Blood transcriptional biomarkers of acute viral infection for detection of pre-symptomatic SARS-CoV-2 infection: a nested, case-control diagnostic accuracy study
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SciScore for 10.1101/2021.01.18.21250044: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical approval: The study was approved by a UK Research Ethics Committee (South Central - Oxford A Research Ethics Committee, reference 20/SC/0149).
Consent: All participants provided written informed consent.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 We searched Medline on 12/10/2020 using comprehensive MeSH and key word terms for “viral infection”, “transcriptome”, “biomarker” and “blood” (full search strategy shown in Table S4). Medlinesuggested: (MEDLINE, RRID:SCR_002185)MeSHsuggested: (MeSH, RRID:SCR_004750)The … SciScore for 10.1101/2021.01.18.21250044: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Ethical approval: The study was approved by a UK Research Ethics Committee (South Central - Oxford A Research Ethics Committee, reference 20/SC/0149).
Consent: All participants provided written informed consent.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 We searched Medline on 12/10/2020 using comprehensive MeSH and key word terms for “viral infection”, “transcriptome”, “biomarker” and “blood” (full search strategy shown in Table S4). Medlinesuggested: (MEDLINE, RRID:SCR_002185)MeSHsuggested: (MeSH, RRID:SCR_004750)The transcript-level output counts and transcripts per million (TPM) values were summed on gene level and annotated with Ensembl gene ID, gene name, and gene biotype using the R/Bioconductor packages tximport and BioMart (39, 40). Ensemblsuggested: (Ensembl, RRID:SCR_002344)R/Bioconductorsuggested: NoneUpstream analysis of transcriptional regulation of the constituent genes in the candidate signatures was performed using Ingenuity Pathway Analysis (Qiagen, Venlo, The Netherlands) and visualized as network diagrams in Gephi v0.9.2, depicting all statistically overrepresented molecules predicted to be upstream >2 target genes, as previously (36). Ingenuity Pathway Analysissuggested: (Ingenuity Pathway Analysis, RRID:SCR_008653)Gephisuggested: (Gephi, RRID:SCR_004293)Open access to RNAseq data and associated essential metadata are available under accession no E-MTAB-10022 at ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). ArrayExpresssuggested: (ArrayExpress, RRID:SCR_002964)Results from OddPub: Thank you for sharing your data.
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.Results from TrialIdentifier: We found the following clinical trial numbers in your paper:
Identifier Status Title NCT04318314 Recruiting COVID-19: Healthcare Worker Bioresource: Immune Protection a… Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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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