Shared N417-Dependent Epitope on the SARS-CoV-2 Omicron, Beta, and Delta Plus Variants
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Abstract
The evolution of SARS-CoV-2 has resulted in variants of concern (VOCs) with distinct spike mutations conferring various immune escape profiles. These variable mutations also influence the cross-reactivity of the antibody response mounted by individuals infected with each of these variants.
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SciScore for 10.1101/2022.04.24.22273395: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical clearance was obtained for each cohort from Human Research Ethics Committees from the University of Pretoria (247/2020) and University of Cape Town (R021/2020). 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 Following cDNA synthesis VH, Vκ, and Vλ antibody genes were amplified as previously described (38, 39). Vλsuggested: NoneMonoclonal antibodies CB6, CA1 and CR3022 were used as controls. CA1suggested: NoneCR3022suggested: NoneSubsequent washing was followed by the addition of an anti-human horseradish peroxidase secondary … SciScore for 10.1101/2022.04.24.22273395: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: Ethical clearance was obtained for each cohort from Human Research Ethics Committees from the University of Pretoria (247/2020) and University of Cape Town (R021/2020). 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 Following cDNA synthesis VH, Vκ, and Vλ antibody genes were amplified as previously described (38, 39). Vλsuggested: NoneMonoclonal antibodies CB6, CA1 and CR3022 were used as controls. CA1suggested: NoneCR3022suggested: NoneSubsequent washing was followed by the addition of an anti-human horseradish peroxidase secondary antibody diluted to 1:3000 and the plates were incubated for a further 1 hour. anti-human horseradish peroxidase secondarysuggested: NoneAntibody-dependent cellular cytotoxicity (ADCC) assay: The ability of the mAb to cross-link between FcγRIIIa (CD16) and spike expressed on cells was used as a proxy for ADCC. CD16suggested: NoneAntibody-dependent cellular phagocytosis (ADCP) Antibody-dependent cellular phagocytosis ( ADCP )suggested: NoneExperimental Models: Cell Lines Sentences Resources Briefly, human embryonic kidney (HEK) 293T cells were co-transfected with the SARS-CoV-2 spike plasmid of interest together with a firefly luciferase encoding lentivirus backbone plasmid for 72 hours. HEKsuggested: None293Tsuggested: NoneSubsequently, 1×104 HEK 293T cells engineered to over-express ACE-2, provided by Michael Farzan, were added and incubated at 37°C, 5% C02 for 72 hours upon which the luminescence of the luciferase gene was measured. HEK 293Tsuggested: NoneFollowing this, Jurkat-Lucia™ NFAT-CD16 cells (Invitrogen) were added to the reaction, and incubated for a further 24 hours at 37°C with 10% CO2. NFAT-CD16suggested: RRID:CVCL_A7ZT)Overnight incubation was carried out with monocytic THP-1 cells, followed by analysis on the FACSAria II (BD Biosciences). THP-1suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)Results 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 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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