Mapping the antigenic diversification of SARS-CoV-2

  1. Karlijn van der Straten
  2. Denise Guerra
  3. Marit J. van Gils
  4. Ilja Bontjer
  5. Tom G. Caniels
  6. Hugo D.G. van Willigen
  7. Elke Wynberg
  8. Meliawati Poniman
  9. Judith A. Burger
  10. Joey H. Bouhuijs
  11. Jacqueline van Rijswijk
  12. Wouter Olijhoek
  13. Marinus H. Liesdek
  14. A. H. Ayesha Lavell
  15. Brent Appelman
  16. Jonne J. Sikkens
  17. Marije K. Bomers
  18. Alvin X. Han
  19. Brooke E. Nichols
  20. Maria Prins
  21. Harry Vennema
  22. Chantal Reusken
  23. Menno D. de Jong
  24. Godelieve J. de Bree
  25. Colin A. Russell
  26. Dirk Eggink
  27. Rogier W. Sanders

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

Large-scale vaccination campaigns have prevented countless hospitalizations and deaths due to COVID-19. However, the emergence of SARS-CoV-2 variants that escape from immunity challenges the effectiveness of current vaccines. Given this continuing evolution, an important question is when and how to update SARS-CoV-2 vaccines to antigenically match circulating variants, similar to seasonal influenza viruses where antigenic drift necessitates periodic vaccine updates. Here, we studied SARS-CoV-2 antigenic drift by assessing neutralizing activity against variants-of-concern (VOCs) of a unique set of sera from patients infected with a range of VOCs. Infections with D614G or Alpha strains induced the broadest immunity, while individuals infected with other VOCs had more strain-specific responses. Omicron BA.1 and BA.2 were substantially resistant to neutralization by sera elicited by all other variants. Antigenic cartography revealed that Omicron BA.1 and BA.2 are antigenically most distinct from D614G, associated with immune escape and likely requiring vaccine updates to ensure vaccine effectiveness.

Article activity feed

  1. Version published to 10.1101/2022.01.03.21268582v2 on medRxiv
  2. ScreenIT

    SciScore for 10.1101/2022.01.03.21268582: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    EthicsIRB: The COSCA study, the RECoVERED study and the S3-study were conducted at the Amsterdam University Medical Centres, the Netherlands, and approved the medical ethical review board of the Amsterdam University Medical Centres (NL 73281.018.20, NL73759.018.20, NL73478.029.20, respectively).
    Consent: All individuals provided written informed consent before participating.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Pseudoviruses were procedures by cotransfecting HEK293T cells (American Type Culture Collection, CRL-11268) with the pCR3 SARS-CoV-2-SΔ19 expression plasmid and the pHIV-1NL43 ΔEnv-NanoLuc reporter virus plasmid.
    HEK293T
    suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)
    Shortly, HEK293T/ACE2 cells were kindly provided by P.
    HEK293T/ACE2
    suggested: None
    Recombinant DNA
    SentencesResources
    The spike constructs were ordered as gBlock gene fragments (Integrated DNA Technologies) and cloned SacI and ApaI in the pCR3 SARS-CoV-2–SΔ19 expression plasmid (GenBank: MT449663.1) using Gibson Assembly (Thermo Fisher Scientific).
    pCR3 SARS-CoV-2–SΔ19
    suggested: None
    Pseudoviruses were procedures by cotransfecting HEK293T cells (American Type Culture Collection, CRL-11268) with the pCR3 SARS-CoV-2-SΔ19 expression plasmid and the pHIV-1NL43 ΔEnv-NanoLuc reporter virus plasmid.
    pCR3 SARS-CoV-2-SΔ19
    suggested: None
    pHIV-1NL43 ΔEnv-NanoLuc
    suggested: None
    Software and Algorithms
    SentencesResources
    The inhibitory neutralization titres (ID50) were determined as the serum dilution at which infectivity was inhibited by 50%, using a nonlinear regression curve fit (GraphPad Prism software version 8.3).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Spider plots were made in Excel 2016.
    Excel
    suggested: None

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    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.

  3. Version published to 10.1101/2022.01.03.21268582v1 on medRxiv