Omicron BA.1 and BA.2 are antigenically distinct SARS-CoV-2 variants

  1. Anna Z. Mykytyn
  2. Melanie Rissmann
  3. Adinda Kok
  4. Miruna E. Rosu
  5. Debby Schipper
  6. Tim I. Breugem
  7. Petra B. van den Doel
  8. Felicity Chandler
  9. Theo Bestebroer
  10. Maurice de Wit
  11. Martin E. van Royen
  12. Richard Molenkamp
  13. Bas B. Oude Munnink
  14. Rory D. de Vries
  15. Corine GeurtsvanKessel
  16. Derek J. Smith
  17. Marion P. G. Koopmans
  18. Barry Rockx
  19. Mart M. Lamers
  20. Ron Fouchier
  21. Bart L. Haagmans

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Abstract

The emergence and rapid spread of SARS-CoV-2 variants may impact vaccine efficacy significantly 1 . The Omicron variant termed BA.2, which differs genetically substantially from BA.1, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed 2,3 . Here, we used antigenic cartography to quantify and visualize antigenic differences between SARS-CoV-2 variants using hamster sera obtained after primary infection. Whereas early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape (vaccine-induced) antibody responses as a result of different antigenic characteristics. Close monitoring of the antigenic changes of SARS-CoV-2 using antigenic cartography can be helpful in the selection of future vaccine strains.

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  1. ScreenIT

    SciScore for 10.1101/2022.02.23.481644: (What is this?)

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

    Table 1: Rigor

    EthicsField Sample Permit: Research was conducted under a project license from the Dutch competent authority and the study protocol (#17-4312) was approved by the institutional Animal Welfare Body.
    Euthanasia Agents: Hamsters were euthanized by cardiac puncture under isoflurane anesthesia and cervical dislocation.
    IRB: This study was approved by the institutional review board of the Erasmus MC (medical ethical committee, MEC-2020-0264).
    Sex as a biological variableHamster infections: Female Syrian golden hamsters (Mesocricetus auratus; 6 weeks old; Janvier, France) were handled in an ABSL-3 biocontainment laboratory.
    RandomizationFor unbiased experiments, all animals were randomly assigned to experimental groups.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Two hours posti-infection, cells were washed three times with Opti-MEM I (1×) + GlutaMAX and replaced with medium containing anti-VSV-G neutralizing antibody (Absolute Antibody).
    anti-VSV-G neutralizing antibody
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Viruses and cell lines: HEK-293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FCS, sodium pyruvate (1 mM,
    HEK-293T
    suggested: None
    VeroE6 cells were maintained in DMEM supplemented with 10% FCS, HEPES (20 mM, Lonza) and sodium pyruvate (1 mM), penicillin (100 IU/mL), and streptomycin (100 IU/mL).
    VeroE6
    suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
    Calu-3 cells were maintained in Eagle’s minimal essential medium (ATCC) supplemented with 10% FCS, penicillin (100 IU/mL), and streptomycin (100 IU/mL).
    Calu-3
    suggested: None
    The 614G virus used for hamster infections was cultured to passage 3 on Vero cells and its S protein did not contain additional mutations.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
    Recombinant DNA
    SentencesResources
    Twenty four hours post-infection cells were infected with pseudoviruses expressing VSV-G.
    VSV-G
    suggested: RRID:Addgene_138479)
    Software and Algorithms
    SentencesResources
    The PRNT50 was calculated using Graphpad Prism 9 based on non-linear regression.
    Graphpad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.

  2. Version published to 10.1101/2022.02.23.481644 on bioRxiv