Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data

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1. Version published to 10.1016/s2214-109x(21)00434-4

   Dec 1, 2021
2. 

   ScreenIT

   Jan 6, 2021

   SciScore for 10.1101/2021.01.04.20232520: (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	Specifically, we determined the number of SARS-CoV-2 infections detected on each day since the first case in Zimbabwe, the distribution of detected cases in ten geographical regions of Zimbabwe, the number of infections in males and females, and the number of infection by age stratification.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Sequence analysis: The raw reads were demultiplexed using bcl2fastq (v2.20)	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   Briefly, the reads had adapters trimmed with TrimGalore …

   SciScore for 10.1101/2021.01.04.20232520: (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	Specifically, we determined the number of SARS-CoV-2 infections detected on each day since the first case in Zimbabwe, the distribution of detected cases in ten geographical regions of Zimbabwe, the number of infections in males and females, and the number of infection by age stratification.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   Sequence analysis: The raw reads were demultiplexed using bcl2fastq (v2.20)	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   Briefly, the reads had adapters trimmed with TrimGalore (https://github.com/FelixKrueger/TrimGalore), were aligned to the Wuhan Hu-1 reference genome (accession MN908947.3) using BWA-MEM (v0.7.17) (Li, 2013), the ARTIC amplicons were trimmed and a consensus built using iVAR (v.1.2) (Grubaugh et al., 2019).	TrimGalore suggested: None BWA-MEM suggested: (Sniffles, RRID:SCR_017619)
   All sequences were aligned against the reference Wuhan Hu-1 using MAFFT (Katoh and Standley, 2013), and the maximum likelihood tree was estimated using fasttree and refined with iqtree2 under the HKY+G model (Price et al., 2010; Minh et al., 2019).	MAFFT suggested: (MAFFT, RRID:SCR_011811)

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   Results from OddPub: Thank you for sharing your code.

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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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3. 

   Version published to 10.1101/2021.01.04.20232520v1 on medRxiv

   Jan 6, 2021