Increased resistance of SARS-CoV-2 Omicron variant to neutralization by vaccine-elicited and therapeutic antibodies

Article activity feed

1. Version published to 10.1016/j.ebiom.2022.103944

   Apr 1, 2022
2. 

   ScreenIT

   Jan 3, 2022

   SciScore for 10.1101/2021.12.28.474369: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	Consent: Human sera and monoclonal antibodies: Human sera were collected at the NYU Vaccine Center with written consent of participants under IRB-approved protocols 18-02035 and 18-02037.
   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

   Experimental Models: Cell Lines
   Sentences	Resources
   Cells: 293T, ACE2.293T and Vero cells were grown in Dulbecco’s Modified Eagle’s Medium/10% fetal bovine serum at 37°C under 5% CO2.	Vero suggested: None
   SARS-CoV-2 spike protein lentiviral pseudotypes: Spike protein pseudotyped lentiviruses were produced by cotransfection of 293T cells with pMDL …

   SciScore for 10.1101/2021.12.28.474369: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Ethics	Consent: Human sera and monoclonal antibodies: Human sera were collected at the NYU Vaccine Center with written consent of participants under IRB-approved protocols 18-02035 and 18-02037.
   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

   Experimental Models: Cell Lines
   Sentences	Resources
   Cells: 293T, ACE2.293T and Vero cells were grown in Dulbecco’s Modified Eagle’s Medium/10% fetal bovine serum at 37°C under 5% CO2.	Vero suggested: None
   SARS-CoV-2 spike protein lentiviral pseudotypes: Spike protein pseudotyped lentiviruses were produced by cotransfection of 293T cells with pMDL Gag/Pol packaging vector, lentiviral vector plenti.	293T suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)
   Recombinant DNA
   Sentences	Resources
   Plasmids: Plasmid expression vectors used in the production of lentiviral pseudotypes pMDL, pcVSV.G, pRSV.	pRSV suggested: RRID:Addgene_106453)
   Rev and the lentiviral dual reporter virus genome pLenti.	pLenti suggested: RRID:Addgene_125133)
   The full-length coding sequence was generated by overlap extension PCR with the two fragments amplified with external primers containing a Kpn-I and Xho-I sites and then cloned into pcDNA6	pcDNA6 suggested: RRID:Addgene_134280)
   Expression vectors encoding spike proteins with the individual mutations of the Omicron spike protein were generated by overlap extension PCR mutagenesis using the D614G spike protein plasmid pcCOV2.Δ19.D614G as template.	pcCOV2.Δ19.D614G suggested: None
   SARS-CoV-2 spike protein lentiviral pseudotypes: Spike protein pseudotyped lentiviruses were produced by cotransfection of 293T cells with pMDL Gag/Pol packaging vector, lentiviral vector plenti.	pMDL Gag/Pol suggested: None
   Software and Algorithms
   Sentences	Resources
   Data were analyzed using GraphPad Prism 8 software and statistical significance was determined by the two-tailed unpaired t-test or nonparametric ANOVA test.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Analyses of the structures of the SARS-CoV-2 spike protein with antibody Fabs was performed with the PyMOL Molecular Graphics System,	PyMOL suggested: (PyMOL, RRID:SCR_000305)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Study Limitations: This study was done on a relatively small number of participants which limits the resolution of fine difference in antibody titers in the different groups. In addition, it depends entirely on pseudotyped viruses rather than antibody neutralization of live virus. While pseudotyped virus has been shown to provide similar data to that of the live virus assays, it is conceivable that there could be differences [30].

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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.

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   Results from scite Reference Check: We found no unreliable references.

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3. 

   Version published to 10.1101/2021.12.28.474369v1 on bioRxiv

   Dec 30, 2021