Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model

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1. Version published to 10.1016/j.ebiom.2021.103675

   Nov 1, 2021
2. 

   ScreenIT

   Jul 16, 2021

   SciScore for 10.1101/2021.07.11.451964: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: All procedures followed standard operating procedures (SOPs) approved by the RML Institutional Biosafety Committee (
   Sex as a biological variable	Animal study: Fifty female Syrian golden hamsters (5-8 weeks of age) were used in this study14.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After three washes with PBST, the bound antibodies were labeled using 50 μl of 1:2,500 peroxidase anti-hamster IgG (H+L) (SeraCare Life Sciences) diluted in 1% skim milk in PBST.	anti-hamster IgG suggested: None
   The secondary antibody was the Vector Laboratories ImPress VR anti-mouse IgG polymer …

   SciScore for 10.1101/2021.07.11.451964: (What is this?)

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

   Table 1: Rigor

   Ethics	IACUC: All procedures followed standard operating procedures (SOPs) approved by the RML Institutional Biosafety Committee (
   Sex as a biological variable	Animal study: Fifty female Syrian golden hamsters (5-8 weeks of age) were used in this study14.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   After three washes with PBST, the bound antibodies were labeled using 50 μl of 1:2,500 peroxidase anti-hamster IgG (H+L) (SeraCare Life Sciences) diluted in 1% skim milk in PBST.	anti-hamster IgG suggested: None
   The secondary antibody was the Vector Laboratories ImPress VR anti-mouse IgG polymer (cat# MP-7422).	anti-mouse IgG suggested: (Vector Laboratories Cat# MP-7422, RRID:AB_2336527)
   Experimental Models: Cell Lines
   Sentences	Resources
   Cells and Viruses: VeroE6 cells were grown at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, St. Louis, MO) containing 10% fetal bovine serum (FBS) (Wisent Inc., St. Bruno, Canada), 2 mM L-glutamine (Thermo Fisher Scientific, Waltham, MA), 50 U/mL penicillin (Thermo Fisher Scientific), and 50 μg/mL streptomycin (Thermo Fisher Scientific).	VeroE6 suggested: JCRB Cat# JCRB1819, RRID:CVCL_YQ49)
   Software and Algorithms
   Sentences	Resources
   RNA-Seq reads were demultiplexed, quality-filtered and trimmed using Trim Galore (average Phred score cut-off of 30, minimum length of 50 bp).	Trim Galore suggested: (Trim Galore, RRID:SCR_011847)
   Hisat2 was used to align reads to the reference genome Mesocricetus auratus (Mesocricetus_auratus.MesAur1.0.dna.toplevel.fa) and the Mesocricetus_auratus.MesAur1.0.103.gtf file was used for annotation.	Hisat2 suggested: (HISAT2, RRID:SCR_015530)
   Raw expression values (gene-level read counts) were generated using the summarizeOverlaps function and normalized (read per kilobase of transcript per million mapped reads, rpkm) using the edgeR package.	edgeR suggested: (edgeR, RRID:SCR_012802)
   Functional enrichment of DEGs was performed using Metascape to identify relevant GO terms70.	Metascape suggested: (Metascape, RRID:SCR_016620)
   Digital cell quantification was performed using ImmQuant with the IRIS database.	IRIS suggested: None
   , Venn diagrams and violin plots were generated using R packages ggplot2 and VennDiagrams.	ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Graphs were generated using GraphPad Prism software (version 8).	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   FastQC was used to generate quality reports.	FastQC suggested: (FastQC, RRID:SCR_014583)
   MaskPrimers.py from the pRESTO R package was used to remove primers prior to alignment to the SARS-CoV-2 genome using BWA-mem software version 0.7.17.	pRESTO suggested: (pRESTO, RRID:SCR_001782) BWA-mem suggested: (Sniffles, RRID:SCR_017619)
   Statistical analyses: All statistical analysis was performed in Prism 8 (GraphPad).	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)

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

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3. 

   Version published to 10.1101/2021.07.11.451964v1 on bioRxiv

   Jul 12, 2021