Activity of convalescent and vaccine serum against a B.1.1.529 variant SARS-CoV-2 isolate

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   ScreenIT

   Dec 24, 2021

   SciScore for 10.1101/2021.12.20.21268134: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: The study was reviewed and approved by the Mount Sinai Hospital Institutional Review Board (IRB-20-03374). Consent: All participants signed written consent forms prior to sample and data collection.
   Sex as a biological variable	The B.1.1.529 isolate USA/NY-MSHSPSP-PV44488/2021 represents one of the first cases diagnosed in New York State (female, age bracket: 30-40 years, mild COVID-19 symptoms, vaccinated and boosted) in late November 2021.
   Randomization	not detected.
   Blinding	All samples were analyzed in a blinded manner.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After 2-hour incubation, plates were washed three times with …

   SciScore for 10.1101/2021.12.20.21268134: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: The study was reviewed and approved by the Mount Sinai Hospital Institutional Review Board (IRB-20-03374). Consent: All participants signed written consent forms prior to sample and data collection.
   Sex as a biological variable	The B.1.1.529 isolate USA/NY-MSHSPSP-PV44488/2021 represents one of the first cases diagnosed in New York State (female, age bracket: 30-40 years, mild COVID-19 symptoms, vaccinated and boosted) in late November 2021.
   Randomization	not detected.
   Blinding	All samples were analyzed in a blinded manner.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After 2-hour incubation, plates were washed three times with PBS-T and 50 μl/well of the pre-diluted secondary antibody anti-human IgG (Fab-specific) horseradish peroxidase (HRP) antibody (produced in goat; Sigma-Aldrich, Cat# A0293, RRID: AB_257875) diluted 1:3,000 in PBS-T containing 1% milk powder were added.	anti-human IgG detected: (Sigma-Aldrich Cat# A0293, RRID:AB_257875)
   During this time the primary antibody was biotinylated according to manufacturer protocol (Thermo Scientific EZ-Link NHS-PEG4-Biotin).	NHS-PEG4-Biotin suggested: None
   Blocking solution was removed and 100 μl/well of biotinylated mAb 1C7C723, a mouse anti-SARS nucleoprotein monoclonal antibody generated at the Center for Therapeutic Antibody Development at The Icahn School of Medicine at Mount Sinai ISMMS (Millipore Sigma, Cat# ZMS1075) at a concentration of 1μg/ml in PBS, 1% BSA was added for 1 hour at RT.	anti-SARS suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   FreeStyle™ 293-F cells (Gibco, #R79007) were cultured in ESF-SFM medium (Expression Systems, cat. no. 98-001) supplemented with 100 U/ml penicillin and 100 μg/ml streptomycin (Gibco, #15140122).	293-F suggested: RRID:CVCL_6642)
   Supplemental Table 3 summarizes the amino acid substitutions, insertions and deletions in the spike region of each of the three viral isolates Viruses were grown by adding 200ul of viral transport media from the nasopharyngeal swabs to Vero-E6-TMPRSS2 cells in culture media supplemented with 0.5 μg/ml amphotericin B (Gibco, # 15290-018).	Vero-E6-TMPRSS2 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Recombinant DNA
   Sentences	Resources
   The proteins were cloned into a mammalian expression vector, pCAGGS as described earlier19,20 and purified after transient transfections with each respective plasmid.	pCAGGS suggested: RRID:Addgene_127347)
   21,22 The NTD protein constructs (residues 1-306) were cloned into pVRC8400 expression vector between SalI and NotI endonuclease restriction sites yielding an NTD with an human rhinovirus (HRV) 3C protease-cleavable C-terminal hexahistidine and a streptavidin-binding protein tags.	pVRC8400 suggested: RRID:Addgene_63163)
   Software and Algorithms
   Sentences	Resources
   Analysis was performed using Prism 7 software (GraphPad).	Prism suggested: (PRISM, RRID:SCR_005375) 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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   Version published to 10.1101/2021.12.20.21268134 on medRxiv

   Dec 21, 2021