Predictions of the SARS-CoV-2 Omicron Variant (B.1.1.529) Spike Protein Receptor-Binding Domain Structure and Neutralizing Antibody Interactions
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Abstract
The genome of the SARS-CoV-2 Omicron variant (B.1.1.529) was released on November 22, 2021, which has caused a flurry of media attention due the large number of mutations it contains. These raw data have spurred questions around vaccine efficacy. Given that neither the structural information nor the experimentally-derived antibody interaction of this variant are available, we have turned to predictive computational methods to model the mutated structure of the spike protein's receptor binding domain and posit potential changes to vaccine efficacy. In this study, we predict some structural changes in the receptor-binding domain that may reduce antibody interaction without completely evading existing neutralizing antibodies (and therefore current vaccines).
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SciScore for 10.1101/2021.12.03.471024: (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 This analysis was performed on the antibody-RBD structure pairs shown in Table 1. antibody-RBDsuggested: NoneSoftware and Algorithms Sentences Resources Sequence Comparison among VBMs and VOCs: We downloaded the reference genome of SARS-CoV-2 (Wuhan-Hu-1, NCBI’s RefSeq accession no. NC_045512.2) as well as the first 100 complete genome sequences (≥29,000 bp) of each Variant of Concern (VOC) and Variant Being Monitored (VBM). RefSeqsuggested: (RefSeq, RRID:SCR_003496)We aligned all of these complete genomes using MAFFT version 7.475 (7) with the “auto” option and trimmed the alignment to remove the 5’-UTR … SciScore for 10.1101/2021.12.03.471024: (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 This analysis was performed on the antibody-RBD structure pairs shown in Table 1. antibody-RBDsuggested: NoneSoftware and Algorithms Sentences Resources Sequence Comparison among VBMs and VOCs: We downloaded the reference genome of SARS-CoV-2 (Wuhan-Hu-1, NCBI’s RefSeq accession no. NC_045512.2) as well as the first 100 complete genome sequences (≥29,000 bp) of each Variant of Concern (VOC) and Variant Being Monitored (VBM). RefSeqsuggested: (RefSeq, RRID:SCR_003496)We aligned all of these complete genomes using MAFFT version 7.475 (7) with the “auto” option and trimmed the alignment to remove the 5’-UTR and 3’-UTR regions. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Once we had all the predicted spike proteins for each of the 1,026 genomes, we aligned those sequences based on their translation with the help of MAFFT using the TranslatorX pipeline (9). TranslatorXsuggested: (TranslatorX, RRID:SCR_014733)We then calculated the pairwise p-distances between each pair of sequences were calculated using MEGA version 11.0.10 (10). MEGAsuggested: (Mega BLAST, RRID:SCR_011920)Further, interfacing residues between the RBD and Fab structures were determined to by identifying residues that are within a distance of 1.0 Å2 or less between the chains of the RBD and the Fab using the InterafaceResidues functionality in PyMol version 2.4.1 (17). PyMolsuggested: (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.
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