SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway
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Abstract
Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.
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SciScore for 10.1101/2022.01.03.21268111: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All participants gave written informed consent to take part in the study.
IRB: The DOVE study was approved by the North-West Liverpool Central Research Ethics Committee (REC reference 21/NW/0073).Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Measurement of SARS-CoV-2, HCoVs and influenza antibody response by electrochemiluminescence: IgG antibody titres were measured quantitatively against SARS-CoV-2 trimeric spike (S) protein, N-terminal domain (NTD), receptor binding domain (RBD) or nucleocapsid (N), human seasonal coronaviruses … SciScore for 10.1101/2022.01.03.21268111: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics Consent: All participants gave written informed consent to take part in the study.
IRB: The DOVE study was approved by the North-West Liverpool Central Research Ethics Committee (REC reference 21/NW/0073).Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources Measurement of SARS-CoV-2, HCoVs and influenza antibody response by electrochemiluminescence: IgG antibody titres were measured quantitatively against SARS-CoV-2 trimeric spike (S) protein, N-terminal domain (NTD), receptor binding domain (RBD) or nucleocapsid (N), human seasonal coronaviruses (HCoVs) 229E, OC43, NL63 and HKU1; and influenza A (Michigan H1, Hong Kong H3 and Shanghai H7) and B (Phuket HA and Brisbane) using MSD V-PLEX COVID-19 Coronavirus Panel 2 (K15369) and Respiratory Panel 1 (K15365) kits. SARS-CoV-2 trimeric spike (S) protein, N-terminal domain (NTD), receptor binding domain (RBD) or nucleocapsid (N)suggested: NoneExperimental Models: Cell Lines Sentences Resources Caco-2 are an immortalized cell line derived from human colorectal adenocarcinoma, primarily used as a model of the intestinal epithelial barrier. Caco-2suggested: CLS Cat# 300137/p1665_CaCo-2, RRID:CVCL_0025)A549 cells, a human alveolar adenocarcinoma line, were modified to stably express human ACE-2 and TMPRSS2. A549suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)Baby Hamster Kidney clone 21 cells and Vero ACE-2 TMPRSS2 cells were used in the isolation of live Omicron SARS-CoV-2. ACE-2 TMPRSS2suggested: NoneAll cell lines were maintained at 37°C and 5% CO2 in DMEM supplemented with 10% foetal bovine serum (FBS), except for Calu-3 cells which were supplemented with 20% FBS. Calu-3suggested: NoneGeneration of cell line expressing human ACE2 receptor: Lentiviral vectors encoding human ACE2 (GenBank NM_001371415.1) were produced as described previously69 and BHK-21 transduced cells were selected with 200µg/ml of hygromycin B. BHK-21suggested: NoneGeneration of cell lines used for fusion assays: Retrovirus vectors were produced by transfecting HEK- 293T cells with plasmid pQCXIP-GFP1-10 (Addgene #68715) or pQCXIP-BSR-GFP11 (Addgene #68716)53 and packaging vectors expressing MLV gal-pol and VSV-G using Lipofectamine 3000 (Invitrogen) according to manufacturer’s instructions. 293Tsuggested: NoneBHK-hACE2 cells previously seeded at a cell density of 3x10^5 cells in T25 flask were inoculated with 400-500µL of resuspended samples in 5ml of complete medium (DMEM 2% FCS supplemented with gentamicin, penicillin- streptomycin and amphotericin B as above). BHK-hACE2suggested: NoneBriefly, HEK293, HEK293T, and 293-ACE269 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 200mM L-glutamine, 100µg/ml streptomycin and 100 IU/ml penicillin. HEK293suggested: None293-ACE269suggested: NoneHEK293T cells were transfected with the appropriate SARS-CoV-2 S gene expression vector (wild type or variant) in conjunction with p8.9171 and pCSFLW72 using polyethylenimine (PEI, Polysciences, Warrington, USA). HEK293Tsuggested: NoneFusion assay: AAT-GFP1-10 and AAT-BSR-GFP11 cells were trypsinized and mixed at a ratio of 1:1 to seed a total of 2x10^4 cells/well in black 96-well plate (Greiner) in FluoroBrite DMEM medium (Thermo Fischer Scientific) supplemented with 2% FBS. AAT-BSR-GFP11suggested: NoneRecombinant DNA Sentences Resources Generation of cell lines used for fusion assays: Retrovirus vectors were produced by transfecting HEK- 293T cells with plasmid pQCXIP-GFP1-10 (Addgene #68715) or pQCXIP-BSR-GFP11 (Addgene #68716)53 and packaging vectors expressing MLV gal-pol and VSV-G using Lipofectamine 3000 (Invitrogen) according to manufacturer’s instructions. pQCXIP-GFP1-10suggested: RRID:Addgene_68715)pQCXIP-BSR-GFP11suggested: RRID:Addgene_68716)VSV-Gsuggested: RRID:Addgene_138479)HEK293T cells were transfected with the appropriate SARS-CoV-2 S gene expression vector (wild type or variant) in conjunction with p8.9171 and pCSFLW72 using polyethylenimine (PEI, Polysciences, Warrington, USA). pCSFLW72suggested: NoneSoftware and Algorithms Sentences Resources Sequences were aligned by mapping to the SARS-CoV-2 reference Wuhan-Hu-1 using Minimap2 (https://doi.org/10.1093/bioinformatics/bty191). Minimap2suggested: (Minimap2, RRID:SCR_018550)Data were analysed using MARS software and plotted with GraphPad prims 9 software. GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Structural modelling: The file 6vsb_1_1_1.pdb containing a complete model of the full-length glycosylated spike homotrimer in open conformation with one monomer having the receptor-binding domain in the ‘up’ position was obtained from the CHARMM-GUI Archive [cite Woo et al. 2020, cite CHARMM-GUI 2021]. CHARMM-GUI Archivesuggested: NoneResults from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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 found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).
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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