Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail
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Abstract
The SARS-CoV-2 pandemic has led to an urgent need to understand the molecular basis for immune recognition of SARS-CoV-2 spike (S) glycoprotein antigenic sites. To define the genetic and structural basis for SARS-CoV-2 neutralization, we determined the structures of two human monoclonal antibodies COV2-2196 and COV2-2130 1 , which form the basis of the investigational antibody cocktail AZD7442, in complex with the receptor binding domain (RBD) of SARS-CoV-2. COV2-2196 forms an “aromatic cage” at the heavy/light chain interface using germline-encoded residues in complementarity determining regions (CDRs) 2 and 3 of the heavy chain and CDRs 1 and 3 of the light chain. These structural features explain why highly similar antibodies (public clonotypes) have been isolated from multiple individuals 1–4 . The structure of COV2-2130 reveals that an unusually long LCDR1 and HCDR3 make interactions with the opposite face of the RBD from that of COV2-2196. Using deep mutational scanning and neutralization escape selection experiments, we comprehensively mapped the critical residues of both antibodies and identified positions of concern for possible viral escape. Nonetheless, both COV2-2196 and COV2-2130 showed strong neutralizing activity against SARS-CoV-2 strain with recent variations of concern including E484K, N501Y, and D614G substitutions. These studies reveal germline-encoded antibody features enabling recognition of the RBD and demonstrate the activity of a cocktail like AZD7442 in preventing escape from emerging variant viruses.
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SciScore for 10.1101/2021.01.27.428529: (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 Sentences Resources The bound antibodies were detected using goat antihuman IgG conjugated with horseradish peroxidase (Southern Biotech) and TMB substrate (Thermo Fischer Scientific). antihuman IgGsuggested: (GeneTex Cat# GTX28798, RRID:AB_374523)After the antibody incubations, the libraries were secondarily labeled with 1:100 FITC-conjugated anti-MYC antibody (Immunology Consultants Lab, CYMC-45F) to label for RBD expression and 1:200 PE-conjugated goat anti-human-IgG (Jackson ImmunoResearch 109-115-098) to label for bound antibody. anti-MYCsuggested: Noneanti-human-IgGsuggested: NoneFor each antibody selection, we … SciScore for 10.1101/2021.01.27.428529: (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 Sentences Resources The bound antibodies were detected using goat antihuman IgG conjugated with horseradish peroxidase (Southern Biotech) and TMB substrate (Thermo Fischer Scientific). antihuman IgGsuggested: (GeneTex Cat# GTX28798, RRID:AB_374523)After the antibody incubations, the libraries were secondarily labeled with 1:100 FITC-conjugated anti-MYC antibody (Immunology Consultants Lab, CYMC-45F) to label for RBD expression and 1:200 PE-conjugated goat anti-human-IgG (Jackson ImmunoResearch 109-115-098) to label for bound antibody. anti-MYCsuggested: Noneanti-human-IgGsuggested: NoneFor each antibody selection, we computed the “escape fraction” for each barcoded variant using the deep sequencing counts for each variant in the original and antibody-escape populations and the total fraction of the library that escaped antibody binding via a previously described formula27. antibody-escapesuggested: NoneNote that these filtering criteria are slightly more stringent than those previously used to map a panel of human antibodies27 but are identical to those used in recent studies defining RBD residues that impact the binding of mAbs65 and polyclonal serum40. antibodies27suggested: NoneSoftware and Algorithms Sentences Resources The diffraction data were processed with XDS59 and CCP4 suite60. CCP4suggested: (CCP4, RRID:SCR_007255)PyMOL software64 was used to make all of the structural figures. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Additionally, the germline revertant forms of COV2-2196 were generated by aligning the sequence to identified germline sequences using IgBlast, and reverting back the residues that were not germline-encoded. IgBlastsuggested: (IgBLAST, RRID:SCR_002873)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.
- 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.
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