Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo–electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)–binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies—including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404—that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants.
Article activity feed
-
-
SciScore for 10.1101/2021.12.27.474307: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources For antibodies where vectors were unavailable (e.g., S309, CB6, REGN10933, REGN10987, COV2-2196, COV2-2130, CT-P59, C144, C135, S2E12) (12, 13, 21, 22, 25, 27–31), published amino acids sequences were used for synthesis and cloning into corresponding pVRC8400 vectors (Genscript) (46, 47). C144suggested: (Leinco Technologies Cat# C144, RRID:AB_2828501)TMPRSS2 and ACE2 expression profiles in 293 Flpin-TMPSS2-ACE2 were characterized by flow cytometry using a mouse monoclonal antibody … SciScore for 10.1101/2021.12.27.474307: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources For antibodies where vectors were unavailable (e.g., S309, CB6, REGN10933, REGN10987, COV2-2196, COV2-2130, CT-P59, C144, C135, S2E12) (12, 13, 21, 22, 25, 27–31), published amino acids sequences were used for synthesis and cloning into corresponding pVRC8400 vectors (Genscript) (46, 47). C144suggested: (Leinco Technologies Cat# C144, RRID:AB_2828501)TMPRSS2 and ACE2 expression profiles in 293 Flpin-TMPSS2-ACE2 were characterized by flow cytometry using a mouse monoclonal antibody against TMPRSS2 (MillliporeSigma) followed by an anti-mouse IgG1 APC conjugate (Jackson laboratories) and a molecular probe containing the SARS-CoV-2 receptor binding domain tagged with biotin (Sino biological) followed by staining with a BV421 conjugated streptavidin probe (BD Biosciences). TMPRSS2suggested: Noneanti-mouse IgG1suggested: NoneAfter incubation with the antibodies or ACE2, the cells were washed and incubated with an allophycocyanin conjugated anti-human IgG (709-136-149, Jackson Immunoresearch Laboratories) or BV421 conjugated streptavidin conjugate for another 30 minutes. ACE2suggested: Noneanti-human IgGsuggested: (Jackson ImmunoResearch Labs Cat# 709-136-149, RRID:AB_2340526)Experimental Models: Cell Lines Sentences Resources Proteins were expressed in Expi293 cells by transfection with expression vectors encoding corresponding genes. Expi293suggested: RRID:CVCL_D615)Generation of 293 Flpin-TMPRSS2-ACE2 cell line: 293 Flpin-TMPRSS2-ACE2 isogenic cell line was prepared by co-transfecting pCDNA5/FRT plasmid encoding TMPRSS2-T2A-ACE2 and pOG44 plasmid encoding Flp recombinase in 293 Flpin parental cell line (Thermo Fisher, Cat R75007) Flpin-TMPRSS2-ACE2suggested: Nonetransducing plasmid pHR’ CMV-Luc, a TMPRSS2 plasmid and S plasmids from SARS CoV-2 variants into 293T cells using Lipofectamine 3000 transfection reagent (L3000-001, ThermoFisher Scientific, Asheville, NC) (48, 49). 293Tsuggested: None293T-ACE2 cells (provided by Dr. Michael Farzan) or 293 flpin-TMPRSS2-ACE2 cells were plated into 96-well white/black Isoplates (PerkinElmer, Waltham, MA) at 75,00 cells per well the day before infection of SARS CoV-2 pseudovirus. 293T-ACE2suggested: NoneCell surface binding: HEK293T cells were transiently transfected with plasmids encoding full length SARS CoV-2 spike variants using lipofectamine 3000 (L3000-001, ThermoFisher) following manufacturer’s protocol. HEK293Tsuggested: NoneRecombinant DNA Sentences Resources Variable heavy chain sequences were human codon optimized, synthesized and cloned into a VRC8400 (CMV/R expression vector)-based IgG1 vector containing an HRV3C protease site (44) as previously described (45). IgG1suggested: NoneGeneration of 293 Flpin-TMPRSS2-ACE2 cell line: 293 Flpin-TMPRSS2-ACE2 isogenic cell line was prepared by co-transfecting pCDNA5/FRT plasmid encoding TMPRSS2-T2A-ACE2 and pOG44 plasmid encoding Flp recombinase in 293 Flpin parental cell line (Thermo Fisher, Cat R75007) pCDNA5/FRTsuggested: RRID:Addgene_31984)pOG44suggested: NoneS-containing lentiviral pseudovirions were produced by co-transfection of packaging plasmid pCMVdR8.2, pCMVdR8.2suggested: RRID:Addgene_8455)transducing plasmid pHR’ CMV-Luc, a TMPRSS2 plasmid and S plasmids from SARS CoV-2 variants into 293T cells using Lipofectamine 3000 transfection reagent (L3000-001, ThermoFisher Scientific, Asheville, NC) (48, 49). pHR’suggested: NoneTMPRSS2suggested: RRID:Addgene_53887)Software and Algorithms Sentences Resources The samples were then acquired in a BD LSRFortessa X-50 flow cytometer (BD biosciences) and analyzed using Flowjo (BD biosciences). Flowjosuggested: (FlowJo, RRID:SCR_008520)Iterative manual model building and real-space refinement were carried out in Coot (48) and in Phenix (51), respectively. Cootsuggested: (Coot, RRID:SCR_014222)Data process workflow, including motion correction, CTF estimation, particle picking and extraction, 2D classification, ab initio reconstruction, homogeneous refinement, heterogeneous refinement, non-uniform refinement, local refinement and local resolution estimation, were carried out with C1 symmetry in cryoSPARC 3.3 (50). cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)Iterative manual model building and real-space refinement were carried out in Coot (48) and in Phenix 1.19.2 (51), respectively. Phenixsuggested: (Phenix, RRID:SCR_014224)Molprobity (52) was used to validate geometry and check structure quality at each iteration step. Molprobitysuggested: (MolProbity, RRID:SCR_014226)The graphs were generated in GraphPad Prism. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 49, 53, 54 and 55. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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.
-