Primary exposure to SARS-CoV-2 variants elicits convergent epitope specificities, immunoglobulin V gene usage and public B cell clones

  1. Noemia S. Lima
  2. Maryam Musayev
  3. Timothy S. Johnston
  4. Danielle A. Wagner
  5. Amy R. Henry
  6. Lingshu Wang
  7. Eun Sung Yang
  8. Yi Zhang
  9. Kevina Birungi
  10. Walker P. Black
  11. Sijy O’Dell
  12. Stephen D. Schmidt
  13. Damee Moon
  14. Cynthia G. Lorang
  15. Bingchun Zhao
  16. Man Chen
  17. Kristin L. Boswell
  18. Jesmine Roberts-Torres
  19. Rachel L. Davis
  20. Lowrey Peyton
  21. Sandeep R. Narpala
  22. Sarah O’Connell
  23. Leonid Serebryannyy
  24. Jennifer Wang
  25. Alexander Schrager
  26. Chloe Adrienna Talana
  27. Geoffrey Shimberg
  28. Kwanyee Leung
  29. Wei Shi
  30. Rawan Khashab
  31. Asaf Biber
  32. Tal Zilberman
  33. Joshua Rhein
  34. Sara Vetter
  35. Afeefa Ahmed
  36. Laura Novik
  37. Alicia Widge
  38. Ingelise Gordon
  39. Mercy Guech
  40. I-Ting Teng
  41. Emily Phung
  42. Tracy J. Ruckwardt
  43. Amarendra Pegu
  44. John Misasi
  45. Nicole A. Doria-Rose
  46. Martin Gaudinski
  47. Richard A. Koup
  48. Peter D. Kwong
  49. Adrian B. McDermott
  50. Sharon Amit
  51. Timothy W. Schacker
  52. Itzchak Levy
  53. John R. Mascola
  54. Nancy J. Sullivan
  55. Chaim A. Schramm
  56. Daniel C. Douek

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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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  1. Version published to 10.1038/s41467-022-35456-2
  2. Version published to 10.1101/2022.03.28.486152v2 on bioRxiv
  3. ScreenIT

    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

    EthicsIRB: 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 variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    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 IgG
    suggested: None
    Directly 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)
    CD14
    suggested: (BD Biosciences Cat# 750381, RRID:AB_2874552)
    CD3
    suggested: (BD Biosciences Cat# 563546, RRID:AB_2744387)
    CD4
    suggested: (BD Biosciences Cat# 566104, RRID:AB_2739506)
    CD8a
    suggested: (Abcam Cat# ab34397, RRID:AB_2291359)
    CD45RA
    suggested: (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)
    CD56
    suggested: (DSHB Cat# 5.1H11, RRID:AB_531857)
    CCR7
    suggested: (GenWay Biotech Inc. Cat# GWB-EA1DA7, RRID:AB_10269678)
    CD69
    suggested: (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-histidine
    suggested: None
    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.
    A19-61.1
    suggested: (ABclonal Cat# A19611, RRID:AB_2862699)
    A23-80.1
    suggested: None
    CR3022
    suggested: None
    The 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-BV510
    suggested: None
    CD56-BV510
    suggested: None
    CD14-BV510
    suggested: None
    CD3-APC-Cy7
    suggested: None
    Samples 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-C
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    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.
    B1-182
    suggested: None
    Software and Algorithms
    SentencesResources
    Data were acquired on a modified BD FACSymphony and analyzed using FlowJo software (version 10.7.1).
    FlowJo
    suggested: (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 Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    The resulting sequences were annotated using SONAR v4.2 (81) in single-cell mode.
    SONAR
    suggested: (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:

    IdentifierStatusTitle
    NCT00067054RecruitingApheresis 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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  4. Version published to 10.1101/2022.03.28.486152v1 on bioRxiv