Differences in neuroinflammation in the olfactory bulb between D614G, Delta and Omicron BA.1 SARS-CoV-2 variants in the hamster model

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   ScreenIT

   Mar 27, 2022

   SciScore for 10.1101/2022.03.24.485596: (What is this?)

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

   Table 1: Rigor

   Ethics	Field Sample Permit: Research was conducted under a project license from the Dutch competent authority and the study protocol (#17-4312) was approved by the institutional Animal Welfare Body. Euthanasia Agents: Hamsters were euthanized by cardiac puncture under isoflurane anesthesia and cervical dislocation.
   Sex as a biological variable	Animals and experimental setup: Female Syrian golden hamsters (Mesocricetus auratus; 6 weeks old; Janvier, France) were handled in an ABSL-3 biocontainment laboratory.
   Randomization	For unbiased experiments, all animals were randomly assigned to experimental groups.
   Blinding	Counting of IBA-1+ cells was determined by manual counting by two independent blinded …

   SciScore for 10.1101/2022.03.24.485596: (What is this?)

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

   Table 1: Rigor

   Ethics	Field Sample Permit: Research was conducted under a project license from the Dutch competent authority and the study protocol (#17-4312) was approved by the institutional Animal Welfare Body. Euthanasia Agents: Hamsters were euthanized by cardiac puncture under isoflurane anesthesia and cervical dislocation.
   Sex as a biological variable	Animals and experimental setup: Female Syrian golden hamsters (Mesocricetus auratus; 6 weeks old; Janvier, France) were handled in an ABSL-3 biocontainment laboratory.
   Randomization	For unbiased experiments, all animals were randomly assigned to experimental groups.
   Blinding	Counting of IBA-1+ cells was determined by manual counting by two independent blinded observes.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: Both cells were grown at 37°C in a humidified CO2◻incubator and routinely tested for mycoplasma.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Cells were incubated in 3% BSA (bovine serum albumin; Sigma) in PBS and stained with a rabbit anti-nucleocapsid antibody (Sino biological; 1:2000) in PBS containing 0.1% BSA, washed thrice in PBS, and stained with donkey anti-rabbit Alexa Fluor 488 (Invitrogen; 1:4000) in PBS containing 0.1% BSA.	anti-nucleocapsid suggested: None anti-rabbit suggested: None
   Slides were then incubated with a rabbit polyclonal antibody against SARS-CoV/SARS-CoV-2-nucleoprotein (40143-T62, Sino Biological, Pennsylvania, USA) (1:1000), mouse CD3 (ab16669, Abcam, Cambridge, UK) (1:10, 20μg/ml), human Iba-1 (019-19741	SARS-CoV/SARS-CoV-2-nucleoprotein ( 40143-T62 , Sino Biological , Pennsylvania , USA ) suggested: None CD3 suggested: (Abcam Cat# ab16669, RRID:AB_443425)
   Experimental Models: Cell Lines
   Sentences	Resources
   Drosten) was propagated to passage three on Vero E6 cells in Opti-MEM I (1X) + GlutaMAX (Gibco), supplemented with penicillin (10,000 IU/mL) and streptomycin (10,000 IU/mL).	Vero E6 suggested: None
   Virus Titrations: Ten-fold serial diluted samples were added to monolayers of Calu-3 cells.	Calu-3 suggested: KCLB Cat# 30055, RRID:CVCL_0609)
   Software and Algorithms
   Sentences	Resources
   Plaque assay analysis was performed using ImageQuant TL 8.2 software (GE Healthcare).	ImageQuant suggested: (ImageQuant, RRID:SCR_014246)
   Images were taken with a 200x magnification (20x air objective; Olympus) with CellSens software.	CellSens suggested: None
   Graphs and statistical tests were made with GraphPad Prism version 9.	GraphPad Prism suggested: (GraphPad Prism, RRID:SCR_002798)
   Figures were prepared with Adobe Illustrator CC2019	Adobe Illustrator suggested: (Adobe Illustrator, RRID:SCR_010279)
   , Adobe Photoshop CC2019 and Biorender.	Adobe Photoshop suggested: (Adobe Photoshop, RRID:SCR_014199)

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   Results from OddPub: Thank you for sharing your data.

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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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   Version published to 10.1101/2022.03.24.485596v1 on bioRxiv

   Mar 24, 2022