Omicron BA.2 specifically evades broad sarbecovirus neutralizing antibodies
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Abstract
Omicron sub-lineage BA.2 has rapidly surged globally, accounting for over 60% of recent SARS-CoV-2 infections. Newly acquired RBD mutations and high transmission advantage over BA.1 urge the investigation of BA.2’s immune evasion capability. Here, we show that BA.2 causes strong neutralization resistance, comparable to BA.1, in vaccinated individuals’ plasma. However, BA.2 displays more severe antibody evasion in BA.1 convalescents, and most prominently, in vaccinated SARS convalescents’ plasma, suggesting a substantial antigenicity difference between BA.2 and BA.1. To specify, we determined the escaping mutation profiles 1,2 of 714 SARS-CoV-2 RBD neutralizing antibodies, including 241 broad sarbecovirus neutralizing antibodies isolated from SARS convalescents, and measured their neutralization efficacy against BA.1, BA.1.1, BA.2. Importantly, BA.2 specifically induces large-scale escape of BA.1/BA.1.1-effective broad sarbecovirus neutralizing antibodies via novel mutations T376A, D405N, and R408S. These sites were highly conserved across sarbecoviruses, suggesting that Omicron BA.2 arose from immune pressure selection instead of zoonotic spillover. Moreover, BA.2 reduces the efficacy of S309 (Sotrovimab) 3,4 and broad sarbecovirus neutralizing antibodies targeting the similar epitope region, including BD55-5840. Structural comparisons of BD55-5840 in complexes with BA.1 and BA.2 spike suggest that BA.2 could hinder antibody binding through S371F-induced N343-glycan displacement. Intriguingly, the absence of G446S mutation in BA.2 enabled a proportion of 440-449 linear epitope targeting antibodies to retain neutralizing efficacy, including COV2-2130 (Cilgavimab) 5 . Together, we showed that BA.2 exhibits distinct antigenicity compared to BA.1 and provided a comprehensive profile of SARS-CoV-2 antibody escaping mutations. Our study offers critical insights into the humoral immune evading mechanism of current and future variants.
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SciScore for 10.1101/2022.02.07.479349: (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 B cells were then stained with FITC anti-human CD19 antibody (BioLegend, 392508) anti-human CD19suggested: (BioLegend Cat# 392508, RRID:AB_2750099)FITC anti-human CD20 antibody (BioLegend, 302304) anti-human CD20suggested: (BioLegend Cat# 302304, RRID:AB_314252)Brilliant Violet 421™ anti-human CD27 antibody (BioLegend, 302824) anti-human CD27suggested: (BioLegend Cat# 302824, RRID:AB_11150782)anti-human IgM antibody (BioLegend, 314532) anti-human IgMsuggested: (BioLegend Cat# 314532, RRID:AB_2566485)High-throughput antibody-escape mutation profiling: The previously described high-throughput MACS … SciScore for 10.1101/2022.02.07.479349: (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 B cells were then stained with FITC anti-human CD19 antibody (BioLegend, 392508) anti-human CD19suggested: (BioLegend Cat# 392508, RRID:AB_2750099)FITC anti-human CD20 antibody (BioLegend, 302304) anti-human CD20suggested: (BioLegend Cat# 302304, RRID:AB_314252)Brilliant Violet 421™ anti-human CD27 antibody (BioLegend, 302824) anti-human CD27suggested: (BioLegend Cat# 302824, RRID:AB_11150782)anti-human IgM antibody (BioLegend, 314532) anti-human IgMsuggested: (BioLegend Cat# 314532, RRID:AB_2566485)High-throughput antibody-escape mutation profiling: The previously described high-throughput MACS (magnetic-activated cell sorting)-based antibody-escape mutation profiling system was used to characterize RBD escaping mutation profile for neutralizing antibodies. antibody-escapesuggested: NoneA, E, n are parameters, where E is the desired EC50 value for the specific antibody and antigen. antigen .suggested: NoneFor protein production, these expression plasmids, as well as the plasmids encoding the antigen-binding fragments (Fabs) of the antibodies described in this paper, were transfected into the HEK293F cells using polyethylenimine (Polysciences). antigen-bindingsuggested: NoneExperimental Models: Cell Lines Sentences Resources Pseudovirus detection of PCoV-GD and RaTG13 was performed in 293T cells overexpressing human angiotensin-converting enzyme 2 (293T-hACE2 cells) 293Tsuggested: None293T-hACE2suggested: NoneOther pseudovirus neutralization assays were performed using the Huh-7 cell line (Japanese Collection of Research Bioresources [JCRB], 0403) Huh-7suggested: JCRB Cat# JCRB0403, RRID:CVCL_0336)About 104 digested Vero cells (ATCC, CCL-81) were seeded in plates and cultured for 5 days. Verosuggested: NoneHealthy HEK293 cells were passaged into a new cell culture and grown in suspension at 37 °C, 120 RPM, 8% CO2 to logarithmic growth phase and transfected with the recombinant constructs by using liposomal vesicles as DNA carrier. HEK293suggested: NoneFor protein production, these expression plasmids, as well as the plasmids encoding the antigen-binding fragments (Fabs) of the antibodies described in this paper, were transfected into the HEK293F cells using polyethylenimine (Polysciences). HEK293Fsuggested: RRID:CVCL_6642)Recombinant DNA Sentences Resources Pseudovirus neutralization assay: SARS-CoV-2 spike (GenBank: MN908947) , Pangolin-GD spike (GISAID: EPI_ISL_410721), RaTG13 spike (GISAID: EPI_ISL_402131), SARS-COV-1 spike (GenBank: AY278491), Omicron BA.1 spike (A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F), BA.2 spike (GISAID: EPI_ISL_7580387), BA.1.1 spike (BA.1+R346K), plasmid is constructed into pcDNA3.1 vector. pcDNA3.1suggested: RRID:Addgene_79663)The purified PCR products were ligated to the secretory expression vector pCMV3 with CMV promoter, and then transformed into E. coli competent cells XL1-blue. pCMV3suggested: RRID:Addgene_161029)Software and Algorithms Sentences Resources FACS data were analyzed using FlowJo™ v10.8 (BD Biosciences) FlowJo™suggested: (FlowJo, RRID:SCR_008520)V(D)J gene annotation was performed using NCBI IgBlast (v1.17.1) with the IMGT reference. IgBlastsuggested: (IgBLAST, RRID:SCR_002873)The V-J pairs were visualized by R package circlize (v0.4.10) circlizesuggested: (circlize, RRID:SCR_002141)VarianceThreshold of scikit-learn Python package (v0.24.2) with the variance threshold as 0.1. Pythonsuggested: (IPython, RRID:SCR_001658)TSNE of scikit-learn. scikit-learnsuggested: (scikit-learn, RRID:SCR_002577)All t-SNE plots were generated by R package ggplot2 (v3.3.3) ggplot2suggested: (ggplot2, RRID:SCR_014601)To improve the density surrounding the RBD-Fab region, UCSF Chimera55 and Relion56 were used to generate the masks, and local refinement was then performed using cryoSPARC. cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)Figures were prepared using USCF ChimeraX59 and Pymol (Schrödinger, LLC.). 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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