Immune recall improves antibody durability and breadth to SARS-CoV-2 variants

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1. Version published to 10.1126/sciimmunol.abp8328

   Dec 16, 2022
2. 

   ScreenIT

   Sep 14, 2021

   SciScore for 10.1101/2021.09.09.459504: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Human subjects: Mass General Brigham Institutional Review Board approved this study and protocol.
   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

   Antibodies
   Sentences	Resources
   For the anti-S and anti-RBD antibody standard, the monoclonal antibody CR3022 was serially diluted 2 times from 0.5 μg/mL.	anti-S suggested: None anti-RBD suggested: None
   Cells were stained with Biolegend antibodies FITC anti-CD27 (356404), PE anti-CCR7 (353204), Percp	anti-CD27 suggested: (BioLegend Cat# 356404, RRID:AB_2561788) anti-CCR7 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell…

   SciScore for 10.1101/2021.09.09.459504: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Human subjects: Mass General Brigham Institutional Review Board approved this study and protocol.
   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

   Antibodies
   Sentences	Resources
   For the anti-S and anti-RBD antibody standard, the monoclonal antibody CR3022 was serially diluted 2 times from 0.5 μg/mL.	anti-S suggested: None anti-RBD suggested: None
   Cells were stained with Biolegend antibodies FITC anti-CD27 (356404), PE anti-CCR7 (353204), Percp	anti-CD27 suggested: (BioLegend Cat# 356404, RRID:AB_2561788) anti-CCR7 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Cell lines: HEK293T cell line (ATCC) was maintained in DMEM containing 10% FBS, 100 U/mL penicillin and 100 U/mL streptomycin (Gibco).	HEK293T suggested: None
   SARS-CoV-2 pseudovirus neutralization assay: 293T cells were co-transfected with pHDM vector expressing SARS-CoV-2 variants, pLenti CMV Puro LUC (w168-1), and psPAX2 (Addgene) with lipofetamine 3000.	293T suggested: None
   Recombinant DNA
   Sentences	Resources
   To be consistent with the pHDM-Wuhan-Hu-1-delta21 and pHDM-D614G-delta21 plasmids obtained from Addgene, the c-terminal 21 amino acid on all the variants were deleted (Crawford et al., 2020).	pHDM-Wuhan-Hu-1-delta21 suggested: None pHDM-D614G-delta21 suggested: None
   Binding signals were scored positive if OD405 values were above 5x PBS control on the same plate. mAb spike binding EC50 measurement: 293T cells were co-transfected with pHDM-Wuhan-Hu-1 and pMAX-GFP plasmids at a 4:1 ratio by lipofectamine 3000 (Thermo fisher).	pHDM-Wuhan-Hu-1 suggested: None pMAX-GFP suggested: RRID:Addgene_16007)
   293T cell pool cotransfected with pHEF-VsVg and pMAX-GFP plasmids at a 4:1 ratio was used as a negative control.	pHEF-VsVg suggested: RRID:Addgene_22501)
   SARS-CoV-2 pseudovirus neutralization assay: 293T cells were co-transfected with pHDM vector expressing SARS-CoV-2 variants, pLenti CMV Puro LUC (w168-1), and psPAX2 (Addgene) with lipofetamine 3000.	pHDM suggested: None psPAX2 suggested: RRID:Addgene_12260)
   Software and Algorithms
   Sentences	Resources
   After enrollment, clinical team identified one subject was not diagnosed by nasopharyngeal swab RT-PCR test, but by Quest Diagnostics antibody test and symptoms consistent with COVID-19 (Chen et al., 2020).	Quest suggested: (QUEST, RRID:SCR_005210)
   Graphpad software generated standard curves for each plate by non-linear regression.	Graphpad suggested: (GraphPad, RRID:SCR_000306)
   The EC50 for each S-binding mAb was reported as the concentration with 50% of maximal binding determined by non-linear regression using Graphpad Prism.	Graphpad Prism 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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   Read the original source
3. 

   Version published to 10.1101/2021.09.09.459504 on bioRxiv

   Sep 10, 2021