Integrated characterization of SARS-CoV-2 genome, microbiome, antibiotic resistance and host response from single throat swabs

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   ScreenIT

   Oct 19, 2020

   SciScore for 10.1101/2020.10.15.340794: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethics statement: The study and use of all samples were approved by the Ethics Committee of Wuhan Institue of Virology (No. WIVH17202001).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   preprocessing: Raw reads from sequencing were firstly subjected to Trim Galore (v0.6.4_dev) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming.	Trim Galore suggested: (Trim Galore, RRID:SCR_011847)
   Host transcriptional profiling analysis: Filtered reads were mapped to human genome (hg19) and …

   SciScore for 10.1101/2020.10.15.340794: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: Ethics statement: The study and use of all samples were approved by the Ethics Committee of Wuhan Institue of Virology (No. WIVH17202001).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   preprocessing: Raw reads from sequencing were firstly subjected to Trim Galore (v0.6.4_dev) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality control and adaptor trimming.	Trim Galore suggested: (Trim Galore, RRID:SCR_011847)
   Host transcriptional profiling analysis: Filtered reads were mapped to human genome (hg19) and transcriptome using STAR (v2.7.1a) (35).	STAR suggested: (STAR, RRID:SCR_015899)
   Multidimensional scaling and differential gene expression analysis were conducted using EdgeR (v3.28.1) (37) with gene count data generated by HTSeq (v0.11.2) (38).	EdgeR suggested: (edgeR, RRID:SCR_012802) HTSeq suggested: (HTSeq, RRID:SCR_005514)
   Gene Ontology Enrichment Analysis for biological processes was performed by DAVID (v6.8) (39) with all significantly up-regulated genes as input.	DAVID suggested: (DAVID, RRID:SCR_001881)
   Due to the redundancy of enriched GO terms, GO terms and their p values were further summarized using REViGO (40).	REViGO suggested: (REViGO, RRID:SCR_005825)
   Discrimination and de-novo assembly of SARS-CoV-2: After removal of human reads, the remaining data were aligned to the reference genome of Wuhan-Hu-1 (GenBank accession number: NC_045512) using Bowtie2 (v2.2.9) (41) for SARS-CoV-2 identification.	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   The coverage and sequencing depth of SARS-CoV-2 genome were calculated by Samtools (v1.9) (42).	Samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   On the other hand, to verify the method could screen for aetiologic agents and obtain pathogen genome, all non-human reads were processed for de-novo assembly using MEGAHIT (v1.2.9) with default parameters (43), and then all contigs were searched against NCBI nt database using blastn for classification(44).	MEGAHIT suggested: (MEGAHIT, RRID:SCR_018551) blastn suggested: (BLASTN, RRID:SCR_001598)
   Microbiome analysis: After removing human reads, the remaining reads were subjected to microbial taxonomic classification using Kraken2 (v2.0.8-beta) (45) with a custom database.	Kraken2 suggested: None
   To build the custom database, standard RefSeq complete bacterial genomes were downloaded through “kraken2-build --download-library bacteria” and complete genomes of human viruses and genome assemblies of fungi were downloaded from NCBI’s RefSeq and added to the custom database’s genomic library using the “--add-to-library” switch.	RefSeq suggested: (RefSeq, RRID:SCR_003496)
   Distances between samples were calculated using Morisita-horn dissimilarity index by vegdist command from vegan package version 2.5-6 (https://CRAN.R-project.org/package=vegan).	vegan suggested: (vegan, RRID:SCR_011950)
   All corresponding graphs were plotted using R scripts by RStudio (v1.2.5033) (https://rstudio.com/).	RStudio suggested: (RStudio, RRID:SCR_000432)

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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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2. 

   Version published to 10.1101/2020.10.15.340794 on bioRxiv

   Oct 15, 2020