸, Elizabeth E Fry², Juthathip Mongkolsapaya¹⁹, Jingshan Ren²⁰, David I Stuart²¹, Gavin R Screaton²²

Affiliations

¹ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
² Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
³ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
⁴ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁵ Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
⁶ National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.
⁷ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
⁸ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
⁹ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
¹⁰ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹¹ NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
¹² Worthing Hospital, Worthing, UK.
¹³ Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
¹⁴ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
¹⁵ Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁶ Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁷ Sir William Dunn School of Pathology University of Oxford, Oxford, UK.
¹⁸ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.
¹⁹ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand. Electronic address: jmongkol@well.ox.ac.uk.
²⁰ Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK. Electronic address: ren@strubi.ox.ac.uk.
²¹ Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK. Electronic address: dave@strubi.ox.ac.uk.
²² Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK. Electronic address: gavin.screaton@medsci.ox.ac.uk.

PMID: 33743891
PMCID: PMC7891044
DOI: 10.1016/j.cell.2021.02.033

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

Piyada Supasa et al. Cell. 2021.

. 2021 Apr 15;184(8):2201-2211.e7.

doi: 10.1016/j.cell.2021.02.033. Epub 2021 Feb 18.

Authors

Affiliations

¹ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
² Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK.
³ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
⁴ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁵ Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
⁶ National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.
⁷ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
⁸ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Centre For Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
⁹ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, Oxford, UK; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
¹⁰ Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹¹ NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
¹² Worthing Hospital, Worthing, UK.
¹³ Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK; MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
¹⁴ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
¹⁵ Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁶ Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁷ Sir William Dunn School of Pathology University of Oxford, Oxford, UK.
¹⁸ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.
¹⁹ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Siriraj Center of Research Excellence in Dengue & Emerging Pathogens, Dean Office for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand. Electronic address: jmongkol@well.ox.ac.uk.
²⁰ Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK. Electronic address: ren@strubi.ox.ac.uk.
²¹ Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK. Electronic address: dave@strubi.ox.ac.uk.
²² Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK. Electronic address: gavin.screaton@medsci.ox.ac.uk.

PMID: 33743891
PMCID: PMC7891044
DOI: 10.1016/j.cell.2021.02.033

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.

Keywords: B.1.1.7; IGHV3-53; Kent; SARS-CoV-2; antibody; escape; neutralization; variant.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests G.R.S. sits on the GSK Vaccines Scientific Advisory Board. Oxford University holds intellectual property related to the Oxford-AstraZeneca vaccine. A.J.P. is Chair of UK Department Health and Social Care’s (DHSC) Joint Committee on Vaccination & Immunisation (JCVI) but does not participate in the JCVI COVID19 committee and is a member of the WHO’s SAGE. S.G. is co-founder of Vaccitech (collaborators in the early development of this vaccine candidate) and named as an inventor on a patent covering use of ChAdOx1-vectored vaccines and a patent application covering this SARS-CoV-2 vaccine. T.L. is named as an inventor on a patent application covering this SARS-CoV-2 vaccine and consultant to Vaccitech. The views expressed in this article do not necessarily represent the views of DHSC, JCVI, or WHO. The University of Oxford has entered into a partnership with AstraZeneca on coronavirus vaccine development. The University of Oxford has protected intellectual property disclosed in this publication.

Figures

**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 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 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 (K_D501Y/K_D501N). 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 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 S2**
Electron density maps for residue 501, related to Figure 3 Electron density maps for RBD_N501Y/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 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 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 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.

See this image and copyright information in PMC

Comment in

SARS-CoV-2 variants: a new challenge to convalescent serum and mRNA vaccine neutralization efficiency.
Li M, Lou F, Fan H. Li M, et al. Signal Transduct Target Ther. 2021 Apr 10;6(1):151. doi: 10.1038/s41392-021-00592-6. Signal Transduct Target Ther. 2021. PMID: 33839737 Free PMC article. No abstract available.

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

Comment in

References

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Miscellaneous