Cross-reactive antibodies after SARS-CoV-2 infection and vaccination
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands
- Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Université Paris-Saclay, INSERM, CEA, France
- Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands
- Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands
- National Institute for Public Health and the Environment, RIVM, Netherlands
- Department of Infectious Diseases, Public Health Service of Amsterdam, GGD, Netherlands
- Department of Internal Medicine, Tergooi Hospital, Netherlands
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Australia
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, United States
Figures
Figure 1 with 1 supplement
SARS-CoV-2 antibody response in COVID-19 patients.
(a) IgG binding of sera to SARS-CoV-2 S protein measured with a custom Luminex assay. Convalescent COVID-19 sera (COVID-19, blue dots, n = 50) were compared to sera of pre-pandemic healthy donors …
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Figure 1—source data 1
Source data of all panels of Figure 1.
- https://cdn.elifesciences.org/articles/70330/elife-70330-fig1-data1-v2.xlsx
Figure 1—figure supplement 1
Principal component analysis showing the influence of sex and disease severity on the SARS-CoV-2 IgG response.
A principal component analysis was performed using the following variables: IgG antibodies to SARS-CoV-2 S protein (S), RBD and nucleocapsid protein (N), SARS-CoV-2 neutralization, age and days …
Figure 2 with 6 supplements
Cross-reactivity to hCoV S proteins in convalescent COVID-19 sera.
(a) IgG binding to all hCoV S proteins measured with a custom Luminex assay in convalescent COVID-19 sera (COVID-19, blue dots, n = 50) were compared to pre-pandemic sera from healthy donors (HD, …
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Figure 2—source data 1
Source data of all panels of Figure 2.
- https://cdn.elifesciences.org/articles/70330/elife-70330-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Antibody reactivity to tetanus toxoid in convalescent COVID-19 sera and depletion of antibodies binding to all proteins in healthy donors.
(a) IgG binding to tetanus toxoid protein measured with a custom Luminex assay in sera of convalescent COVID-19 sera (COVID-19, orange dots, n = 50) compared to sera of pre-pandemic healthy donors …
Figure 2—figure supplement 2
Correlation between sequence identity and reduction of cross-reactive antibodies in depletion assay for S, S1, and S2.
The correlation between S protein (a), S1 subdomain (b), and S2 subdomain (c) sequence identity of SARS-CoV-2 with the different hCoV S proteins (also shown in Supplementary file 2) and the …
Figure 2—figure supplement 3
Spearman’s correlations between SARS-CoV-2 neutralization and antibody reactivity to hCoV S and tetanus toxoid.
Figure 2—figure supplement 4
Principal component analysis including SARS-CoV-2 binding antibodies, neutralization, clinical characteristics, and cross-reactivity.
The principal component analysis was performed using the following variables: IgG binding to all hCoV S proteins including SARS-CoV-2, IgG binding to SARS-CoV-2 RBD and nucleocapsid protein (N), …
Figure 2—figure supplement 5
Native PAGE analysis of hCoV proteins.
Photographs of colloidal blue stainings of 4–12% NuPAGE Bis-Tris gels showing protein integrity and composition of the trimeric human coronavirus spike proteins. Marker sizes are indicated in kilo …
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Figure 2—figure supplement 5—source data 1
Raw, unedited, and uncropped pictures of colloidal blue stainings of 4–12% NuPAGE Bis-Tris gels, and uncropped pictures with the sizes of the marker in kilo Dalton and the relevant bands indicated.
The numbers match with the numbers in Figure 2—figure supplement 5: (M) Marker HMW-Native Protein Mixture; (1) SARS-CoV spike; (2) MERS-CoV spike; (3) hCoV-229E spike; (4) hCoV-OC43 spike; (5) SARS-CoV-2 spike; (6) hCoV-HKU1 spike; and (7) hCoV-NL63 spike.
- https://cdn.elifesciences.org/articles/70330/elife-70330-fig2-figsupp5-data1-v2.zip
Figure 2—figure supplement 6
Reproducibility of the Luminex assay.
The reproducibility of the custom Luminex assay is shown by plotting data from two independent assays performed on different days with the same samples. The data on the Y axis are found in Figure 3, …
Figure 3 with 2 supplements
Depletion of S1 and S2 subdomain-specific cross-reactivity in convalescent COVID-19 sera.
Percent decrease of IgG binding to all other hCoV S proteins in convalescent COVID-19 sera (n = 50) after depletion with soluble recombinant monomeric SARS-CoV-2 S1 or S2 subdomains. Bars represent …
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Figure 3—source data 1
Source data of all panels of Figure 3.
- https://cdn.elifesciences.org/articles/70330/elife-70330-fig3-data1-v2.xlsx
Figure 3—figure supplement 1
Raw data and control data from depletion assays on convalescent COVID-19 sera.
(a) Median fluorescent intensity (MFI) values of IgG binding to all hCoV S proteins and tetanus toxoid control protein, measured with a custom Luminex assay in sera of convalescent COVID-19 sera (n …
Figure 3—figure supplement 2
Raw data and control data from depletion assays on healthy donor sera.
(a) Median fluorescent intensity (MFI) values of IgG binding to all hCoV S proteins (top and middle rows) and control proteins (bottom row) measured with a custom Luminex assay in sera of …
Figure 4 with 2 supplements
Cross-reactivity and depletion of cross-reactivity to hCoV S proteins in immunized macaques.
(a) SARS-CoV-2 S protein-specific IgG binding and cross-reactive IgG binding to SARS-CoV S protein at week 0 (pre-immunization baseline) and week 12 (after a total of three immunizations), measured …
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Figure 4—source data 1
Source data of all panels of Figure 4.
- https://cdn.elifesciences.org/articles/70330/elife-70330-fig4-data1-v2.xlsx
Figure 4—figure supplement 1
Antibodies binding to hCoV S and tetanus toxoid in immunized cynomolgus macaques over time.
(a) IgG response over time in serum of six cynomolgus macaques immunized at weeks 0, 4, and 10 with a SARS-CoV-2 spike nanoparticle vaccine, measured at 1:50,000 serum dilution for SARS-CoV-2 and …
Figure 4—figure supplement 2
Reactivity and depletion of antibodies to hCoV S proteins and tetanus toxoid in immunized cynomolgus macaques.
(a) Median fluorescent intensity (MFI) values of IgG binding to all hCoV S proteins and tetanus toxoid control protein with and without depletion with soluble recombinant SARS-CoV-2 S protein, …
Figure 5 with 1 supplement
Cross-reactivity to hCoV S proteins following COVID-19 mRNA vaccination in human IgG binding to hCoVs S proteins measured with a custom Luminex assay in 1:100,000 diluted serum of 45 SARS-CoV-2-naïve individuals at baseline (gray dots), 3 weeks after their first vaccination (blue dots) and 4 weeks after their second vaccination (dark blue dots) with Pfizer-BioNTech mRNA vaccine.
IgG binding to tetanus toxoid control protein is shown in Figure 5—figure supplement 1. Friedman test with Dunn’s multiple comparisons test was used to compare medians of different time points and …
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Figure 5—source data 1
Source data of all panels of Figure 5.
- https://cdn.elifesciences.org/articles/70330/elife-70330-fig5-data1-v2.xlsx
Figure 5—figure supplement 1
Antibodies binding to tetanus toxoid protein following Pfizer-BioNTech mRNA vaccination in humans.
IgG binding to tetanus toxoid control protein measured with a custom Luminex assay in 1:100,000 diluted sera of vaccinated SARS-CoV-2-naïve individuals at baseline, at 3 weeks after their first …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (viral structural protein) | SARS-CoV-2 spike | GenBank | ID: MN908947.3 | N/A |
| Gene (viral structural protein) | SARS-CoV spike | GenBank | ID: ABD72984.1 | N/A |
| Gene (viral structural protein) | MERS-CoV spike | GenBank | ID: AHI48550.1 | N/A |
| Gene (viral structural protein) | hCoV-OC43 spike | GenBank | ID: AAT84362.1 | N/A |
| Gene (viral structural protein) | hCoV-HKU1 spike | GenBank | ID: Q0ZME7 | N/A |
| Gene (viral structural protein) | hCoV-229E spike | GenBank | ID: NP_073551.1 | N/A |
| Gene (viral structural protein) | hCoV-NL63 spike | GenBank | ID: AKT07952.1 | N/A |
| Cell line (human) | FreeStyle HEK293F cells | Thermo Fisher | Cat#: R79007; RRID:CVCL_D603 | N/A |
| Cell line (human) | HEK293T/ACE2 cells | Schmidt et al | Ref: 51 | N/A |
| Biological sample (human) | Human sera, post-infection | Brouwer et al., 2020 | Ref: 52 | N/A |
| Biological sample (human) | Human sera, post-vaccination | Appelman et al. | Ref: 53 | N/A |
| Biological sample (cynomolgus macaque) | Cynomolgus macaque sera | Brouwer et al., 2021 | Ref: 32 | N/A |
| Antibody | Goat-anti-human IgG-PE (goat polyclonal) | Southern Biotech | Cat#: 2040-09;RRID: AB_2795648 | ‘Used at 1.3 µg/mL’ |
| Peptide, recombinant protein | Prefusion-stabilized S protein ectodomain of SARS-CoV-2 | Brouwer et al., 2020 | Ref: 52 | N/A |
| Peptide, recombinant protein | Prefusion-stabilized S protein ectodomain of SARS-CoV | . | Ref: 52 | N/A |
| Peptide, recombinant protein | SARS-CoV-2 nucleocapsid | Sanquin Research | Ref: 54 | Provided by Gestur Vidarsson and Federica Linty of Sanquin Research, Amsterdam, the Netherlands |
| Peptide, recombinant protein | tetanus toxoid | Creative Biolabs | Cat#: Vcar-Lsx003 | N/A |
| Peptide, recombinant protein | SARS-CoV-2 S1 subdomain | ABclonal Biotechnology | Cat#: RP01262 | N/A |
| Peptide, recombinant protein | SARS-CoV2 S2 subdomain | ABclonal Biotechnology | Cat#: RP01267 | N/A |
| Chemical compound, drug | 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide | Thermo Fisher Scientific | Cat#: A35391 | N/A |
| Chemical compound, drug | Sulfo-N-hydroxysulfosuccinimide | Thermo Fisher Scientific | Cat#: A39269 | N/A |
| Chemical compound, drug | Polyethylenimine hydrochloride (PEI) MAX | Polysciences | Cat#: 24765-1 | N/A |
| Software, algorithm | GraphPad Prism 8.3.0 | GraphPad | N/A | N/A |
| Software, algorithm | MATLAB 9.6 (R2019a) | MATLAB | N/A | N/A |
| Other | Luminex Magplex beads | Luminex | Cat#: MC10043-01 | N/A |
| Other | MAGPIX | Luminex | Cat#: MAGPIX-XPON4.1-RUO | N/A |
| Other | NiNTA agarose beads | QIAGEN | Cat#: R90115 | N/A |
| Other | Superose6 increase 10/300 GL column | Cytiva | Cat#: 29091596 | N/A |
| Other | 4–12% NuPAGE Bis-Tris | Thermo Fisher | Cat#: NP0321BOX | N/A |
| Other | Novex colloidal blue staining kit | Invitrogen | Cat#: LC6025 | N/A |
| Other | HMW-Native Protein Mixture | GE Healthcare | Cat#: 17044501 | N/A |
| Other | Nano-Glo Luciferase Assay System | Promega | Cat#: N1130 | N/A |
| Other | GloMax | Turner BioSystems | Cat#: 9101-002 | N/A |
Additional files
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Supplementary file 1
Sociodemographics, clinical characteristics, and severity scoring for COVID-19 patients.
- https://cdn.elifesciences.org/articles/70330/elife-70330-supp1-v2.docx
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Supplementary file 2
Sequence identity matrices for the ectodomains of all hCoV S proteins.
Sequence identity matrices were composed of all coronavirus spike proteins in this study. All sequences comprise only the truncated ectodomain of each spike as was used to generate the recombinant proteins. S1, S2, and RBD were defined as noted in the corresponding GenBank sequences (see Materials and methods). Multiple sequence alignments were performed and sequence identities calculated using Clustal Omega 1.2.4.
- https://cdn.elifesciences.org/articles/70330/elife-70330-supp2-v2.docx
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Supplementary file 3
Overview of statistical tests, exact p-values, and 95% confidence intervals.
- https://cdn.elifesciences.org/articles/70330/elife-70330-supp3-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/70330/elife-70330-transrepform1-v2.pdf
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Source data 1
Source data of all panels of all figure supplements.
- https://cdn.elifesciences.org/articles/70330/elife-70330-supp4-v2.xlsx
