Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones
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Abstract
An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. However, the basis for such cross-protection at the molecular level is incompletely understood. Here, we characterized the repertoire and epitope specificity of antibodies elicited by infection with the Beta, Gamma and WA1 ancestral variants and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a method to obtain immunoglobulin sequences with concurrent rapid production and functional assessment of monoclonal antibodies from hundreds of single B cells sorted by flow cytometry. Infection with any variant elicited similar cross-binding antibody responses exhibiting a conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may account for the continued efficacy of vaccines based on a single ancestral variant.
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SciScore for 10.1101/2022.03.28.486152: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: NIAID), National Institutes of Health protocol VRC 200 (NCT00067054) in compliance with the NIH Institutional Review Board (IRB) approved protocol and procedures.
Consent: All subjects met protocol eligibility criteria and agreed to participate in the study by signing the NIH IRB approved informed consent.
Field Sample Permit: Research studies with these samples were conducted by protecting the rights and privacy of the study participants.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources Diluted antibody samples were applied and incubated 1 hr at 37°C followed by 6 washes with … SciScore for 10.1101/2022.03.28.486152: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: NIAID), National Institutes of Health protocol VRC 200 (NCT00067054) in compliance with the NIH Institutional Review Board (IRB) approved protocol and procedures.
Consent: All subjects met protocol eligibility criteria and agreed to participate in the study by signing the NIH IRB approved informed consent.
Field Sample Permit: Research studies with these samples were conducted by protecting the rights and privacy of the study participants.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources Diluted antibody samples were applied and incubated 1 hr at 37°C followed by 6 washes with PBS-T; plates were the incubated with HRP-conjugated anti-human IgG (Jackson ImmunoResearch) diluted 1:10,000 in B3T buffer for 1 h at 37°C. anti-human IgGsuggested: NoneDirectly conjugated antibodies purchased from BD Biosciences include CD19 PE-Cy5 (Clone HIB19; cat. 302210), CD14 BB660 (Clone M0P9; cat. 624925), CD3 BUV395 (Clone UCHT1; cat. 563546), CD4 BV480 (Clone SK3; cat. 566104), CD8a BUV805 (Clone SK1; cat. 612889), CD45RA BUV496 (Clone H100; cat. 750258) CD14suggested: (BD Biosciences Cat# 750381, RRID:AB_2874552)CD3suggested: (BD Biosciences Cat# 563546, RRID:AB_2744387)CD4suggested: (BD Biosciences Cat# 566104, RRID:AB_2739506)CD8asuggested: (Abcam Cat# ab34397, RRID:AB_2291359)CD45RAsuggested: (BD Biosciences Cat# 750258, RRID:AB_2874456)Antibodies from Biolegend include CD16 BV570 (Clone 3G8; cat. 302036), CD56 BV750 (Clone 5.1H11; cat. 362556), CCR7 BV605 (Clone G043H7; cat. 353244) and CD69 APC-Fire750 (Clone FN50; cat. 310946) CD56suggested: (DSHB Cat# 5.1H11, RRID:AB_531857)CCR7suggested: (GenWay Biotech Inc. Cat# GWB-EA1DA7, RRID:AB_10269678)CD69suggested: (BioLegend Cat# 310946, RRID:AB_2616709)Anti-histidine antibody was immobilized on Series S Sensor Chip CM5 (Cytiva) through primary amine coupling using a His capture kit (Cytiva). Anti-histidinesuggested: NoneHuman IgG monoclonal antibodies (mAb) used for these analyses include: B1-182, CB6, A20-29.1, A19-46.1, LY-COV555, A19-61.1, S309, A23-97.1, A19-30.1, A23-80.1, and CR3022. A19-61.1suggested: (ABclonal Cat# A19611, RRID:AB_2862699)A23-80.1suggested: NoneCR3022suggested: NoneThe antibodies used in the staining cocktail were: CD8-BV510 (Biolegend, clone RPA-T8, cat# 301048), CD56-BV510 (Biolegend, clone HCD56, cat# 318340), CD14-BV510 (Biolegend, clone M5E2, cat# 301842), CD16-BUV496 (BD Biosciences, clone 3G8, cat# 612944), CD3-APC-Cy7 (BD Biosciences, clone SP34-2, cat# 557757), CD19-PECy7 CD8-BV510suggested: NoneCD56-BV510suggested: NoneCD14-BV510suggested: NoneCD3-APC-Cy7suggested: NoneSamples sorted for 10x Genomics single-cell RNAseq were individually labelled with an oligonucleotide-linked hashing antibody (Totalseq-C, Biolegend) in addition to the staining cocktail and sorted into a single tube according to the gating strategy shown in Fig. Totalseq-Csuggested: NoneExperimental Models: Organisms/Strains Sentences Resources Human IgG monoclonal antibodies (mAb) used for these analyses include: B1-182, CB6, A20-29.1, A19-46.1, LY-COV555, A19-61.1, S309, A23-97.1, A19-30.1, A23-80.1, and CR3022. B1-182suggested: NoneSoftware and Algorithms Sentences Resources Data were acquired on a modified BD FACSymphony and analyzed using FlowJo software (version 10.7.1). FlowJosuggested: (FlowJo, RRID:SCR_008520)Results are reported as percent competition and statistical analysis was performed using unpaired, two-tailed t-test (Graphpad Prism v.8.3.1). Graphpad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)The resulting sequences were annotated using SONAR v4.2 (81) in single-cell mode. SONARsuggested: (Edgerton Digital Collections, RRID:SCR_005962)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:LIMITATIONS OF THE STUDY: Our study is limited by sampling of paired heavy and light chain sequences from fewer than 1,000 SARS-CoV-2-specific B cells across 13 individuals. This scale is small in comparison to bulk IG sequencing studies (32, 61) and even a few single-cell studies (58, 60, 75). We are also limited in our ability to make functional repertoire comparisons due to varied sorting strategies and differences in functional assays used to assess isolated mAbs. Moreover, our cohort was sampled only at a single time point early in convalescence and included only one individual with high serum neutralization titers. It will be important to verify that our findings extend to later time points when the antibody repertoire has matured. In addition, further studies are needed to examine the response elicited by more recent SARS-CoV-2 variants such as Delta and Omicron.
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT00067054 Recruiting Apheresis and Specimen Collection Procedures to Obtain Plasm… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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