. 2021 Aug 5;184(16):4220-4236.e13.

doi: 10.1016/j.cell.2021.06.020. Epub 2021 Jun 17.

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Chang Liu¹, Helen M Ginn², Wanwisa Dejnirattisai³, Piyada Supasa³, Beibei Wang³, Aekkachai Tuekprakhon³, Rungtiwa Nutalai³, Daming Zhou⁴, Alexander J Mentzer⁵, Yuguang Zhao⁴, Helen M E Duyvesteyn⁴, César López-Camacho³, Jose Slon-Campos³, Thomas S Walter⁴, Donal Skelly⁶, Sile Ann Johnson⁷, Thomas G Ritter⁸, Chris Mason⁸, Sue Ann Costa Clemens⁹, Felipe Gomes Naveca¹⁰, Valdinete Nascimento¹⁰, Fernanda Nascimento¹⁰, Cristiano Fernandes da Costa¹¹, Paola Cristina Resende¹², Alex Pauvolid-Correa¹³, Marilda M Siqueira¹², Christina Dold¹⁴, Nigel Temperton¹⁵, Tao Dong¹⁶, Andrew J Pollard¹⁴, Julian C Knight¹⁷, Derrick Crook¹⁸, Teresa Lambe¹⁹, Elizabeth Clutterbuck¹⁴, Sagida Bibi¹⁴, Amy Flaxman¹⁹, Mustapha Bittaye¹⁹, Sandra Belij-Rammerstorfer¹⁹, Sarah C Gilbert¹⁹, Tariq Malik²⁰, Miles W Carroll²¹, Paul Klenerman²², Eleanor Barnes²², Susanna J Dunachie²³, Vicky Baillie²⁴, Natali Serafin²⁴, Zanele Ditse²⁴, Kelly Da Silva²⁴, Neil G Paterson², Mark A Williams², David R Hall², Shabir Madhi²⁴, Marta C Nunes²⁴, Philip Goulder²⁵, Elizabeth E Fry⁴, Juthathip Mongkolsapaya²⁶, Jingshan Ren²⁷, David I Stuart²⁸, Gavin R Screaton²⁹

Affiliations

¹ 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.
² Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK.
³ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁴ Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁵ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁶ 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.
⁷ Peter Medawar Building for Pathogen Research, Oxford, UK.
⁸ Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁹ Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK.
¹⁰ Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil.
¹¹ Fundação de Vigilância em Saúde do Amazonas, Manaus, Amazonas, Brazil.
¹² Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil.
¹³ Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
¹⁴ NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
¹⁵ Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK.
¹⁶ 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.
¹⁷ 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; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁸ Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁹ Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
²⁰ National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.
²¹ 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.
²² 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.
²³ 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; Department of Medicine, University of Oxford, Oxford, UK.
²⁴ South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
²⁵ Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK.
²⁶ 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.
²⁷ Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK. Electronic address: ren@strubi.ox.ac.uk.
²⁸ 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; Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK; Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK. Electronic address: dave@strubi.ox.ac.uk.
²⁹ 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: 34242578
PMCID: PMC8218332
DOI: 10.1016/j.cell.2021.06.020

Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Chang Liu et al. Cell. 2021.

. 2021 Aug 5;184(16):4220-4236.e13.

doi: 10.1016/j.cell.2021.06.020. Epub 2021 Jun 17.

Authors

Affiliations

¹ 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.
² Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK.
³ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁴ Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
⁵ Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁶ 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.
⁷ Peter Medawar Building for Pathogen Research, Oxford, UK.
⁸ Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
⁹ Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK.
¹⁰ Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz, Manaus, Amazonas, Brazil.
¹¹ Fundação de Vigilância em Saúde do Amazonas, Manaus, Amazonas, Brazil.
¹² Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil.
¹³ Laboratorio de vírus respiratórios-IOC/FIOCRUZ, Rio de Janeiro, Brazil; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
¹⁴ NIHR Oxford Biomedical Research Centre, Oxford, UK; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
¹⁵ Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich, Chatham Maritime, Kent ME4 4TB, UK.
¹⁶ 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.
¹⁷ 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; Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁸ Nuffield Department of Medicine, University of Oxford, Oxford, UK.
¹⁹ Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
²⁰ National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK.
²¹ 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.
²² 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.
²³ 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; Department of Medicine, University of Oxford, Oxford, UK.
²⁴ South African Medical Research Council, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Department of Science and Technology/National Research Foundation, South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
²⁵ Peter Medawar Building for Pathogen Research, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK.
²⁶ 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.
²⁷ Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK. Electronic address: ren@strubi.ox.ac.uk.
²⁸ 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; Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK; Division of Structural Biology, The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK. Electronic address: dave@strubi.ox.ac.uk.
²⁹ 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: 34242578
PMCID: PMC8218332
DOI: 10.1016/j.cell.2021.06.020

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone progressive change, with variants conferring advantage rapidly becoming dominant lineages, e.g., B.1.617. With apparent increased transmissibility, variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the United Kingdom. Here we study the ability of monoclonal antibodies and convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2, complement this with structural analyses of Fab/receptor binding domain (RBD) complexes, and map the antigenic space of current variants. Neutralization of both viruses is reduced compared with ancestral Wuhan-related strains, but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2, suggesting that individuals infected previously by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insights for immunization policy with future variant vaccines in non-immune populations.

Keywords: B.1.617; Delta variant; Receptor-binding-domain; SARS-CoV-2; antibody; escape; neutralization; structure; vaccine; variant.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests G.R.S. is 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. 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. S.C.G. is co-founder of Vaccitech (collaborators in the early development of this vaccine candidate) and is named as an inventor on a patent covering use of ChAdOx1-vectored vaccines and a patent application covering this SARS-CoV-2 vaccine (PCT/GB2012/000467). T.L. is named as an inventor on a patent application covering this SARS-CoV-2 vaccine and was a consultant to Vaccitech for an unrelated project during the conduct of the study.

Figures

**Figure 1**
Mutational landscape of the B.1.617 lineage (A) Evolution plot showing trajectories of various mutations in the COG-UK data. Certain mutations were used to select for sequences typically belonging to a given strain: 501Y and Δ69 to select the B.1.1.7 variant; 501Y, 484K, and 417N to select the B.1.351 variant; 501Y, 484K, and 417T to select the P.1 variant; E484Q and L452R to select the B.1.617.1 variant; and T478K and L452R to select the B.1.617.2 variant. (B and C) Schematic showing the locations of amino acid substitutions in B.1.617.1 (B) and B.1.617.2 (C) relative to the ChAdOx1 SARS-CoV-2 sequence, as drawn in previous studies (Dejnirattisai et al., 2021a, 2021b; Supasa et al., 2021; Zhou et al., 2021), with all amino acid mutations above 5% explicitly labeled. Mutations colored in bold were included in the constructs used in this study for the given strain. Under the structural cartoon is a linear representation of S with changes marked for B.1.617.2 live virus, and the three subvariants of B.1.617.1 (a, b, and c) used in this study are detailed. Where there is a charge change introduced by mutations, the change is colored (red when the change makes the mutant more acidic/less basic and blue for more basic/less acidic).

**Figure 2**
Neutralization of B.1.617.1 and B.1.617.2 by mAbs (A) Neutralization of B.1.617.1-B and B.1.617.2 by a panel of 20 potent human mAbs. Neutralization of B.1.617.1-B, as measured by pseudovirus assay, is shown as open triangles, and neutralization of B.1.617 virus, as measured by FRNT, is shown as closed circles; comparison is made with neutralization curves for Victoria, which we have generated previously (Supasa et al., 2021). Neutralization titers are reported in Table S1. (B) Equivalent plots for the Vir, Regeneron, AstraZeneca, Lilly, and Adagio antibodies.

**Figure S1**
Neutralization curves of human mAbs against SARS-CoV-2 pseudotyped lentiviruses expressing full-length S of the B.1.617.1, B.1.617.2, B.1.1.519, and B.1.429 variants, related to Figure 2 FRNT50 titers are given in Table S2.

**Figure 3**
Interaction of B.1.617.1 and B.1.617.2 with ACE2 (A) BLI experiments showing binding of ACE2 to RBDs of B.1.617.1, B.1.617.2, and the T478K mutant. Experimental data for the dilution series are shown in different colors and the models as red lines. (B) Neutralization FRNT50 data (NT50) and BLI data (K_D) mapped onto the RBD using the method described (Dejnirattisai et al., 2021a). The top two panels show the NT50 and K_D values for B.1.617.1, and the bottom two panels show the corresponding values for B.1.617.2. Front and back views of the RBD are shown. Spheres represent the antibody binding sites, colored according to the ratio of the values for B.1.617.1/Wuhan and B.1.617.2/Wuhan. The NT50 plots are colored white for a ratio of 1, and red for less than 0.001 (i.e., at least a 1,000-fold reduction); blue indicates that the binding is increased. For the K_D plots, white denotes a ratio of 1, red less than 0.1 (i.e., at least a 10-fold reduction). Black dots indicate mapped antibodies not included in this analysis, dark green indicates the RBD ACE2 binding surface, and blue shows the mutated residues in each variant. Note the strong agreement between NT50 and K_D. All relevant data are shown in Table S1. (C) K_Ds of RBD/mAbs interactions, measured by BLI for RBDs of Victoria (original), B.1.1.7, B.1.351, P.1, B.1.617.1 and B.1.617.261 (left to right).

**Figure 4**
Crystal structures of RBD-Fab complexes and mechanism of reduced antibody potency to B.1.617 variants (A) Cartoon depiction of the ternary complex of Wuhan RBD (gray, magenta balls represent the mutations in the B.1.617 lineage, and this representation is also used in other panels) with antibody 278 (light chain, blue; heavy chain, red) and antibody 222 (light chain, pale blue; heavy chain, pink), which was used as a crystallization chaperone. The heavy chain of antibody 278 binds to an epitope comprising residue 452, explaining its reduced ability to neutralize B.1.617.1 and B.1.617.2. (B) Simplification of (A), showing CDR loop H3 from antibody 278 (HC, red; LC, blue) interacting with residue 452 on the Wuhan RBD, depicted as a gray surface (the B.1.617 lineage mutations are highlighted in magenta). (C and D) Specifics of antibody 278 interaction. (C) Residue D108 of H3 forms salt bridges with R346, K444 and a hydrogen bond to N450. L452R would sterically inhibit binding. (D) L1 hydrogen bonds via S31 to R346 of the RBD, and Y32 hydrogen bonds to the carbonyl of D442. L3 forms backbone hydrogen bond interactions between Y92 and K444, T94, and G446. (E and F) The binding mode of Fab 384 (E) and its interactions with L452 and E484 of the RBD (F) (PDB: 7BEP). (G) Cartoon depiction of the ternary complex of antibody 253 (HC, red [sugar shown as red sticks]; LC, blue) with mutant L452R RBD (gray, with sugar shown as sticks) with antibody 75 (HC, pink; LC, green) used as a crystallization chaperone. Antibody 253 makes no contact with R452, in line with no observed loss of neutralization. (H) Cartoon depiction of the ternary complex of antibody 253 (HC, red; LC, blue; sugar, red sticks) with T478K RBD (gray) and antibody 45 (HC, pink; LC, green) as a crystallization chaperone. (I and J) Close ups showing 253 interacting with residue 478 in the two mutant RBDs, revealing a modest shift in the binding pose of 253. The L452R mutant RBD is shown in dark gray, with antibody 253 in crimson (HC) and blue (LC), and the T478K RBD is shown in white, with 253 in pink (HC) and pale blue (LC). The Thr and Lysine at 478 are shown as magenta sticks (I). In the T478K mutant RBD, the lysine folds back away from the antibody (J). (K and L) The binding mode of Fab 316 to the RBD (K) and its interactions with E484 of the RBD (L) (PDB: 7BEH).

**Figure S2**
Structure features of SARS-CoV-2 mAbs and effects of B.1.617 mutations, related to Figure 4 (A) In the left panel, comparing the binding modes of fab 278 (red and blue) and Fab 75 (salmon and teal), and the right panel showing the CDR loops of the two Fabs involved in contacts with the RBD. The mutation sites, L452, T478 and E484, of B.1.617 variants are highlighted in magenta. (B) The left panel comparing the binding mode of fab 278 (red and blue) with that of REGN-10987 (salmon and teal, PDB ID 6XDG), and the right panel showing the CDR loops of the two Fabs involved in contacts with the RBD. (C) Electron density maps contoured at 1.0 σ showing the density for R452 in the L452R-RBD/75-253 complex (left), and K478 in the T478K-RBD/45-253 complex. (D), (E) Positions of the mutation sites in the NTD of the B.1.617.1 (D) and B.1.617.2 (E) spike relative to the bound antibody 159 (PDB ID 7NDC). The VhVl domains of mAb 159 are shown as surfaces and the NTD as gray ribbons with mutation and deletion sites marked with green and magenta spheres, respectively.

**Figure 5**
Neutralization of B.1.617.1 by convalescent serum (A) Neutralization of three (A, B, and C) B.1.617.1 pseudotyped lentiviruses by convalescent plasma (n = 34) collected from volunteers 4–9 weeks following SARS-CoV-2 infection; all samples were collected before June 2020 and therefore represent infection before the emergence of B.1.1.7 in the United Kingdom. Comparison is made with neutralization curves for pseudovirus Victoria. (B) Comparison of FRNT50 titers for B.1.617-A, B.1.617-B, and B.1.617-C with Victoria; geometric mean titers are shown above each column. (C and D) Neutralization titers for Victoria and B.1.617-B pseudovirus using (C) B.1.1.7 convalescent serum, (D) B.1.351 convalescent serum, and (C) P.1 convalescent serum. Wilcoxon matched-pairs signed-rank test was used for the analysis, and two-tailed p values were calculated. For the data presented for B.1.1.7 in (B), the sample with extremely high titers was excluded from the statistical analysis.

**Figure S3**
Neutralization curves against SARS-CoV-2 pseudotyped lentiviruses expressing full-length S of Victoria and B.1.617.1 strains by plasma from 18 individuals infected with B.1.1.7, serum from 14 individuals infected with B.1.351, and serum from 17 individuals infected with P.1, related to Figure 5 FRNT50 titers are given in Table S3.

**Figure 6**
Neutralization of B.1.617.2 by convalescent plasma (A) Neutralization of B.1.617.2 live virus, measured by FRNT using the 34 convalescent samples described in Figure 5A; comparison is made with neutralization titers to Victoria, B.1.1.7, B.1.351, and P.1 (filled squares), reported previously in Supasa et al. (2021), Zhou et al. (2021), and Dejnirattisai et al. (2021b), and geometric mean titers are shown above each column. (B–D) Neutralization titers for Victoria, B.1.1.7, B.1.351, P.1, and B.1.617.2 using (B) B.1.1.7 convalescent plasma, (C) B.1.351 convalescent serum, and (D) P.1 convalescent serum. The green arrow in (C) represents serum from an individual who was infected with B.1.351 and subsequently received a vaccine. Wilcoxon matched-pairs signed-rank test was used for the analysis, and two-tailed p values were calculated. For the data presented for B.1.1.7 in (B), the sample with extremely high titers was excluded from the statistical analysis. (E and F) Neutralization curves for Victoria, B.1.1.7, B.1.351, P.1, and B.1.617.2 using convalescent serum from (E) B.1.351- and (F) P.1-infected individuals.

**Figure S4**
Neutralization curves against authentic SARS-CoV-2-Victoria, B.1.1.7, B.1.351, P.1. and B.1.617.2 strains by plasma from 34 individuals during the early pandemic in the United Kingdom and serum from 14 individuals infected with B.1.1.7, related to Figure 6 FRNT50 titers given in Table S3.

**Figure 7**
Neutralization by vaccine serum and mapping variants in antigenic space For the Pfizer vaccine, serum (n = 25) was taken 7–17 days following the second dose of the Pfizer-BioNTech vaccine. For the AstraZenca vaccine, serum was taken 14 or 28 days following the second dose of the Oxford-AstraZeneca vaccine (n = 25). (A) NT50 titers of Pfizer-BioNTech serum against B.1.617.1-B pseudovirus. (B) FRNT50 titers of Oxford-AstraZeneca serum against B.1.617.1-B pseudovirus. (C) FRNT50 titers of Pfizer-BioNTech serum against B.1.617.2 virus. (D) FRNT50 against of Oxford-AstraZeneca serum against B.1.617.2 virus. (A–D) Comparison is made with Victoria pseudo virus (A and B) or wild-type Victoria, B.1.1.7, B.1.351, and P.1 (filled squares), reported previously (Supasa et al., 2021; Zhou et al., 2021; Dejnirattisai et al., 2021b) (C and D). Subsequent panels analyze responses following a single dose of Pfizer vaccine. Serum (n = 20) was taken 28 or 70 days following the first dose of the Pfizer-BioNTech vaccine. (E and F) Comparison of FRNT50 titers for individual samples obtained 28 or 70 days after the first dose against Victoria or B.1.617.2. (G and H) Comparison of percent virus neutralization at serum dilution of 1:20 against SARS-CoV-2 Victoria and B.1.617.2 strains. Mean values are indicated above each column. (E–H) Mann-Whitney unpaired test was used for the analysis in (E) and (G). Wilcoxon matched-pairs signed rank test was used for the analysis in (F) and (H). (I) Map of variants in antigenic space. Wall-eyed stereo pair plots show output of principal-component analysis converting serum/virus strain pair neutralization capacities to antigenic space. Circle size denotes depth along the axis connecting the reader’s nose to the origin. See also Video S1. (J) Positions and charge effects of RBD mutations found in variants of concern. Shown is an incoming ACE2 view of the surface of the RBD, with the footprint of ACE2 shown in green and mutations occurring in variants, including B.1.1.7, P.1, P.1.351, B.1.617.1, and B.1.617.2, shown in a range of other colors.

**Figure S5**
Neutralization curves against SARS-CoV-2 pseudotyped lentiviruses expressing full-length S of Victoria and B.1.617.1 strains by serum from 25 recipients of the Pfizer-BioNTech vaccine and Oxford-AstraZeneca vaccine, related to Figure 7 FRNT50 titers given in Table S4.

**Figure S6**
Neutralization curves against authentic SARS-CoV-2-Victoria, B.1.1.7, B.1.351, P.1, and B.1.617.2 strains by serum from 25 recipients of the Pfizer-BioNTech vaccine and Oxford-AstraZeneca vaccine, related to Figure 7 FRNT50 titers given in Table S4.

See this image and copyright information in PMC

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Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

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Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

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