Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model

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1. Version published to 10.1371/journal.ppat.1010807

   Sep 6, 2022
2. 

   ScreenIT

   Mar 18, 2022

   SciScore for 10.1101/2022.03.15.484379: (What is this?)

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

   Table 1: Rigor

   Ethics	Euthanasia Agents: Viral inocula were made in sterile phosphate buffered saline (PBS) and delivered via intranasal instillation (200μL total with 100μL per nare) with animals sedated using isoflurane. IACUC: UKHSA) Porton Down by the Animal Welfare and Ethical Review Body (AWERB) as required by the Home Office Animals (Scientific Procedures) Act 1986.
   Sex as a biological variable	The animals were randomly assigned into groups and individually housed, with equal allocation of male and female animals to each study.
   Randomization	The animals were randomly assigned into groups and individually housed, with equal allocation of male and female animals to each study.
   Blinding	All slides were evaluated …

   SciScore for 10.1101/2022.03.15.484379: (What is this?)

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

   Table 1: Rigor

   Ethics	Euthanasia Agents: Viral inocula were made in sterile phosphate buffered saline (PBS) and delivered via intranasal instillation (200μL total with 100μL per nare) with animals sedated using isoflurane. IACUC: UKHSA) Porton Down by the Animal Welfare and Ethical Review Body (AWERB) as required by the Home Office Animals (Scientific Procedures) Act 1986.
   Sex as a biological variable	The animals were randomly assigned into groups and individually housed, with equal allocation of male and female animals to each study.
   Randomization	The animals were randomly assigned into groups and individually housed, with equal allocation of male and female animals to each study.
   Blinding	All slides were evaluated subjectively by a qualified pathologist, blinded to treatment details and were randomised prior to examination to limit bias (blind evaluation).
   Power Analysis	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Staining was performed with the BOND Polymer Refine Detection kit, a rabbit anti-SARS-CoV-2 nucleocapsid antibody (Sinobiological; clone: #001; dilution: 1:5000) and counterstained with haematoxylin.	anti-SARS-CoV-2 suggested: (Leinco Technologies Cat# LT5000, RRID:AB_2893962)
   Membranes were blocked in 5% milk in PBS/0.1% Tween-20 and incubated with anti-HIF-1α (BD Biosciences), anti-β-Actin (Sigma) or SARS-CoV-2 nucleocapsid (EY-2A, a kind gift from Prof Alain Townsend) primary antibodies and appropriate HRP-conjugated secondary antibodies (DAKO).	anti-HIF-1α suggested: (Cayman Chemical Cat# 10006421, RRID:AB_409037) anti-HIF-1α (BD Biosciences), anti-β-Actin (Sigma) suggested: None anti-β-Actin suggested: None
   Experimental Models: Cell Lines
   Sentences	Resources
   Virus infectivity was determined by plaque assay on Vero-TMPRSS2 cells as previously reported (Wing et al., 2021a)	Vero-TMPRSS2 suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
   Calu-3 cells were infected with the above strain of SARS-CoV-2 at an MOI of 0.01 for 2h.	Calu-3 suggested: KCLB Cat# 30055, RRID:CVCL_0609)
   Software and Algorithms
   Sentences	Resources
   FPKM values were enumerated, and differential expression quantified using the DeSeq2 package (Love et al., 2014).	DeSeq2 suggested: (DESeq2, RRID:SCR_015687)
   Membranes were blocked in 5% milk in PBS/0.1% Tween-20 and incubated with anti-HIF-1α (BD Biosciences), anti-β-Actin (Sigma) or SARS-CoV-2 nucleocapsid (EY-2A, a kind gift from Prof Alain Townsend) primary antibodies and appropriate HRP-conjugated secondary antibodies (DAKO).	BD Biosciences suggested: (BD Biosciences, RRID:SCR_013311)
   P values were determined using the Mann-Whitney test (two group comparisons) or with the Kruskal–Wallis ANOVA (multi group comparisons) using PRISM version 8.	PRISM suggested: (PRISM, RRID:SCR_005375)

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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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • 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 10.1101/2022.03.15.484379v1 on bioRxiv

   Mar 15, 2022