Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody

Abstract

In this study, by characterizing several human monoclonal antibodies (mAbs) isolated from single B cells of the COVID-19–recovered individuals in India who experienced ancestral Wuhan strain (WA.1) of SARS-CoV-2 during early stages of the pandemic, we found a receptor binding domain (RBD)–specific mAb 002-S21F2 that has rare gene usage and potently neutralized live viral isolates of SARS-CoV-2 variants including Alpha, Beta, Gamma, Delta, and Omicron sublineages (BA.1, BA.2, BA.2.12.1, BA.4, and BA.5) with IC ₅₀ ranging from 0.02 to 0.13 μg/ml. Structural studies of 002-S21F2 in complex with spike trimers of Omicron and WA.1 showed that it targets a conformationally conserved epitope on the outer face of RBD (class 3 surface) outside the ACE2-binding motif, thereby providing a mechanistic insights for its broad neutralization activity. The discovery of 002-S21F2 and the broadly neutralizing epitope it targets have timely implications for developing a broad range of therapeutic and vaccine interventions against SARS-CoV-2 variants including Omicron sublineages.

SciScore for 10.1101/2022.05.13.491770: (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	4 colonies from each transformed plate were randomly picked and the insert was checked by performing colony PCR using nested PCR primers.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
Cells were incubated with an anti-SARS-CoV spike primary antibody directly conjugated with alexaflour-647 (CR3022-AF647) for up to 4 hours at room temperature.	anti-SARS-CoV spike suggested: None
Ten million PBMCs of select COVID-19 recovered donors were stained with RBD-Alexa Fluor 488 for 1 hour at 4°C, followed by washing with PBS containing 2% FBS (FACS buffer) …

SciScore for 10.1101/2022.05.13.491770: (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	4 colonies from each transformed plate were randomly picked and the insert was checked by performing colony PCR using nested PCR primers.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	not detected.

Table 2: Resources

Antibodies
Sentences	Resources
Cells were incubated with an anti-SARS-CoV spike primary antibody directly conjugated with alexaflour-647 (CR3022-AF647) for up to 4 hours at room temperature.	anti-SARS-CoV spike suggested: None
Ten million PBMCs of select COVID-19 recovered donors were stained with RBD-Alexa Fluor 488 for 1 hour at 4°C, followed by washing with PBS containing 2% FBS (FACS buffer) and incubation with efluor780 Fixable Viability (Live Dead) dye (Life Technologies, #65-0865-14) and anti-human CD3, CD19, CD20, CD27, CD38 and IgD antibodies (BD Biosciences) for 30 minutes.	anti-human CD3 suggested: (RayBiotech Cat# CS-11-0105, RRID:AB_1227994) CD19 suggested: (Agilent Cat# TC67401, RRID:AB_579635) CD20 suggested: None CD27 , CD38 suggested: None IgD suggested: None
mAb antibody binding was then detected with 50 μl/well of MSD SULFO-TAG anti-human IgG antibody (diluted 1:200) incubated for one hour at room temperature with shaking at 700rpm.	anti-human IgG suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Briefly, 100 pfu of SARS-CoV-2 (2019-nCoV/USA_WA1/2020), Alpha, Beta, Gamma, Delta and Omicron (BA.1 and BA.2) were used on Vero TMPRSS2 cells.	Vero TMPRSS2 suggested: None
Software and Algorithms
Sentences	Resources
IC50 titers were calculated by non-linear regression analysis using the 4PL sigmoidal dose curve equation on Prism 9 (Graphpad Software).	Graphpad suggested: (GraphPad, RRID:SCR_000306)
Data were analyzed using FlowJo software 10	FlowJo suggested: (FlowJo, RRID:SCR_008520)
CryoEM data analysis and model building: CryoEM movies were motion-corrected either in Motioncorr2 in Relion3.0 (30) or using Patch motion correction implemented in Cryosparc v3.3.1 (31).	Cryosparc suggested: (cryoSPARC, RRID:SCR_016501)
The combined Focused Map tool in Phenix was used to integrate high resolution locally refined maps into an overall map.	Phenix suggested: (Phenix, RRID:SCR_014224)
Glycans with visible density were modelled in Coot (36).	Coot suggested: (Coot, RRID:SCR_014222)
Model validation was performed using Molprobity (37).	Molprobity suggested: (MolProbity, RRID:SCR_014226)
Figures were prepared in ChimeraX(34) and PyMOL (39).	PyMOL suggested: (PyMOL, RRID:SCR_000305)

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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Structural insights for neutralization of Omicron variants BA.1, BA.2, BA.4, and BA.5 by a broadly neutralizing SARS-CoV-2 antibody

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