Spike-Dependent Opsonization Indicates Both Dose-Dependent Inhibition of Phagocytosis and That Non-Neutralizing Antibodies Can Confer Protection to SARS-CoV-2

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1. Version published to 10.3389/fimmu.2021.808932

   Jan 14, 2022
2. 

   ScreenIT

   Oct 22, 2021

   SciScore for 10.1101/2021.10.14.464464: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All participants gave written informed consent to participate in the study which was approved by the Swedish ethical review authority (2020/01747). IRB: All the animal experiments were performed under the approval of the regional animal experimental ethics committee in Stockholm (16765-2020).
   Sex as a biological variable	Animal experiments: Forty-two nine-week old female K18 hACE2 (B6.Cg-Tg(K18-ACE2)2Prlmn/J) mice were inoculated intranasally with 105 PFU of SARS-CoV-2 (Wuhan strain, isolate SARS-CoV-2/01/human/2020/SWE, sourced from the Swedish Health Authorities).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: …

   SciScore for 10.1101/2021.10.14.464464: (What is this?)

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

   Table 1: Rigor

   Ethics	Consent: All participants gave written informed consent to participate in the study which was approved by the Swedish ethical review authority (2020/01747). IRB: All the animal experiments were performed under the approval of the regional animal experimental ethics committee in Stockholm (16765-2020).
   Sex as a biological variable	Animal experiments: Forty-two nine-week old female K18 hACE2 (B6.Cg-Tg(K18-ACE2)2Prlmn/J) mice were inoculated intranasally with 105 PFU of SARS-CoV-2 (Wuhan strain, isolate SARS-CoV-2/01/human/2020/SWE, sourced from the Swedish Health Authorities).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The cells were then washed with PBS, blocked in 2% BSA and stained with antibodies against CD19-PE (BD-555413), CD3-BV510 (BD-564713), IgG-BV421 (BD-562581) and a live/Dead Sytox stain.	CD19-PE suggested: None CD3-BV510 suggested: None BD-564713) , IgG-BV421 suggested: None BD-562581 suggested: None
   After 1 hour incubation at room temperature the wells were washed and bound scFv was detected by incubation for 40 minutes at room temperature with peroxidase labelled monoclonal anti-FLAG® M2 antibody (Sigma Aldrich (30 µl diluted 1/4000 in assay buffer) and development using 1-Step™ Ultra TMB-ELISA Substrate Solution (Thermo Fisher Scientific)	anti-FLAG® suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   HEK293 cells constitutively expressing the ACE2 receptor were acquired from BEI resources (NR-52511).	HEK293 suggested: None
   THP-1 cells were washed twice with PBS and reconstituted in Sodium medium.	THP-1 suggested: CLS Cat# 300356/p804_THP-1, RRID:CVCL_0006)
   Pseudotyped lentiviruses displaying the SARS-CoV-2 pandemic founder variant (Wu-Hu-1) packaging a firefly luciferase reporter gene were generated by the co-transfection of HEK293T cells using Lipofectamine 3000 (Invitrogen) per the manufacturer’s protocols.	HEK293T suggested: None
   For these experiments, the HEK293T-hACE2 cell culture was supplemented with penicillin/streptomycin antibiotics to avoid contamination.	HEK293T-hACE2 suggested: RRID:CVCL_A7UK)
   Bead-based neutralization assay: HEK293T-ACE2 cells were seeded at density of 35,000 cells per well in a Poly-D-Lysine coated flat bottom 96 well plate.	HEK293T-ACE2 suggested: None
   Experimental Models: Organisms/Strains
   Sentences	Resources
   Animal experiments: Forty-two nine-week old female K18 hACE2 (B6.Cg-Tg(K18-ACE2)2Prlmn/J) mice were inoculated intranasally with 105 PFU of SARS-CoV-2 (Wuhan strain, isolate SARS-CoV-2/01/human/2020/SWE, sourced from the Swedish Health Authorities).	B6.Cg-Tg(K18-ACE2)2Prlmn/J suggested: RRID:IMSR_JAX:034860)
   Software and Algorithms
   Sentences	Resources
   Once received, we collated the V(D)J regions from our antibodies of interest using the V-Loupe software (10X Genomics software platform).	Genomics suggested: (UTHSCSA Genomics Core, RRID:SCR_012239)
   Multiple sequence alignment using the ClustalW algorithm was performed on the light chain sequences and the heavy chain sequences.	ClustalW suggested: (ClustalW, RRID:SCR_017277)
   Apparent reaction rate kinetics was determined using a Langmuir 1:1 model using the Sierra Analyser software version 3.4.3 (Bruker).	Sierra Analyser suggested: (OMICtools, RRID:SCR_002250)

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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: Please consider improving the rainbow (“jet”) colormap(s) used on page 4. 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 10.1101/2021.10.14.464464 on bioRxiv

   Oct 15, 2021