Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant–neutralizing antibody that is a strong candidate for clinical development.

SciScore for 10.1101/2022.05.08.491108: (What is this?)

Please note, not all rigor criteria are appropriate for all manuscripts.

Table 1: Rigor

Ethics	IRB: HAARVI) study and was approved by the University of Washington Human Subjects Division Institutional Review Board (STUDY00000959). Consent: All donors provided written informed consent for the use of blood and blood derivatives (such as peripheral blood mononuclear cells, sera or plasma) for research. Euthanasia Agents: At day 4 post-inoculation, the animals were euthanized with an excess of anesthetics (ketamine and xylazine) and exsanguination.
Sex as a biological variable	For the results shown in Fig.4 (A-C), 64 male golden Syrian hamsters (Mesocricetus auratus; RjHan:AURA) of 5-6 weeks of age (average weight 60-80 grams) were purchased from Janvier Laboratories (Le Genest-Saint-Isle, France) and handled under specific pathogen-free conditions.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Cell Line Authentication	Contamination: Cell lines were routinely tested for mycoplasma contamination.

Table 2: Resources

Antibodies
Sentences	Resources
goat anti-human IgG secondary antibody (Southern Biotech, 2040-04) was added and incubated for 1 h at room temperature.	goat anti-human IgG secondary antibody suggested: None anti-human IgG suggested: (SouthernBiotech Cat# 2040-04, RRID:AB_2795643)
Plates were washed 4 × in TBST, then anti-human (Invitrogen) horseradish peroxidase-conjugated antibodies were diluted 1:5,000 and 50 μL added to each well and incubated at 37°C for 1 h.	anti-human suggested: None
Twenty-four hours before infection, the hamsters received an intraperitoneal injection of different concentrations of the hamsterized monoclonal antibodies (mAb) S309 (0.6, 1.7, 5 and 15 mg/kg), S2X324 (0.2, 0.6, 1.7 and 5 mg/kg) or the control isotype MGH2 (15 mg/kg).	S309 suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Cell lines: Cell lines used in this study were obtained from ATCC (HEK293T and Vero E6), Thermo Fisher Scientific (Expi-CHO-S cells, FreeStyle 293-F cells and Expi293F cells) or Takara (Lenti-X 293T cells)	HEK293T suggested: None 293T suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)
For pseudoviruses expressing spike substitutions that resulted in decreased infectivity using Vero E6 cells, Vero E6-TMPRSS2 cells were substituted as target cells for neutralization assays.	Vero E6-TMPRSS2 suggested: None
Cell-surface mAb-mediated S1 shedding: CHO cells stably expressing the prototypic SARS-CoV-2 S were harvested, washed in wash buffer (PBS 1% BSA 2 mM EDTA) and resuspended in PBS.	CHO suggested: CLS Cat# 603479/p746_CHO, RRID:CVCL_0213)
Vero E6 cells were seeded into 12 well plates overnight.	Vero E6 suggested: None
After a 25-minute incubation, Jurkat cells stably expressing FcγRIIIa receptor (V158 variant) or FcγRIIa receptor (H131 variant) and NFAT-driven luciferase gene (effector cells) were added at an effector to target ratio of 6:1 for FcγRIIIa and 5:1 for FcγRIIa.	Jurkat suggested: None
ADCC assays were performed using SARS-CoV2 CHO-K1 cells (genetically engineered to stably express a HaloTag-HiBit-tagged) as target cells and PBMC as effector cells at a E:T ratio of 30:1.	CHO-K1 suggested: None
Experimental Models: Organisms/Strains
Sentences	Resources
The coordinates of the Wuhan-Hu-1 RBD were obtained from PDB 6M0J (42) for which ACE2 was removed and as previously described (25) the glycan at position 343 added in the RBD using ISOLDE (99) to visually place, link and minimize each monosaccharide beyond the N-acetylglucosamine for which there was density.	Wuhan-Hu-1 RBD suggested: None
Software and Algorithms
Sentences	Resources
After 30 min incubation, absorbance at 405 nm was measured by a plate reader (Biotek) and data were plotted using Prism GraphPad 9.1.0.	Prism GraphPad suggested: None
Plates were immediately read at 450 nm on a VarioSkanLux plate reader (ThermoFisher) and data plotted and fit in Prism (GraphPad) using nonlinear regression sigmoidal, 4PL, X is log(concentration) to determine EC50 values from curve fits.	Prism suggested: (PRISM, RRID:SCR_005375) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
Binding at each time point (MFI) was determined normalizing to the MFI at 5 minutes time point and data plotted using GraphPad Prism v.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
Two rounds of reference-free 2D classification were performed using CryoSPARC (80) to select well-defined particle images.	CryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
Model building and refinement: UCSF Chimera (87) and Coot (88) were used to fit atomic models into the cryoEM maps.	Coot suggested: (Coot, RRID:SCR_014222)
Data were analyzed using FlowJo software.	FlowJo suggested: (FlowJo, RRID:SCR_008520)
The 3 RBD structures were each parameterized using tleap with the Amber ff14SB force field (100) for the protein, GLYCAM_06j-1 for the glycan (101), TIP3P for water (truncated octahedral cell with 18 Å buffer around solute) (102); the Joung & Cheatham parameters (103) were used for the ions neutralizing the charged solute (2 Cl- ions for Wuhan-Hu-1, 6 Cl- ions for BA.1 and BA.2) and the additional 0.15 M excess Na+ and Cl- ions (80 Na+ and 80 Cl- for Wuhan- Hu-1, 76 of each for BA.1 and BA.2).	Amber suggested: (AMBER, RRID:SCR_016151)

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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:

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Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

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