Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

Version published to 10.1016/j.chom.2020.08.004

Oct 1, 2020

SciScore for 10.1101/2020.06.25.172403: (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

Experimental Models: Cell Lines
Sentences	Resources
The expression construct was transfected in HEK293F cells using polyethylenimine.	HEK293F suggested: RRID:CVCL_6642)
ppVSV-SARS-2-S): 293T cells were transfected with an expression plasmid encoding SARS-CoV-2 Spike (pcDNAintron-SARS-2-SΔ19).	293T suggested: None
Target cells VeroE6 were seeded in 24-well plates (5×105 cells/mL) at a density of 80% coverage.	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
To quantify the ability of various SARS-CoV-2 S mutants to mediate fusion, effector cells (HEK293T) were transiently transfected with the indicated pcDNAintron-SARS-2-S expression …

SciScore for 10.1101/2020.06.25.172403: (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

Experimental Models: Cell Lines
Sentences	Resources
The expression construct was transfected in HEK293F cells using polyethylenimine.	HEK293F suggested: RRID:CVCL_6642)
ppVSV-SARS-2-S): 293T cells were transfected with an expression plasmid encoding SARS-CoV-2 Spike (pcDNAintron-SARS-2-SΔ19).	293T suggested: None
Target cells VeroE6 were seeded in 24-well plates (5×105 cells/mL) at a density of 80% coverage.	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
To quantify the ability of various SARS-CoV-2 S mutants to mediate fusion, effector cells (HEK293T) were transiently transfected with the indicated pcDNAintron-SARS-2-S expression vector or measles virus H and F (78)	HEK293T suggested: None
To visualize cell-to-cell fusion, Vero cells were co-transfected with pGFP and the pcDNAintron-SARS-2-S constructs.	Vero suggested: None
Software and Algorithms
Sentences	Resources
Detection and relative quantification of the prevalence of individual glycans was accomplished using the total ion mapping (TIM) and neutral loss scan (NL scan) functionality of the Xcalibur software package version 2.0 (Thermo Fisher Scientific) as previously described (38,39).	Xcalibur suggested: (Thermo Xcalibur, RRID:SCR_014593)
Proteome Discoverer 1.4) with mass tolerance set as 20 ppm for precursors and 0.5 Da for fragments.	Proteome Discoverer suggested: (Proteome Discoverer, RRID:SCR_014477)
The search output was filtered using ProteoIQ (v2.7) to reach a 1% false discovery rate at protein level and 10% at peptide level.	ProteoIQ suggested: (PremierBiosoft Proteo IQ Software, RRID:SCR_018072)
The S protein sequences from all of those genomes were aligned using EMBOSS needle v6.6.0 (61) via the EMBL-EBI provided web service (69).	EMBOSS suggested: (EMBOSS, RRID:SCR_008493)
For further sequence analysis of SARS-CoV-2 S variants, the genomes of SARS-CoV-2 were downloaded from NCBI and GISAID and further processed using Biopython 1.76 to extract all sequences annotated as “surface glycoprotein” and to remove any incomplete sequence as well as any sequence containing unassigned amino acids.	Biopython suggested: (Biopython, RRID:SCR_007173)
For sequence analysis of human ACE2 variants, the single nucleotide polymorphisms (SNPs) of ACE2 were extracted from the NCBI dbSNP database and filtered for missense mutation entries with a reported minor allele frequency.	dbSNP suggested: (dbSNP, RRID:SCR_002338)

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 rtransparent:

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No protocol registration statement was detected.

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Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

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