Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

SciScore for 10.1101/2020.10.07.326462: (What is this?)

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

Table 1: Rigor

Institutional Review Board Statement	not detected.
Randomization	not detected.
Blinding	not detected.
Power Analysis	not detected.
Sex as a biological variable	Cell culture: Lenti-X 293T™ cells (H. sapiens; sex: female) obtained from Takara (cat. #632180) and Huh-7.5 cells (H. sapiens; sex: male) (Blight et al., 2002) were maintained at 37 °C and 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM, Fisher Scientific, cat. #11995065) supplemented with 0.1 mM nonessential amino acids (NEAA, Fisher Scientific, cat. #11140076) and 10% hyclone fetal bovine serum (FBS, HyClone Laboratories, Lot. #AUJ35777)
Cell Line Authentication	Contamination: Both cell lines have tested negative for contamination with mycoplasma.

Table 2: Resources

Antibodies
Sentences	Resources
To stain for SARS-CoV-2, a rabbit polyclonal anti-SARS-CoV-2 nucleocapsid antibody (GeneTex: catalog no. GTX135357) was added to the cells at a 1:1,000 dilution in blocking solution and incubated at 4 °C overnight.	anti-SARS-CoV-2 suggested: None
To detect infected cells for HCoV-229E, HCoV-OC43 and HCoV-NL63, a mouse monoclonal anti-dsRNA antibody (Scicons: catalog no. 10010500) was used under similar conditions.	anti-dsRNA suggested: (Millipore Cat# MABE1134, RRID:AB_2819101)
Goat anti-rabbit AlexaFluor 488 (Life Technologies: catalog no. A-11012) and goat anti-mouse AlexaFluor 488 (Life Technologies: catalog no. A-11001) were used as a secondary antibody at a dilution of 1:2,000.	anti-rabbit suggested: None anti-mouse suggested: None
Experimental Models: Cell Lines
Sentences	Resources
Production and titration of coronavirus stocks: SARS-CoV-2 (strain: USA-WA1/2020) and HCoV-NL63 were obtained from BEI Resources (NR-52281 and NR-470).	HCoV-NL63 suggested: RRID:CVCL_RW88)
All viruses were amplified at 33 °C in Huh-7.5 cells to generate a P1 stock.	Huh-7.5 suggested: RRID:CVCL_7927)
Huh-7.5-Cas9 cells transduced with the Brunello sgRNA library were seeded in p150 plates at 4.5 × 106 cells/plate with two plates per replicate (e.g., 9 × 106 cells) and three replicates for each condition (mock, HCoV-229E, HCoV-NL63, HCoV-OC43).	Huh-7.5-Cas9 suggested: None
Software and Algorithms
Sentences	Resources
Nuclei were stained with Hoechst 33342 (ThermoFisher Scientific: catalog no. 62249) at a 1:1,000 dilution.	ThermoFisher Scientific suggested: None
Briefly, enriched pathways were identified from the NIH NCATS BioPlanet database (Huang et al., 2019), which aggregates currates pathways from multiple sources, using competitive gene set testing of z scores in pre-ranked mode (Wu and Smyth, 2012).	NCATS BioPlanet suggested: None
For construction of the network in Figure 3, significant CRISPR hits from any virus were searched using the STRING database (string-db.org) (Szklarczyk et al., 2019) using default parameters and imported into Cytoscape (Shannon et al., 2003)	STRING suggested: (STRING, RRID:SCR_005223) Cytoscape suggested: (Cytoscape, RRID:SCR_003032)
Overlapping hits per virus were calculated and subsequently depicted as pie charts per node in Adobe Illustrator.	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)
Analysis of scRNAseq data: For scRNAseq analysis, Seurat objects were downloaded from FigShare (https://doi.org/10.6084/m9.figshare.12436517) (Chua et al., 2020).	FigShare suggested: (FigShare, RRID:SCR_004328)

Results from OddPub: Thank you for sharing your data.

Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

The results of this study should be interpreted within the context of its limitations. If a gene did not score in our screens, it does not rule out that gene being an important SARS-CoV-2 factor for a number of reasons. First, pooled CRISPR screens may not identify functionally redundant or buffering genes (Ewen-Campen et al., 2017). Second, Huh-7.5 cells were chosen based on their infectivity by multiple coronaviruses; however, it should be understood that they are not airway cells. Nevertheless, a recent study demonstrated that hits in Huh-7 cells translate to human cells of lung origin (Baggen et al., 2020). Furthermore, as shown in Figure S6, the vast majority of genes identified here are expressed in human cells and tissues known to be infected by SARS-CoV-2. Lastly, our current experimental system is limited to assessing survival and can not interrogate host factors that act in late stages of the viral life cycle, nor can it identify genes that play important roles in immune modulation and pathogenesis. It is essential to understand the underlying biology of a disease in order to develop new strategies for treatment and prevention. For infectious diseases, this entails studying the biology of the pathogen and the host. We identified complex, interconnected networks of coronavirus host factors and pathways that are essential for virus infection, nominating hundreds of new host proteins that represent liabilities for SARS-CoV-2 and potential opportunities for therapeutic ...

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:

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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Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks

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