A potent SARS-CoV-2 antibody neutralizes Omicron variant by disassembling the spike trimer

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Abstract

The continuous emergence of novel SARS-CoV-2 variants poses new challenges to the fight against the COVID-19 pandemic. The newly emerging Omicron strain caused serious immune escape and raised unprecedented concern all over the world. The development of antibody targeting conserved and universal epitope is urgently needed. A subset neutralizing antibody(nAbs) against COVID-19 from convalescent patients were isolated in our previous study. Here in this study, we investigated the accommodation of these nAbs to SARS-CoV-2 variants of concerns (VOCs), revealing that IgG 553-49 neutralizes pseudovirus of SARS-CoV-2 Omicron variant. In addition, we determined the cryo-EM structure of SARS-CoV-2 spike complexed with three antibodies targeting different epitopes, including 553-49, 553-15 and 553-60. Notably, 553-49 targets a novel conserved epitope and neutralizes virus by disassembling spike trimers. 553-15, an antibody that neutralizes all the other VOCs except omicron, cross-links two spike trimers to form trimer dimer, demonstrating that 553-15 neutralizes virus by steric hindrance and virion aggregation. These findings suggest the potential to develop 49 and other antibody targeting this highly conserved epitope as promising cocktail therapeutics reagent for COVID-19.

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  1. SciScore for 10.1101/2022.03.21.485243: (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

    Experimental Models: Cell Lines
    SentencesResources
    Expression and Purification of recombinant antibodies: A pair of plasmids separately expressing the heavy- and the light-chain of antibodies were transiently co-transfected into HEK293F cells.
    HEK293F
    suggested: RRID:CVCL_6642)
    Serial 1/3 dilutions of antibodies were incubated with pseudoviruses at 37°C for 1 hour, and then the mixtures were added in ACE2 expressed Huh-7 cells (104 per well in 96-well plates).
    Huh-7
    suggested: None
    Recombinant DNA
    SentencesResources
    Production of recombinant D614G and variants spike ectodomain: The gene encoding SARS-CoV-2 S ectodomain (residues 1-1208, Gene Bank: MN908947) was synthesized (GeneScript) and cloned into mammalian expression constructs pcDNA-3.1, proline substitutions at residues 986 and 987, “GSAS” substitution at furin cleavage site (residues 682-685), a T4 fibritin trimerization motif, an HRV3C protease cleavage site, a TwinStrepTag, and an 8XHisTag at C-terminal were introduced simultaneously by MultiS one step cloning kit (Vazyme).
    pcDNA-3.1
    suggested: None
    Using the SARS-CoV-2 WT plasmid as the template, mutations such as D614G, B.1.17 (Del 69H70V, N501Y, P681H, S982A, Del 145Y, A570D, T716I, D1118H), B.1.351 (K417N, E484K, N501Y) and P1 (K417T, E484K, N501Y) was introduced by Multi Site-Directed Mutagenesis Kit (Yeasen).
    SARS-CoV-2 WT
    suggested: None
    The expression plasmid of Omicron S with HexaPro mutations(26), “GSAS” substitution at furin cleavage site (residues 682-285), a T4 fibritin trimerization motif, a TwinStrep Tag, and a C-terminal 8 × His Tag was constructed into pcDNA3.1 vector by MultiS one step cloning kit (Vazyme).
    pcDNA3.1
    suggested: RRID:Addgene_79663)
    Briefly, whole spike glycoprotein sequences of SARS-CoV, wild type or variants of SARS-CoV-2 were inserted into the vector of pcDNA3.1+ and severally co-transfected into 293 T cells (ATCC, Manassas, VA, USA) with a defective HIV-1 genome that encodes luciferase reporter.
    pcDNA3.1+
    suggested: RRID:Addgene_117272)
    Software and Algorithms
    SentencesResources
    A nonlinear regression analysis was performed on the resulting curves using Prism (GraphPad) to calculate half-maximal inhibitory concentration (IC50) values.
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)
    Automated data acquisition was carried out with SerialEM software(27).
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)
    Cryo-EM image processing: All the data processing was carried out using either modules on, or through, RELION v3.0 and cryoSPARC(28).
    RELION
    suggested: (RELION, RRID:SCR_016274)
    For S-15 complex (Fig.S10), a total of 6,943 movie stacks was binned 2 × 2, dose weighted, and motion corrected using MotionCor2(29).
    MotionCor2
    suggested: (MotionCor2, RRID:SCR_016499)
    After blob-picking in cryoSPARC and 2D classification, trimer and monomer particles were observed.
    cryoSPARC
    suggested: (cryoSPARC, RRID:SCR_016501)
    For model building of S-15 and S-60, the apo-S trimer model and the antibody (15 and 60) model generated by swiss-model were fitted into the map using UCSF Chimera(31) and followed by manually adjustment in COOT(33), as well as real space refinement in Phenix.
    Phenix
    suggested: (Phenix, RRID:SCR_014224)
    Model validation was performed using MolProbity.
    MolProbity
    suggested: (MolProbity, RRID:SCR_014226)

    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.


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