Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence
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SciScore for 10.1101/2020.07.30.230102: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study was approved by the ethics review committee of Guangzhou Women and Children’s Medical Center.
Consent: Written informed consents were obtained from the legal guardians of all children.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 Clean reads were mapped to SARS-CoV-2 reference genome Wuhan-Hu-1 (GenBank MN908947.3) using BWA mem v0.7.12 (11), followed by duplicate reads removal with Picard v2.18.22 (http://broadinstitute.github.io/picard). BWAsuggested: (BWA, RRID:SCR_010910)Picardsuggested: (Picard, RRID:SCR_006525)Mpileup… SciScore for 10.1101/2020.07.30.230102: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: This study was approved by the ethics review committee of Guangzhou Women and Children’s Medical Center.
Consent: Written informed consents were obtained from the legal guardians of all children.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 Clean reads were mapped to SARS-CoV-2 reference genome Wuhan-Hu-1 (GenBank MN908947.3) using BWA mem v0.7.12 (11), followed by duplicate reads removal with Picard v2.18.22 (http://broadinstitute.github.io/picard). BWAsuggested: (BWA, RRID:SCR_010910)Picardsuggested: (Picard, RRID:SCR_006525)Mpileup files were generated with samtools v1.8 (12). samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Intra-host variants were identified using VarScan v2.3.9 and an in-house script (13). VarScansuggested: (VARSCAN, RRID:SCR_006849)Criteria for variants included: (1) sequencing depth ≥ 50, (2) minor allele frequency ≥ 5%, (3) minor allele frequency ≥ 2% on each strand, (4) minor allele counts ≥ 10 on each strand, (5) strand bias of the minor allele < 10 fold, (6) minor allele was supported by the inner part of the read (excluding 10 base pairs on each end), and (7) minor allele was supported by ≥ 10 reads that were classified as Betacoronavirus by Kraken v2.0.8-beta (14) on each strand. Krakensuggested: (Kraken, RRID:SCR_005484)The ratio of the number of non-synonymous substitutions per non-synonymous site (Ka) to the number of synonymous substitutions per synonymous site (Ks) was calculated using KaKs_Calculator 2.0 (15) with the MS method. KaKs_Calculatorsuggested: NoneResults 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: No clinical trial numbers were referenced.
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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