Omicron BA.1 and BA.2 neutralizing activity elicited by a comprehensive panel of human vaccines

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   ScreenIT

   Mar 19, 2022

   SciScore for 10.1101/2022.03.15.484542: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: donors: Convalescent plasma, Ad26.COV2.S, and some BNT162b2 samples were obtained from the HAARVI study approved by the University of Washington Human Subjects Division Institutional Review Board (STUDY00000959).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: None of the cell lines used were authenticated or tested for mycoplasma contamination. Contamination: None of the cell lines used were authenticated or tested for mycoplasma contamination.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Infected cells were then washed an additional five times with DMEM prior to adding media …

   SciScore for 10.1101/2022.03.15.484542: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: donors: Convalescent plasma, Ad26.COV2.S, and some BNT162b2 samples were obtained from the HAARVI study approved by the University of Washington Human Subjects Division Institutional Review Board (STUDY00000959).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Authentication: None of the cell lines used were authenticated or tested for mycoplasma contamination. Contamination: None of the cell lines used were authenticated or tested for mycoplasma contamination.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Infected cells were then washed an additional five times with DMEM prior to adding media supplemented with anti-VSV-G antibody (I1-mouse hybridoma supernatant diluted 1:25, from CRL-2700, ATCC) to reduce parental background.	anti-VSV-G suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: Cell lines used in this study were obtained from ThermoFisher Scientific (HEK293T) or were kindly gifted by Florian	HEK293T suggested: RRID:CVCL_HA71)
   Briefly, HEK-293T cells seeded in poly-D-lysine coated 100 mm dishes at ∼75 % confluency were washed five times with Opti-MEM and transfected using 24 μg of the S glycoprotein plasmid with Lipofectamine 2000 (Life Technologies).	HEK-293T suggested: None
   Pseudotyped VSV neutralization assay: To evaluate neutralization of SARS-CoV-2 G614 and Omicron BA.1 and BA.2 pseudotypes by plasma of vaccinees or previously infected individuals, Vero-TMPRSS2 cells in DMEM supplemented with 10% FBS, 1% PenStrep, and 8 ug/mL puromycin were seeded at 60-70% confluency into white clear-bottom 96 well plates (Corning) and incubated at 37°C.	Vero-TMPRSS2 suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
   Media was removed from the cells and 40 μL from each well (containing plasma and pseudovirus) was transferred to the 96-well plate seeded with Vero-TMPRESS2 cells and incubated at 37°C for 2 h.	Vero-TMPRESS2 suggested: None
   Recombinant DNA
   Sentences	Resources
   The plasmids encoding the SARS-CoV-2 Omicron S variants BA.1 and BA.2 were generated by overlap PCR mutagenesis of the wildtype plasmid, pcDNA3.1(+)-spike-D19 (Table S1) (64)	pcDNA3.1 suggested: RRID:Addgene_79663)
   Software and Algorithms
   Sentences	Resources
   Relative luciferase units were plotted and normalized in Prism (GraphPad): 100% neutralization being cells lacking pseudovirus and 0% neutralizing being cells containing virus but lacking plasma.	Prism suggested: (PRISM, RRID:SCR_005375)
   Prism (GraphPad) nonlinear regression with “[inhibitor] versus normalized response with a variable slope” was used to determine ID50 values from curve fits with 2-3 repeats.	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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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2. 

   Version published to 10.1101/2022.03.15.484542v1 on bioRxiv

   Mar 16, 2022