SARS-CoV-2 infection results in lasting and systemic perturbations post recovery

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1. 

   Rapid Reviews Infectious Diseases

   Jun 7, 2022

   Rajkumar Kalra

   Review 1: "SARS-CoV-2 infection results in lasting and systemic perturbations post recovery"

   Reviewer: Rajkumar Kalra (Okinawa Institute of Science and Technology Graduate University) | 📒📒📒 ◻️◻️

   Read the original source
2. 

   Rapid Reviews Infectious Diseases

   Jun 7, 2022

   Rajkumar Kalra

   Review of "SARS-CoV-2 infection results in lasting and systemic perturbations post recovery"

   Reviewer: Rajkumar Kalra (Okinawa Institute of Science and Technology Graduate University) | 📒📒📒 ◻️◻️

   Read the original source
3. 

   ScreenIT

   Jan 21, 2022

   SciScore for 10.1101/2022.01.18.476786: (What is this?)

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

   Table 1: Rigor

   Ethics

   Euthanasia Agents: Hamsters were euthanized via intraperitoneal injection of pentobarbital and cardiac perfusion with 60 mL PBS. IACUC: All animal experiments were performed according to protocols approved by the Institutional Animal Care and Use Committee (IACUC) and Institutional Biosafety Committee at ISMMS and NYUL. IRB: The Tissue Procurement Facility operates under Institutional Review Board (IRB) approved protocol and follows guidelines set by Health Insurance Portability and Accountability Act (HIPAA). Consent: All autopsies have consent for research use from next of kin, and these studies were determined as exempt by IRB at Weill Cornell Medicine under those protocol numbers.

   Sex as a …

   SciScore for 10.1101/2022.01.18.476786: (What is this?)

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

   Table 1: Rigor

   Ethics	Euthanasia Agents: Hamsters were euthanized via intraperitoneal injection of pentobarbital and cardiac perfusion with 60 mL PBS. IACUC: All animal experiments were performed according to protocols approved by the Institutional Animal Care and Use Committee (IACUC) and Institutional Biosafety Committee at ISMMS and NYUL. IRB: The Tissue Procurement Facility operates under Institutional Review Board (IRB) approved protocol and follows guidelines set by Health Insurance Portability and Accountability Act (HIPAA). Consent: All autopsies have consent for research use from next of kin, and these studies were determined as exempt by IRB at Weill Cornell Medicine under those protocol numbers.
   Sex as a biological variable	Hamster experiments: 6–7 week-old male Golden Syrian hamsters (Mesocricetus auratus) were obtained from Charles River Laboratories.
   Randomization	Hamsters were randomly assigned to the different treatment groups and all IAV and SARS-CoV-2 infections were performed in the BSL-3 facility. qRT-PCR: RNA was isolated from homogenized samples by TRIzol/phenol-chloroform extraction.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: All cells were tested for the presence of mycoplasma using MycoAlert Mycoplasma Detection Kit (Lonza).

   Table 2: Resources

   Antibodies
   Sentences	Resources
   Slides were washed once again and HRP-conjugated secondary antibody was added at a 1:5000 concentration (Goat anti-mouse: ThermoFisher, Cat #A21426; Goat anti-rabbit: Abcam, Ab6721).	anti-rabbit suggested: (Abcam Cat# ab6721, RRID:AB_955447) anti-mouse suggested: (Innovative Research Cat# A21426, RRID:AB_1500929) Ab6721 suggested: (Abcam Cat# ab6721, RRID:AB_955447)
   Primary antibody (MX-A: Millipore Sigma, MABF938; IBA-1: Wako, 019-19741; CD3: Dako, A0452; MPO: Dako, A0398) was added to slides at a dilution (MX-A, 1:100; IBA-1, 1:1000; CD3, 1:1000; MPO: 1:5000), and sections were incubated overnight at 4 degrees Celsius.	CD3 suggested: None
   Slides were washed once again and HRP-conjugated secondary antibody was added at a 1:5000 concentration (Goat anti-mouse: ThermoFisher, Cat #A21426; Goat anti-rabbit: Abcam, Ab6721).	anti-rabbit suggested: (Abcam Cat# ab6721, RRID:AB_955447) anti-mouse suggested: (Innovative Research Cat# A21426, RRID:AB_1500929) Ab6721 suggested: (Abcam Cat# ab6721, RRID:AB_955447)
   Experimental Models: Cell Lines
   Sentences	Resources
   Virus and cells: SARS-CoV-2 isolate USA-WA1/2020 was propagated in Vero-E6 cells in DMEM supplemented with 2% FBS, 1mM HEPES and 1% penicillin/streptomycin.	Vero-E6 suggested: None
   Influenza A virus H1N1 isolate A/California/04/2009 was propagated in MDCK cells in DMEM supplemented with 0.35% BSA.	MDCK suggested: CLS Cat# 602280/p823_MDCK_(NBL-2, RRID:CVCL_0422)
   Software and Algorithms
   Sentences	Resources
   Data visualization: All non-RNA-Seq statistical analyses, box and bar graphs, and Kaplan-Meyer plots were prepared using prism 9 as described in figure legends (GraphPad Software, San Diego, California USA;	GraphPad suggested: (GraphPad Prism, RRID:SCR_002798)
   Fastq files were generated with bcl2fastq (Illumina) and aligned to the Syrian golden hamster genome (MesAur 1.0, ensembl) using the RNA-Seq Alignment application (Basespace, Illumina).	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   Salmon files were analyzed using the DESeq2 analysis pipeline (Love et al., 2014).	DESeq2 suggested: (DESeq, RRID:SCR_000154)
   All visualizations of RNA-sequencing differential expression data were created in R using ggplot2, pheatmap, ComplexHeatmap, and gplots packages.	ComplexHeatmap suggested: (ComplexHeatmap, RRID:SCR_017270)
   Assessment of read coverage of viral genome was conducted using Bowtie2 and IGV_2.8.13 and visualized using ggplot2.	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368) ggplot2 suggested: (ggplot2, RRID:SCR_014601)
   Images were morphometrically analyzed using QuPath (Bankhead et al., 2017) and ImageJ (Schneider et al., 2012).	ImageJ suggested: (ImageJ, RRID:SCR_003070)
   Human Heart, Lung, Kidney RNA-sequencing: For RNA library preparation, all samples’ RNA was treated with DNAse 1 (Zymo Research, Catalog # E1010).	Human Heart suggested: (Duke Human Heart Repository, RRID:SCR_013980)
   This workflow involved quality control of the reads with FastQC (Andrews), adapter trimming using Trim Galore!	FastQC suggested: (FastQC, RRID:SCR_014583) Trim Galore suggested: (Trim Galore, RRID:SCR_011847)
   (https://github.com/FelixKrueger/TrimGalore), read alignment with STAR (Dobin et al., 2013), gene quantification with Salmon (Patro et al., 2017), duplicate read marking with Picard MarkDuplicates (https://github.com/broadinstitute/picard), and transcript quantification with StringTie (Kovaka et al., 2019).	STAR suggested: (STAR, RRID:SCR_004463) StringTie suggested: (StringTie , RRID:SCR_016323) Picard suggested: (Picard, RRID:SCR_006525)
   Differential expression of genes was calculated by DESeq2 using FeatureCounts reads.	FeatureCounts suggested: (featureCounts, RRID:SCR_012919)
   All resulting fastq files were aligned to the Homo Sapiens genome (GRCh38, RefSeq) using the RNA-Seq Alignment application (Basespace, Illumina).	RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Libraries were pooled and sent to the WCM Genomics Core or HudsonAlpha for final quantification by Qubit fluorometer (ThermoFisher Scientific), TapeStation 2200 (Agilent), and qRT-PCR using the Kapa Biosystems Illumina library quantification kit.	Agilent suggested: (Agilent Bravo NGS, RRID:SCR_019473)
   Final libraries were quantified using fluorescent-based assays including PicoGreen (Life Technologies) or Qubit Fluorometer (Invitrogen) and Fragment Analyzer (Advanced Analytics) and sequenced on a NovaSeq 6000 sequencer (v1 chemistry) with 2×150bp targeting 60M reads per sample.	PicoGreen suggested: None
   (https://github.com/FelixKrueger/TrimGalore), read alignment with STAR (Dobin et al., 2013), gene quantification with Salmon (Patro et al., 2017), duplicate read marking with Picard MarkDuplicates (https://github.com/broadinstitute/picard), and transcript quantification with StringTie (Kovaka et al., 2019).	STAR suggested: (STAR, RRID:SCR_004463) StringTie suggested: (StringTie , RRID:SCR_016323) Picard suggested: (Picard, RRID:SCR_006525)
   Other quality control measures included RSeQC, Qualimap, and dupRadar.	RSeQC suggested: (RSeQC, RRID:SCR_005275) Qualimap suggested: (QualiMap, RRID:SCR_001209)
   Graphic Creation: All graphics were created using BioRender and Microsoft Powerpoint.	BioRender suggested: (Biorender, RRID:SCR_018361)

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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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   Read the original source
4. 

   Version published to 10.1101/2022.01.18.476786v1 on bioRxiv

   Jan 20, 2022