Potent monoclonal antibodies neutralize Omicron sublineages and other SARS-CoV-2 variants

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1. Version published to 10.1016/j.celrep.2022.111528

   Nov 1, 2022
2. 

   ScreenIT

   Jan 17, 2022

   SciScore for 10.1101/2022.01.12.22269023: (What is this?)

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

   Table 1: Rigor

   Ethics

   IRB: Convalescent COVID-19 plasma donor selection and lymphocyte isolation: Convalescent COVID-19 plasma donors were prospectively enrolled onto an institutional review board-approved protocol (Clinical Trials Registration, NCT04360278)19 and provided written informed consent for the study. Consent: Convalescent COVID-19 plasma donor selection and lymphocyte isolation: Convalescent COVID-19 plasma donors were prospectively enrolled onto an institutional review board-approved protocol (Clinical Trials Registration, NCT04360278)19 and provided written informed consent for the study. IACUC: Prophylactic and therapeutic studies in the hamster model: The preclinical hamster studies were approved …

   SciScore for 10.1101/2022.01.12.22269023: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Convalescent COVID-19 plasma donor selection and lymphocyte isolation: Convalescent COVID-19 plasma donors were prospectively enrolled onto an institutional review board-approved protocol (Clinical Trials Registration, NCT04360278)19 and provided written informed consent for the study. Consent: Convalescent COVID-19 plasma donor selection and lymphocyte isolation: Convalescent COVID-19 plasma donors were prospectively enrolled onto an institutional review board-approved protocol (Clinical Trials Registration, NCT04360278)19 and provided written informed consent for the study. IACUC: Prophylactic and therapeutic studies in the hamster model: The preclinical hamster studies were approved by the NIAID Animal Care and Use Committee. Euthanasia Agents: Animals were euthanized by CO2 inhalation prior to necropsy.
   Sex as a biological variable	In the prophylactic study, 80 male Syrian hamsters, aged 8-9 weeks, were randomly divided into groups of 10 animals each, bled for baseline serology and inoculated intraperitoneally with 0.5 mL of NE12, NA8, or IgG1 control at 12 mg/kg or 4 mg/kg, diluted to the concentration of 2.4 mg/mL or 0.8 mg/mL in PBS.
   Randomization	Single colonies were randomly picked from the third cycle output and screening of specific binders was performed, using phage ELISA against S-2P, with a BSA coated-plate as a negative control.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The plates were washed, and the secondary conjugated antibody (anti-His-HRP, anti-human Fab-HRP, or anti-M13-HRP) was added and incubated for 1 h at room temperature.	anti-His-HRP suggested: None anti-M13-HRP suggested: None
   Following incubation for 2 h at room temperature, the plate was washed, and a secondary anti-human Fab-HRP antibody (Jackson ImmunoResearch) was added for 1 h at room temperature.	anti-human Fab-HRP suggested: (SouthernBiotech Cat# 2085-05, RRID:AB_2795788)
   An in house- produced anti-poliovirus IgG antibody was used as a negative control43.	anti-poliovirus IgG suggested: None
   Following incubation for 2 h at room temperature, the plates were washed, and a secondary anti-human IgG Fc-HRP antibody (Jackson ImmunoResearch) was added and incubated for 1 h at room temperature.	anti-human IgG suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The mixture was then incubated with 104 ACE-2-expressing 293T cells (293T-hACE2.	293T suggested: None
   The SARS-CoV-2 stocks were titrated in Vero E6 cells by determination of the 50% tissue culture infectious dose (TCID50) as previously described46.	Vero E6 suggested: None
   Recombinant DNA
   Sentences	Resources
   The restriction enzyme digested light chain fragments from one donor or pooled from 5 donors were then cloned into the pComb 3H vector by electroporation42.	pComb 3H suggested: None
   One liter of 293 Freestyle cells at concentration of about 0.9 million cells per ml was transfected with 1 mg of S-2P plasmid, pre-mixed with 1 ml of 293fectin™ Transfection Reagent.	S-2P suggested: None
   B.1.1.529/Omicron; luciferase (pHR’ CMV Luc), a lentivirus backbone (pCMV ΔR8.2), and human transmembrane protease serine 2 (TMPRSS2) at a ratio of 1:20:20:0.3 into HEK293T/17 cells (ATCC) using the transfection reagent LiFect293™.	pCMV ΔR8.2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Live virus neutralization assay used in COVID-19 convalescent patients: Neutralization of live virus by patient plasmas was tested using a fluorescence reduction neutralization assay (FRNA) with SARS-CoV-2 [2019-nCoV/USA-WA1-A12/2020 (WA-1) from the US Centers for Disease Control and Prevention, Atlanta, GA, USA] at the NIH-NIAID Integrated Research Facility at Fort Detrick, MD, USA, as previously reported39.	SARS-CoV-2 suggested: (SARS-CoV-2-Sequences, RRID:SCR_018319)
   The data were plotted, and dose-response curves with and without inhibition with RBD were generated using Prism software (Graphpad Software, Inc.	Prism suggested: (PRISM, RRID:SCR_005375)
   Analyses were performed using Prism 9 (GraphPad Software)	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   The following steps were performed using Relion 3.1.051, unless otherwise stated.	Relion suggested: (RELION, RRID:SCR_016274)
   Local resolution was determined with ResMap 1.1.454.	ResMap suggested: None

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   Results from OddPub: Thank you for sharing your data.

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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: We found the following clinical trial numbers in your paper:
   

   Identifier	Status	Title
   NCT04360278	Active, not recruiting	Plasma Collection From Convalescent and/or Immunized Donors …

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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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 32, 33, 29 and 31. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.

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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 10.1101/2022.01.12.22269023v1 on medRxiv

   Jan 13, 2022