Memory B cell repertoire from triple vaccinees against diverse SARS-CoV-2 variants

  1. Kang Wang
  2. Zijing Jia
  3. Linilin Bao
  4. Lei Wang
  5. Lei Cao
  6. Hang Chi
  7. Yaling Hu
  8. Qianqian Li
  9. Yunjiao Zhou
  10. Yinan Jiang
  11. Qianhui Zhu
  12. Yongqiang Deng
  13. Pan Liu
  14. Nan Wang
  15. Lin Wang
  16. Min Liu
  17. Yurong Li
  18. Boling Zhu
  19. Kaiyue Fan
  20. Wangjun Fu
  21. Peng Yang
  22. Xinran Pei
  23. Zhen Cui
  24. Lili Qin
  25. Pingju Ge
  26. Jiajing Wu
  27. Shuo Liu
  28. Yiding Chen
  29. Weijin Huang
  30. Qiao Wang
  31. Cheng-Feng Qin
  32. Youchun Wang
  33. Chuan Qin
  34. Xiangxi Wang

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Abstract

Omicron (B.1.1.529), the most heavily mutated SARS-CoV-2 variant so far, is highly resistant to neutralizing antibodies, raising concerns about the effectiveness of antibody therapies and vaccines 1,2 . Here we examined whether sera from individuals who received two or three doses of inactivated SARS-CoV-2 vaccine could neutralize authentic Omicron. The seroconversion rates of neutralizing antibodies were 3.3% (2 out of 60) and 95% (57 out of 60) for individuals who had received 2 and 3 doses of vaccine, respectively. For recipients of three vaccine doses, the geometric mean neutralization antibody titre for Omicron was 16.5-fold lower than for the ancestral virus (254). We isolated 323 human monoclonal antibodies derived from memory B cells in triple vaccinees, half of which recognized the receptor-binding domain, and showed that a subset (24 out of 163) potently neutralized all SARS-CoV-2 variants of concern, including Omicron. Therapeutic treatments with representative broadly neutralizing monoclonal antibodies were highly protective against infection of mice with SARS-CoV-2 Beta (B.1.351) and Omicron. Atomic structures of the Omicron spike protein in complex with three classes of antibodies that were active against all five variants of concern defined the binding and neutralizing determinants and revealed a key antibody escape site, G446S, that confers greater resistance to a class of antibodies that bind on the right shoulder of the receptor-binding domain by altering local conformation at the binding interface. Our results rationalize the use of three-dose immunization regimens and suggest that the fundamental epitopes revealed by these broadly ultrapotent antibodies are rational targets for a universal sarbecovirus vaccine.

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  1. Version published to 10.1038/s41586-022-04466-x
  2. ScreenIT

    SciScore for 10.1101/2021.12.24.474084: (What is this?)

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

    Table 1: Rigor

    EthicsIACUC: Facility and ethics statements: All procedures associated with SARS-CoV-2 live virus were approved by the Animal experiment Committee Laboratory Animal Center, Beijing Institute of Microbiology and Epidemiology with an approval number of IACUC-IME-2021-022 and performed in Biosafety Level 3 (BSL-3) laboratories in strict accordance with the recommendations in the Guide for Care and Use of Laboratory Animals.
    Consent: All volunteers were provided informed written consent form and the whole study was conducted in accordance with the requirements of Good Clinical Practice of China.
    Sex as a biological variableBriefly, group of 8-month-old female BALB/c mice were infected with 1×104 PFU of SARS-CoV-2 Beta variant strain, then infected mice were treated intraperitoneally with a single dose of different antibodies or antibody cocktails at 1 hour after infection.
    RandomizationFinally, a MD production runs of 100 ns were performed starting from random initial velocities and applying periodic boundary conditions.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    The heat-treated samples or monoclonal antibodies (mAbs) were subject to seral dilution from 1: 4 or 50 ng/μL with DMEM in two-fold steps and mixed with a virus suspension containing 100 TCID50 at 36.5°C for 2h, after which, the mixtures were added to wells seeded with confluence Vero cells and incubated at 36.5°C for another 5 days in a humidified 5% CO2 cell incubator.
    Vero
    suggested: None
    The transfected 293T cells were infected with VSV G pseudotyped virus (G*ΔG-VSV) at a multiplicity of infection (MOI) of 4.
    293T
    suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)
    After that, the mixtures were added to Huh-7 cells and placed back for incubation for another 24 hours.
    Huh-7
    suggested: None
    For protein expression, the plasmids of these proteins were transiently transfected into HEK293 F cells grown in suspension at 37 °C in an incubator supplied with 8% CO2, rotating at 130 rpm.
    HEK293
    suggested: None
    Then the clones were transiently transfected into mammalian HEK293F cells and incubated for 5 days in a 5% CO2 rotating incubator at 37°C for antibody expression, which were further purified using protein A.
    HEK293F
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    Viral stock and cell lines: SARS-CoV-2 wild-type strain CN01 was originally isolated from a patient during the early phase of COVID-19 endemic in China.
    SARS-CoV-2
    suggested: None
    Briefly, group of 8-month-old female BALB/c mice were infected with 1×104 PFU of SARS-CoV-2 Beta variant strain, then infected mice were treated intraperitoneally with a single dose of different antibodies or antibody cocktails at 1 hour after infection.
    BALB/c
    suggested: None
    Software and Algorithms
    SentencesResources
    The area under the curve (AUC) of each mAb were determined using Prism V8.0 (GraphPad).
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Automated single particle data acquisition was carried out by SerialEM, with a calibrated magnification of 22,500 yielding a final pixel size of 1.07 Å.
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)
    The defocus value of each image was calculated by Gctf.
    Gctf
    suggested: (GCTF, RRID:SCR_016500)
    Then, 1,302,103, 756,508, 2,332,045 and 2,320,416 particles of the S-XGv265-complex, S-XGv282-complex, S-XGv289-complex and S-XGv347-complex, respectively were picked and extracted for reference-free 2D alignment by cryoSPARC 32, based of which, 422,083, 190,154, 837,832 and 614,852 particles were selected and applied for 3D classification by Relion3.0 for S-XGv265-complex, S-XGv282-complex, S-XGv289-complex and S-XGv347-complex, respectively with no symmetry imposed to produce the potential conformations for the complexes.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    Model fitting and refinement: The atomic models of the complexes were generated by first fitting the chains of the native apo SARS-CoV-2 S trimer (PDB number of 6VYB) and Fabs (PDB number of 7LSS and 7CZW for XGv265, 5MES and 5VAG for XGv282, 6UDA and 7MEG for XGv289 as well as 7E3K for XGv347) into the cyo-EM densities of the final S-Fab-complexes described above by Chimera, followed by manually adjustment and correction according to the protein sequences and densities in Coot, as well as real space refinement using Phenix.
    Coot
    suggested: (Coot, RRID:SCR_014222)
    Phenix
    suggested: (Phenix, RRID:SCR_014224)
    Average structure of the four complexes were generated using the last 10 ns frames and ΔG between the antibodies and RBD was estimated in ROSETTA by InterfaceAnalyzer.
    ROSETTA
    suggested: (Rosetta, RRID:SCR_015701)

    Results from OddPub: Thank you for sharing your data.

    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

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  3. Version published to 10.1101/2021.12.24.474084 on bioRxiv