Considerable escape of SARS-CoV-2 Omicron to antibody neutralization
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SciScore for 10.1101/2021.12.14.472630: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IACUC: This study was approved by the ILE DE FRANCE IV ethical committee.
Consent: At enrolment, written informed consent was collected and participants completed a questionnaire which covered sociodemographic characteristics, virological findings (SARS-CoV-2 RT-PCR results, including date of testing), clinical data (date of symptom onset, type of symptoms, hospitalization), and data related to anti-SARS-CoV-2 vaccination if ever (brand product, date of first and second doses).
Field Sample Permit: The leftover material of the sample was used in this study after performing routine diagnostics, within the context of the mandate that was provided to UZ/KU Leuven as National Reference Center …SciScore for 10.1101/2021.12.14.472630: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IACUC: This study was approved by the ILE DE FRANCE IV ethical committee.
Consent: At enrolment, written informed consent was collected and participants completed a questionnaire which covered sociodemographic characteristics, virological findings (SARS-CoV-2 RT-PCR results, including date of testing), clinical data (date of symptom onset, type of symptoms, hospitalization), and data related to anti-SARS-CoV-2 vaccination if ever (brand product, date of first and second doses).
Field Sample Permit: The leftover material of the sample was used in this study after performing routine diagnostics, within the context of the mandate that was provided to UZ/KU Leuven as National Reference Center (NRC) of respiratory pathogens, as described in detail in the Belgian Royal Decree of 09/02/2011.Sex as a biological variable not detected. Randomization The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. Blinding The experiments were not randomized and the investigators were not blinded to allocation during experiments and outcome assessment. Power Analysis No statistical methods were used to predetermine sample size. Cell Line Authentication Contamination: Cells were tested negative for mycoplasma. Table 2: Resources
Antibodies Sentences Resources The other human SARS-CoV-2 anti-RBD neutralizing antibodies (ADG2 or Adintrevimab, AZD1061 (COV2-2130) or Cilgavimab, AZD8895 (COV2-2196) or Tixagevimab, CT-P59 or Regdanvimab, LY-CoV016 (CB6) or Etesevimab, LY-CoV555 or Bamlanivimab, REGN10933 or Casirivimab, REGN10987 or Imdevimab, and VIR-7831 (S309) or Sotrovimab 13,14,15,16,17,18,19 were produced as followed. anti-RBD neutralizing antibodies ( ADG2suggested: NoneVIR-7831suggested: NonePurified digested DNA fragments were cloned into human Igγ1- and Ig κ-/ Igλ-expressing vectors 38 and recombinant IgG1 antibodies were produced by transient co-transfection of Freestyle™ 293-F suspension cells (Thermo Fisher Scientific) using PEI-precipitation method as previously described 39. recombinant IgG1suggested: NoneIgG1 antibodies were purified by batch/gravity-flow affinity chromatography using protein G sepharose 4 fast flow beads (Cytivia) according to the manufacturer’s instructions, dialyzed against PBS using Slide-A-Lyzer® dialysis cassettes (Thermo Fisher Scientific), quantified using NanoDrop 2000 instrument (Thermo Fisher Scientific) and checked for purity and quality on a silver-stained SDS-PAGE gel (3-8% Tris-Acetate Novex, Thermo Fisher Scientific). IgG1suggested: NoneThe anti-NTD neutralizing antibody NTD-18 and the pan-coronavirus anti-S2 non-neutralizing antibody Ab-10 were previously described 9,10. anti-NTDsuggested: Noneanti-S2 non-neutralizingsuggested: NoneExperimental Models: Cell Lines Sentences Resources The variant strains were isolated from nasal swabs using Vero E6 cells and amplified by one or two passages. Vero E6suggested: RRID:CVCL_XD71)Viruses were sequenced directly on nasal swabs, and after one or two passages on Vero cells. Verosuggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)Software and Algorithms Sentences Resources 1 were prepared with The PyMOL Molecular Graphics System, Version 2.1 Schrödinger, LLC. PyMOLsuggested: (PyMOL, RRID:SCR_000305)Software v3.2.1 (Life Technologies) and analysed with FlowJo 10.7.1 (Becton Dickinson). FlowJosuggested: (FlowJo, RRID:SCR_008520)Figures were drawn on Prism 9 (GraphPad Software). GraphPadsuggested: (GraphPad Prism, RRID:SCR_002798)Statistical analysis was conducted using GraphPad Prism 9. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Potential limitations of our work include a low number of vaccine recipients and convalescents sera analyzed and the lack of characterization of cellular immunity, which is known to be more cross-reactive than the humoral response. Our results may therefore partly underestimate the residual protection offered by vaccines and previous infections against Omicron infection, in particular with regard to the severity of disease. We only analyzed sera sampled 1 month after the booster dose, or after vaccination of infected individuals. Future work with more individuals and longer survey periods will help characterize the duration of the humoral response against Omicron. We focused on immune responses elicited by Pfizer and AstraZeneca vaccination. It will be worth determining the potency of other vaccines against this variant. Our results have important public health consequences regarding the use of therapeutic mAbs and vaccines. Clinical indications of mAbs include pre-exposure prophylaxis in individuals unable to mount an immune response, as well as prevention of COVID-19 in infected individuals at high risk for evolution towards severe disease. Antibody-based treatment strategies need to be rapidy adapted to Omicron. Experiments in preclinical models or clinical trials are warranted to assess whether the drops in IC50 are translated into impaired clinical efficacy of the mAbs that retain efficacy against Omicron. Most of the low-income countries display a weak vaccination rate,...
Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04750720 Recruiting Study of the Kinetics of COVID-19 Antibodies for 24 Months i… 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.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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