Omicron BA.2 specifically evades broad sarbecovirus neutralizing antibodies

  1. Yunlong Cao
  2. Ayijiang Yisimayi
  3. Fanchong Jian
  4. Tianhe Xiao
  5. Weiliang Song
  6. Jing Wang
  7. Shuo Du
  8. Zhiying Zhang
  9. Pulan Liu
  10. Xiaohua Hao
  11. Qianqian Li
  12. Xiaosu Chen
  13. Lei Wang
  14. Peng Wang
  15. Ran An
  16. Yao Wang
  17. Jing Wang
  18. Peng Yang
  19. Haiyan Sun
  20. Lijuan Zhao
  21. Wen Zhang
  22. Dong Zhao
  23. Jiang Zheng
  24. Lingling Yu
  25. Can Li
  26. Na Zhang
  27. Rui Wang
  28. Xiao Niu
  29. Sijie Yang
  30. Xuetao Song
  31. Linlin Zheng
  32. Zhiqiang Li
  33. Qingqing Gu
  34. Fei Shao
  35. Weijin Huang
  36. Youchun Wang
  37. Zhongyang Shen
  38. Xiangxi Wang
  39. Ronghua Jin
  40. Junyu Xiao
  41. Xiaoliang Sunney Xie

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Omicron sub-lineage BA.2 has rapidly surged globally, accounting for over 60% of recent SARS-CoV-2 infections. Newly acquired RBD mutations and high transmission advantage over BA.1 urge the investigation of BA.2’s immune evasion capability. Here, we show that BA.2 causes strong neutralization resistance, comparable to BA.1, in vaccinated individuals’ plasma. However, BA.2 displays more severe antibody evasion in BA.1 convalescents, and most prominently, in vaccinated SARS convalescents’ plasma, suggesting a substantial antigenicity difference between BA.2 and BA.1. To specify, we determined the escaping mutation profiles 1,2 of 714 SARS-CoV-2 RBD neutralizing antibodies, including 241 broad sarbecovirus neutralizing antibodies isolated from SARS convalescents, and measured their neutralization efficacy against BA.1, BA.1.1, BA.2. Importantly, BA.2 specifically induces large-scale escape of BA.1/BA.1.1-effective broad sarbecovirus neutralizing antibodies via novel mutations T376A, D405N, and R408S. These sites were highly conserved across sarbecoviruses, suggesting that Omicron BA.2 arose from immune pressure selection instead of zoonotic spillover. Moreover, BA.2 reduces the efficacy of S309 (Sotrovimab) 3,4 and broad sarbecovirus neutralizing antibodies targeting the similar epitope region, including BD55-5840. Structural comparisons of BD55-5840 in complexes with BA.1 and BA.2 spike suggest that BA.2 could hinder antibody binding through S371F-induced N343-glycan displacement. Intriguingly, the absence of G446S mutation in BA.2 enabled a proportion of 440-449 linear epitope targeting antibodies to retain neutralizing efficacy, including COV2-2130 (Cilgavimab) 5 . Together, we showed that BA.2 exhibits distinct antigenicity compared to BA.1 and provided a comprehensive profile of SARS-CoV-2 antibody escaping mutations. Our study offers critical insights into the humoral immune evading mechanism of current and future variants.

Article activity feed

  1. Version published to 10.1101/2022.02.07.479349v3 on bioRxiv
  2. Version published to 10.1101/2022.02.07.479349v2 on bioRxiv
  3. ScreenIT

    SciScore for 10.1101/2022.02.07.479349: (What is this?)

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

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Antibodies
    SentencesResources
    B cells were then stained with FITC anti-human CD19 antibody (BioLegend, 392508)
    anti-human CD19
    suggested: (BioLegend Cat# 392508, RRID:AB_2750099)
    FITC anti-human CD20 antibody (BioLegend, 302304)
    anti-human CD20
    suggested: (BioLegend Cat# 302304, RRID:AB_314252)
    Brilliant Violet 421™ anti-human CD27 antibody (BioLegend, 302824)
    anti-human CD27
    suggested: (BioLegend Cat# 302824, RRID:AB_11150782)
    anti-human IgM antibody (BioLegend, 314532)
    anti-human IgM
    suggested: (BioLegend Cat# 314532, RRID:AB_2566485)
    High-throughput antibody-escape mutation profiling: The previously described high-throughput MACS (magnetic-activated cell sorting)-based antibody-escape mutation profiling system was used to characterize RBD escaping mutation profile for neutralizing antibodies.
    antibody-escape
    suggested: None
    A, E, n are parameters, where E is the desired EC50 value for the specific antibody and antigen.
    antigen .
    suggested: None
    For protein production, these expression plasmids, as well as the plasmids encoding the antigen-binding fragments (Fabs) of the antibodies described in this paper, were transfected into the HEK293F cells using polyethylenimine (Polysciences).
    antigen-binding
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Pseudovirus detection of PCoV-GD and RaTG13 was performed in 293T cells overexpressing human angiotensin-converting enzyme 2 (293T-hACE2 cells)
    293T
    suggested: None
    293T-hACE2
    suggested: None
    Other pseudovirus neutralization assays were performed using the Huh-7 cell line (Japanese Collection of Research Bioresources [JCRB], 0403)
    Huh-7
    suggested: JCRB Cat# JCRB0403, RRID:CVCL_0336)
    About 104 digested Vero cells (ATCC, CCL-81) were seeded in plates and cultured for 5 days.
    Vero
    suggested: None
    Healthy HEK293 cells were passaged into a new cell culture and grown in suspension at 37 °C, 120 RPM, 8% CO2 to logarithmic growth phase and transfected with the recombinant constructs by using liposomal vesicles as DNA carrier.
    HEK293
    suggested: None
    For protein production, these expression plasmids, as well as the plasmids encoding the antigen-binding fragments (Fabs) of the antibodies described in this paper, were transfected into the HEK293F cells using polyethylenimine (Polysciences).
    HEK293F
    suggested: RRID:CVCL_6642)
    Recombinant DNA
    SentencesResources
    Pseudovirus neutralization assay: SARS-CoV-2 spike (GenBank: MN908947) , Pangolin-GD spike (GISAID: EPI_ISL_410721), RaTG13 spike (GISAID: EPI_ISL_402131), SARS-COV-1 spike (GenBank: AY278491), Omicron BA.1 spike (A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F), BA.2 spike (GISAID: EPI_ISL_7580387), BA.1.1 spike (BA.1+R346K), plasmid is constructed into pcDNA3.1 vector.
    pcDNA3.1
    suggested: RRID:Addgene_79663)
    The purified PCR products were ligated to the secretory expression vector pCMV3 with CMV promoter, and then transformed into E. coli competent cells XL1-blue.
    pCMV3
    suggested: RRID:Addgene_161029)
    Software and Algorithms
    SentencesResources
    FACS data were analyzed using FlowJo™ v10.8 (BD Biosciences)
    FlowJo™
    suggested: (FlowJo, RRID:SCR_008520)
    V(D)J gene annotation was performed using NCBI IgBlast (v1.17.1) with the IMGT reference.
    IgBlast
    suggested: (IgBLAST, RRID:SCR_002873)
    The V-J pairs were visualized by R package circlize (v0.4.10)
    circlize
    suggested: (circlize, RRID:SCR_002141)
    VarianceThreshold of scikit-learn Python package (v0.24.2) with the variance threshold as 0.1.
    Python
    suggested: (IPython, RRID:SCR_001658)
    TSNE of scikit-learn.
    scikit-learn
    suggested: (scikit-learn, RRID:SCR_002577)
    All t-SNE plots were generated by R package ggplot2 (v3.3.3)
    ggplot2
    suggested: (ggplot2, RRID:SCR_014601)
    To improve the density surrounding the RBD-Fab region, UCSF Chimera55 and Relion56 were used to generate the masks, and local refinement was then performed using cryoSPARC.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    Figures were prepared using USCF ChimeraX59 and Pymol (Schrödinger, LLC.).
    Pymol
    suggested: (PyMOL, RRID:SCR_000305)

    Results from OddPub: Thank you for sharing your code and 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.
    • No funding statement was detected.
    • 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 10.1101/2022.02.07.479349v1 on bioRxiv