Sequence variation among SARS-CoV-2 isolates in Taiwan

Article activity feed

1. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.29.014290: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell Culture and Virus Isolation: Vero-E6 (ATCC, Manassas, VA, USA) and MK-2 (ATCC) cells were maintained in Modified Eagle Medium (MEM, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum and 1x penicillin-streptomycin at 37°C in the presence of 5% CO2.	Vero-E6 suggested: None MK-2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Next-generation Sequencing Data Analysis Pipeline: We first trimmed …

   SciScore for 10.1101/2020.03.29.014290: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	not detected.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell Culture and Virus Isolation: Vero-E6 (ATCC, Manassas, VA, USA) and MK-2 (ATCC) cells were maintained in Modified Eagle Medium (MEM, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum and 1x penicillin-streptomycin at 37°C in the presence of 5% CO2.	Vero-E6 suggested: None MK-2 suggested: None
   Software and Algorithms
   Sentences	Resources
   Next-generation Sequencing Data Analysis Pipeline: We first trimmed the raw data by removing low-quality and short reads using Trimmomatic (version 0.39) (4).	Trimmomatic suggested: (Trimmomatic, RRID:SCR_011848)
   Next, quality reads were mapped to the human reference genome to remove host sequences using HISAT2 (version 2.1.0) (5)	HISAT2 suggested: (HISAT2, RRID:SCR_015530)
   SPAdes (version 3.14.0) (6) was used to perform de novo assembly for constructing contig sequences.	SPAdes suggested: (SPAdes, RRID:SCR_000131)
   Viral candidates were identified using the reported top BLASTN hits for each of the queried contig sequences.	BLASTN suggested: (BLASTN, RRID:SCR_001598)
   In total 348 sequences were aligned using MAFFT (version 7.427) (8) for further analyses.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   The phylogenetic tree was inferred using RAxML (version 8.2.12) (9) under the GTRGAMMA model with a bootstrap value of 1000 to investigate the genomic relationships.	RAxML suggested: (RAxML, RRID:SCR_006086)

   ---

   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).

   ---

   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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • 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.

   ---

   Read the original source
2. 

   Version published to 10.1101/2020.03.29.014290v1 on bioRxiv

   Mar 31, 2020
3. Version published to 10.1080/22221751.2020.1782271

   Jan 1, 2020