SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

Version published to 10.1016/j.cell.2021.03.036

Apr 1, 2021

SciScore for 10.1101/2021.02.11.430787: (What is this?)

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

Table 1: Rigor

Institutional Review Board Statement	IRB: Study was approved by the Ethic committee of Ulm university (vote 31/21 – FSt/Sta).
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Sex as a biological variable	not detected.
Cell Line Authentication	Contamination: Further, cell lines were routinely tested for contamination by mycoplasma.

Table 2: Resources

Antibodies
Sentences	Resources
Finally, culture medium containing anti-VSV-G antibody (culture supernatant from I1-hybridoma cells; ATCC no. CRL-2700) was added.	anti-VSV-G suggested: None
Alternatively, pseudotype particles were pre-incubated with different concentrations of either sol-ACE2-Fc, fusion inhibitor (EK-1 or EK-1-C4), …

SciScore for 10.1101/2021.02.11.430787: (What is this?)

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

Table 1: Rigor

Institutional Review Board Statement	IRB: Study was approved by the Ethic committee of Ulm university (vote 31/21 – FSt/Sta).
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Sex as a biological variable	not detected.
Cell Line Authentication	Contamination: Further, cell lines were routinely tested for contamination by mycoplasma.

Table 2: Resources

Antibodies
Sentences	Resources
Finally, culture medium containing anti-VSV-G antibody (culture supernatant from I1-hybridoma cells; ATCC no. CRL-2700) was added.	anti-VSV-G suggested: None
Alternatively, pseudotype particles were pre-incubated with different concentrations of either sol-ACE2-Fc, fusion inhibitor (EK-1 or EK-1-C4), monoclonal antibodies (REGN10933, REGN10987, REGN10989, Bamlaivimab/LY-CoV555), or sera from COVID-19 patients or vaccinated (Pfizer/BioNTech vaccine BNT162b2) individuals (30 min at 37 °C).	EK-1-C4 suggested: None Bamlaivimab/LY-CoV555 suggested: None
Thereafter, samples were washed and incubated for 1 h at room temperature with primary antibody (anti-HA, mouse, 1:500, Sigma-Aldrich) diluted in PBS containing 1 % bovine serum albumin.	anti-HA suggested: None
Next, the samples were washed with PBS and incubated in the dark for 1 h at 4 °C with secondary antibody (Alexa Fluor-568-conjugated anti-mouse antibody, 1:750, Thermo Fisher Scientific).	anti-mouse suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Vero-TMPRSS2 cells additionally received puromycin (0.5 μg/ml, Invivogen).	Vero-TMPRSS2 suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
A549 (human, lung; CRM-CCL-185, ATCC), A549-ACE2 and A549-ACE2/TMPRSS2 cells were cultivated in DMEM/F-12 Medium with Nutrient Mix (ThermoFisher Scientific).	A549-ACE2/TMPRSS2 suggested: None
Caco-2 (human, intestine; HTB-37, ATCC) and Calu-3 cells (human, lung; HTB-55, ATCC; kindly provided by Stephan Ludwig, Institute of Virology, University of Münster, Germany) were cultivated in minimum essential medium supplemented with 1x non-essential amino acid solution (from 100x stock, PAA) and 1 mM sodium pyruvate (Thermo Fisher Scientific)	Caco-2 suggested: None HTB-37 suggested: None Calu-3 suggested: ATCC Cat# HTB-55, RRID:CVCL_0609)
. 293T cells that stably express ACE2 were generated by retroviral (murine leukemia virus, MLV) transduction and selection of parental 293T cells with puromycin (4 μg/ml for initial selection and 0.5 μg/ml for sub-culturing).	293T suggested: None
A549 cells stably expressing ACE2 and TMPRSS2 (A549-ACE2/TMPRSS2) were obtained by retroviral transduction of A549-ACE2 cells and selection with blasticidin (6 μg/ml for initial selection and 1 μg/ml for sub-culturing).	A549 suggested: None A549-ACE2 suggested: None
For the investigation of the entry speed of S protein-bearing pseudotypes, the respective particles were inoculated on Vero76 cells and adsorbed for different time intervals before the inoculum was removed and cells were washed and incubated with fresh medium.	Vero76 suggested: IZSLER Cat# BS CL 101, RRID:CVCL_0603)
Software and Algorithms
Sentences	Resources
Protein models are based on PDB: 6XDG (Hansen et al., 2020) or a template generated by modelling the SARS-2-S sequence on a published crystal structure (PDB: 6XR8,(Cai et al., 2020)), using the SWISS-MODEL online tool (https://swissmodel.expasy.org/), and were generated using the YASARA software (http://www.yasara.org/index.html).	YASARA suggested: (YASARA, RRID:SCR_017591)
Finally, the samples were washed, nuclei were stained with DAPI and coverslips were mounted onto microscopic glass slides with Mowiol/DABCO.	Mowiol/DABCO suggested: None
Data normalization and statistical analysis: Data analysis was performed using Microsoft Excel as part of the Microsoft Office software package (version 2019, Microsoft Corporation) and GraphPad Prism 8 version 8.4.3 (GraphPad Software).	Microsoft Excel suggested: (Microsoft Excel, RRID:SCR_016137) GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798) GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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).

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.

Results from TrialIdentifier: No clinical trial numbers were referenced.

Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

Results from JetFighter: We did not find any issues relating to colormaps.

Results from scite Reference Check: We found no unreliable references.

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SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

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