Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences

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   ScreenIT

   Oct 30, 2020

   SciScore for 10.1101/2020.10.26.354969: (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	Of the 6 cases sequenced, 4 were male; 2 females, there was one death, two recoveries and two active cases.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Of the 451 samples screened by rRT-PCR, ten were confirmed as SARS-CoV-2 cases and 5 as indeterminate cases (positive for the screening gene and negative for the SARS-CoV-2 confirmatory gene) For WGS, four SARS-CoV-2 confirmed cases, one indeterminate case and one negative case were processed Table 1.	WGS suggested: None
   The pool was run at a final concentration of 10 pM on an Illumina …

   SciScore for 10.1101/2020.10.26.354969: (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	Of the 6 cases sequenced, 4 were male; 2 females, there was one death, two recoveries and two active cases.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Of the 451 samples screened by rRT-PCR, ten were confirmed as SARS-CoV-2 cases and 5 as indeterminate cases (positive for the screening gene and negative for the SARS-CoV-2 confirmatory gene) For WGS, four SARS-CoV-2 confirmed cases, one indeterminate case and one negative case were processed Table 1.	WGS suggested: None
   The pool was run at a final concentration of 10 pM on an Illumina MiSeq instrument using MiSeq V3 reagent kit.	MiSeq suggested: (A5-miseq, RRID:SCR_012148)
   Fig 1 summarised the steps involved in sequencing using for both Nanopore and Illumina platform.	Nanopore suggested: None
   SARS-CoV-2 novel Coronavirus bioinformatics protocol; SAMTOOLS).	SAMTOOLS suggested: (SAMTOOLS, RRID:SCR_002105)
   Similarly, 250 bp paired end Illumina reads were quality checked using FASTQC (	FASTQC suggested: (FastQC, RRID:SCR_014583)
   18 Reads with only a minimum Phred score of 30 were included in our downstream analysis.	Phred suggested: (Phred, RRID:SCR_001017)
   Filtered reads were then mapped to the Wuhan-Hu-1 reference genomes (accession number MN908947.3) using BWA-mem (0.7.17-r1188).	BWA-mem suggested: (Sniffles, RRID:SCR_017619)
   Phylogenetic analysis for Illumina and Nanopore platform: Prank (v140603) was used to generate a multiple alignment of all the samples including some available reference genomes around the globe (Downloaded from RefSeq).	Prank suggested: (prank, RRID:SCR_017228) RefSeq suggested: (RefSeq, RRID:SCR_003496)

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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.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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2. 

   Version published to 10.1101/2020.10.26.354969 on bioRxiv

   Oct 26, 2020