Development of potency, breadth and resilience to viral escape mutations in SARS-CoV-2 neutralizing antibodies

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   ScreenIT

   Mar 15, 2021

   SciScore for 10.1101/2021.03.07.434227: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The R683G substitution itself increased pseudovirus sensitivity to some antibodies, including C055, C099, C549 and C512, and antibodies from the C144 and C032 groups.	C099 suggested: None C512 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The R683G substitution itself increased pseudovirus sensitivity to some antibodies, including C055, C099, C549 and C512, and antibodies from the C144 and C032 groups.	C549 suggested: None
   Specifically, virus stocks were harvested 48 hours after transfection of 293T cells with pNL4-3ΔEnv-nanoluc and pSARS-CoV-2 SΔ19 and filtered and stored at −80°C.	293T sugge…

   SciScore for 10.1101/2021.03.07.434227: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   The R683G substitution itself increased pseudovirus sensitivity to some antibodies, including C055, C099, C549 and C512, and antibodies from the C144 and C032 groups.	C099 suggested: None C512 suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   The R683G substitution itself increased pseudovirus sensitivity to some antibodies, including C055, C099, C549 and C512, and antibodies from the C144 and C032 groups.	C549 suggested: None
   Specifically, virus stocks were harvested 48 hours after transfection of 293T cells with pNL4-3ΔEnv-nanoluc and pSARS-CoV-2 SΔ19 and filtered and stored at −80°C.	293T suggested: None
   The antibody/pseudotyped virus mixture was then added to HT1080/ACE2.cl14 cells.	HT1080/ACE2.cl14 suggested: None
   Selection of antibody resistant rVSV/SARS-CoV-2 variants: To select monoclonal antibody-resistant S variants, rVSV/SARS-CoV-2/GFP1D7 and rVSV/SARS-CoV-2/GFP2E1 were passaged to generate diversity, and populations containing 106 PFU were incubated with monoclonal antibodies (0.5µg/ml to 10µg/ml) for 1h at 37°C before inoculation of 2×105 293T/ACE2cl.22 cells in 6-well plates.	293T/ACE2cl.22 suggested: None
   The antibody/recombinant virus mixture was then added to 293T/ACE2.cl22 cells.	293T/ACE2.cl22 suggested: None
   Software and Algorithms
   Sentences	Resources
   The half-maximal inhibitory concentrations for monoclonal antibodies (IC50) were determined using four-parameter nonlinear regression (least squares regression method without weighting) (GraphPad Prism).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   For analysis of the Illumina sequencing data, adapter sequences were removed from the raw reads and low-quality reads (Phred quality score <20) using BBDuk.	Phred suggested: (Phred, RRID:SCR_001017)
   RBD-specific variant frequencies, P-values, and read depth were compiled using Python running pandas (1.0.5), numpy (1.18.5), and matplotlib (3.2.2).	Python suggested: (IPython, RRID:SCR_001658) matplotlib suggested: (MatPlotLib, RRID:SCR_008624)
   Briefly, for all Fab-S complexes, we collected micrographs on a Talos Arctica transmission electron microscope (Thermo Fisher) operating at 200 kV using SerialEM automated data collection software (Mastronarde, 2005).	SerialEM suggested: (SerialEM, RRID:SCR_017293)
   Non-dose-weighted images were used to estimate CTF parameters using a cryoSPARC implementation of the Patch CTF job, and all datasets were processed similarly.	cryoSPARC suggested: (cryoSPARC, RRID:SCR_016501)
   We validated model coordinates using MolProbity (Chen et al., 2010) (Table S3).	MolProbity suggested: (MolProbity, RRID:SCR_014226)
   Data from single crystals were indexed and integrated in XDS (Kabsch, 2010) or iMosflm (Battye, 2011 #796) and merged using AIMLESS in CCP4 (Winn et al., 2011) (Table S2).	iMosflm suggested: (iMosflm , RRID:SCR_014217)
   The structures were refined using an initial round of rigid body and individual B refinement in Phenix (Adams et al., 2010) followed by cycles of manual building in Coot (Emsley et al., 2010) and real space refinement in Phenix with TLS (Table S2).	Coot suggested: (Coot, RRID:SCR_014222) Phenix suggested: (Phenix, RRID:SCR_014224)
   Homology models were generated by MODELLER (version 9.23) (Sali and Blundell, 1993) and further optimized by Protein Preparation Wizard in Maestro Schrodinger (Sastry et al., 2013) including optimization of hydrogens.	MODELLER suggested: (MODELLER, RRID:SCR_008395)
   DATA AND SOFTWARE AVAILABILITY: Coordinates and maps associated with data reported in this manuscript will be deposited in the Electron Microscopy Data Bank (EMDB: https://www.ebi.ac.uk/pdbe/emdb/) and Protein Data Bank (PDB: www.rcsb.org) with accession numbers …	https://www.ebi.ac.uk/pdbe/emdb/ suggested: (Electron Microscopy Data Bank at PDBe (MSD-EBI, RRID:SCR_006506)

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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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   Version published to 10.1101/2021.03.07.434227 on bioRxiv

   Mar 8, 2021