Structural diversity of the SARS-CoV-2 Omicron spike
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SciScore for 10.1101/2022.01.25.477784: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources Assays were run in two formats i.e., antibodies/ACE2 coated, or spike coated. antibodies/ACE2suggested: NoneAntibodies were incubated at room temperature for 1 hour, washed and binding detected with goat anti-human-HRP (Jackson ImmunoResearch Laboratories, PA) and TMB substrate. anti-human-HRPsuggested: NoneMouse anti-monkey IgG-HRP (Southern Biotech, CAT# 4700-05) and Goat anti-human IgG-HRP (Jackson ImmunoResearch Laboratories, CAT# 109-035-098) secondary antibodies were used to detect antibody bound to the spike … SciScore for 10.1101/2022.01.25.477784: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Antibodies Sentences Resources Assays were run in two formats i.e., antibodies/ACE2 coated, or spike coated. antibodies/ACE2suggested: NoneAntibodies were incubated at room temperature for 1 hour, washed and binding detected with goat anti-human-HRP (Jackson ImmunoResearch Laboratories, PA) and TMB substrate. anti-human-HRPsuggested: NoneMouse anti-monkey IgG-HRP (Southern Biotech, CAT# 4700-05) and Goat anti-human IgG-HRP (Jackson ImmunoResearch Laboratories, CAT# 109-035-098) secondary antibodies were used to detect antibody bound to the spike proteins. anti-monkey IgG-HRPsuggested: (SouthernBiotech Cat# 4700-05, RRID:AB_2796069)anti-human IgG-HRPsuggested: NoneSoftware and Algorithms Sentences Resources All spike ectodomains were cloned into the mammalian expression vector pαH and have been deposited to Addgene (10) (https://www.addgene.org). https://www.addgene.orgsuggested: (Addgene, RRID:SCR_002037)Sensogram data were analyzed using the BiaEvaluation software (Cytiva, MA) Negative-stain electron microscopy: Fab-spike complex of DH1044 was generated by mixing 5.9 μg of spike with 6.2 μg of Fab in ~25 μl of HEPES-buffered saline (HBS) containing 20 mM HEPES and 150 mM NaCl, pH 7.4, and incubating at 37 °C for 1 hr and using sample directly for negative stain without further purification. BiaEvaluationsuggested: (BIAevaluation Software, RRID:SCR_015936)Images were analyzed and 3D reconstructions generated using standard protocols with Relion 3.0 (28). Relionsuggested: (RELION, RRID:SCR_016274)The cryoSPARC (29) software was used for data processing. cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)Phenix (30, 31), Coot (32) Cootsuggested: (Coot, RRID:SCR_014222), Pymol (33), Chimera (34), ChimeraX (35) and Isolde (36) were used for model building and refinement. Pymolsuggested: (PyMOL, RRID:SCR_000305)Difference distance matrices (DDM): DDM were generated using the Bio3D package (39) implemented in R (R Core Team (2014). Bio3Dsuggested: NoneThe collected diffraction images were indexed, integrated, and scaled using HKL2000 (40) Initial phases were calculated by molecular replacement using Phenix. Phenixsuggested: (Phenix, RRID:SCR_014224)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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 34 and 27. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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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