Differential Evasion of Delta and Omicron Immunity and Enhanced Fusogenicity of SARS-CoV-2 Omicron BA.4/5 and BA.2.12.1 Subvariants

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   ScreenIT

   May 20, 2022

   SciScore for 10.1101/2022.05.16.492158: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: Demographic information was self-reported, and all subjects provided informed consent.
   Sex as a biological variable	Sera were collected 3-4 weeks post-second vaccine dose for 15 HCWs (7 female and 8 male; median age 37; age range 31-56), which included 4 Moderna mRNA-1273 and 11 Pfizer/BioNTech BNT162b2 vaccinated HCWs.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Once dissociated, cells were fixed in 4% formaldehyde diluted in 1X PBS and stained with primary antibody anti-S1 (Sino Biological, 40150-T62).	anti-S1 suggested: None
   Cells were then stained with secondary antibody …

   SciScore for 10.1101/2022.05.16.492158: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: Demographic information was self-reported, and all subjects provided informed consent.
   Sex as a biological variable	Sera were collected 3-4 weeks post-second vaccine dose for 15 HCWs (7 female and 8 male; median age 37; age range 31-56), which included 4 Moderna mRNA-1273 and 11 Pfizer/BioNTech BNT162b2 vaccinated HCWs.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Once dissociated, cells were fixed in 4% formaldehyde diluted in 1X PBS and stained with primary antibody anti-S1 (Sino Biological, 40150-T62).	anti-S1 suggested: None
   Cells were then stained with secondary antibody anti-rabbit-IgG-FITC (Sigma, F9887) and processed by a Life Technologies Attune NxT flow cytometer.	anti-rabbit-IgG-FITC suggested: None
   Membranes were blotted with anti-S1 (Sino Biological, 40150-T62), anti-p24 (Abcam, ab63917; NIH ARP-1513), and anti-GAPDH (Santa Cruz Biotech, sc-47724).	anti-GAPDH suggested: (Santa Cruz Biotechnology Cat# sc-47724, RRID:AB_627678)
   Anti-mouse-IgG-Peroxidase (Sigma, A5278) and anti-rabbit-IgG-HRP (Sigma, A9169) were used as secondary antibodies accordingly.	Anti-mouse-IgG-Peroxidase suggested: None anti-rabbit-IgG-HRP suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HEK293T (ATCC CRL-11268, RRID: CVCL_1926) and HEK293T-ACE2 (BEI NR-52511, RRID: CVCL_A7UK) cells were maintained in DMEM (Gibco, 11965-092) supplemented with 10% FBS (Sigma, F1051) and 1% penicillin-streptomycin (HyClone, SV30010).	HEK293T detected: (ATCC Cat# CRL-11268, RRID:CVCL_1926) HEK293T-ACE2 detected: ( RRID:CVCL_A7UK)
   CaLu-3 cells (RRID: CVCL_0609) were maintained in EMEM (ATCC 30-2003) supplemented with 10% FBS and 1% penicillin-streptomycin.	CaLu-3 detected: (ATCC Cat# HTB-55, RRID:CVCL_0609)
   pNL4-3-inGluc and spike constructs were transfected into HEK-293T cells in a 2:1 ration using polyethylenimine transfection.	HEK-293T suggested: None
   Pseudotyped virus for each SARS-CoV-2 spike, produced in parallel, were used to infect target HEK293T-ACE2 or CaLu-3 cells.	CaLu-3 suggested: KCLB Cat# 30055, RRID:CVCL_0609)
   Virus and serum were incubated for 1 hr at 37°C and then added to HEK293T-ACE2 cells for infection by neutralized virus.	HEK293T-ACE2 suggested: None
   Spike detection by flow cytometry: HEK293T cells used to produce pseudotyped vectors were harvested and fixed 72 hrs after transfection.	HEK293T suggested: None
   Recombinant DNA
   Sentences	Resources
   GenScript Biotech (Piscataway, NJ) produced and cloned SARS-CoV-2 spike constructs with N- and C-terminal flag tags using Kpn I and BamH I restriction enzyme cloning into a pcDNA3.1 vector.	pcDNA3.1 suggested: RRID:Addgene_79663)
   pNL4-3-inGluc and spike constructs were transfected into HEK-293T cells in a 2:1 ration using polyethylenimine transfection.	pNL4-3-inGluc suggested: None
   Software and Algorithms
   Sentences	Resources
   NT50 values were determined by least-squares-fit, non-linear regression in GraphPad Prism 9 (San Diego, CA).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Results were analyzed using FlowJo v7.6.5 (Ashland, OR).	FlowJo suggested: (FlowJo, RRID:SCR_008520)
   NT50 values were determined by least-squares fit non-linear regression in GraphPad Prism 9.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Western Blot quantification was performed using NIH ImageJ and by setting the ratio of S1/S and S1/p24 of BA.2 to 1.00.	ImageJ suggested: (ImageJ, RRID:SCR_003070)

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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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   Version published to 10.1101/2022.05.16.492158 on bioRxiv

   May 17, 2022