SARS-CoV-2 Genome Sequencing Methods Differ in Their Abilities To Detect Variants from Low-Viral-Load Samples

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1. Version published to 10.1128/jcm.01046-21

   Oct 19, 2021
2. 

   ScreenIT

   May 8, 2021

   SciScore for 10.1101/2021.05.01.442304: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethical and governance approval for the study was granted by the Western Sydney Local Health District Human Research Ethics Committee (2020/ETH02426).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: Routine mycoplasma testing was performed to exclude mycoplasma contamination of the cell line and all culture work was undertaken in physical containment laboratory level 3 (PC3) biosafety conditions.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Viral isolation: SARS-CoV-2 positive respiratory specimens were cultured in Vero C1008 cells (Vero 76, clone E6, Vero E6 …

   SciScore for 10.1101/2021.05.01.442304: (What is this?)

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

   Table 1: Rigor

   Ethics	IRB: Ethical and governance approval for the study was granted by the Western Sydney Local Health District Human Research Ethics Committee (2020/ETH02426).
   Sex as a biological variable	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Cell Line Authentication	Contamination: Routine mycoplasma testing was performed to exclude mycoplasma contamination of the cell line and all culture work was undertaken in physical containment laboratory level 3 (PC3) biosafety conditions.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Viral isolation: SARS-CoV-2 positive respiratory specimens were cultured in Vero C1008 cells (Vero 76, clone E6, Vero E6 [ECACC 85020206]) as previously outlined [32].	Vero C1008 suggested: ATCC Cat# CRL-1586, RRID:CVCL_0574) Vero E6 suggested: None
   Briefly, Vero cell cultures were seeded at 1-3 × 104 cells/cm2 in Dulbecco’s minimal essential medium (DMEM, LONZA, Alpharetta, GA, USA) supplemented with 9% foetal bovine serum (FBS, HyClone, Cytiva, Sydney, Australia).	Vero suggested: RRID:CVCL_ZW93)
   Software and Algorithms
   Sentences	Resources
   Demultiplexed reads were quality trimmed using Trimmomatic v0.36 (sliding window of 4, minimum read quality score of 20, leading/trailing quality of 5 and minimum length of 36 after trimming) [35].	Trimmomatic suggested: (Trimmomatic, RRID:SCR_011848)
   Briefly, reads were mapped to the reference SARS-CoV-2 genome (NCBI GenBank accession MN908947.3) using BWA-mem version 0.7.17, with unmapped reads discarded.	BWA-mem suggested: (Sniffles, RRID:SCR_017619)

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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:

   • 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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3. 

   Version published to 10.1101/2021.05.01.442304v1 on bioRxiv

   May 3, 2021