Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong

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1. Version published to 10.1038/s41467-022-28420-7

   Feb 8, 2022
2. 

   ScreenIT

   Jul 1, 2021

   SciScore for 10.1101/2021.06.19.21259169: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   The base calling of raw read signal and demultiplexing of reads by different samples were performed using Bcl2Fastq (Illumina).	Bcl2Fastq suggested: (bcl2fastq , RRID:SCR_015058)
   Specifically, the raw FASTQ reads were assembled and mapped to the SARS-CoV-2 reference genome (Wuhan-Hu-1, GenBank: MN908947.3) using BWA mem2 (v.2.0pre2) (23).	BWA suggested: (BWA, RRID:SCR_010910)
   The consensus sequences for each sample were called as dominant bases at each position by samtools mpileup (v.1.11) (24) with minimum depth of 100 reads.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   After removing …

   SciScore for 10.1101/2021.06.19.21259169: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   The base calling of raw read signal and demultiplexing of reads by different samples were performed using Bcl2Fastq (Illumina).	Bcl2Fastq suggested: (bcl2fastq , RRID:SCR_015058)
   Specifically, the raw FASTQ reads were assembled and mapped to the SARS-CoV-2 reference genome (Wuhan-Hu-1, GenBank: MN908947.3) using BWA mem2 (v.2.0pre2) (23).	BWA suggested: (BWA, RRID:SCR_010910)
   The consensus sequences for each sample were called as dominant bases at each position by samtools mpileup (v.1.11) (24) with minimum depth of 100 reads.	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   After removing repetitive sequences and trimming masked sites, data quality was evaluated using a root-to-tip regression analysis in TempEst (v.1.5.3) (25), resulting in a final set of 3,437 sequences.	TempEst suggested: (TempEst, RRID:SCR_017304)
   Time-scaled phylogenies were generated using the strict clock model with 0.001 substitutions per site per year which is within 95% credible interval of SARS-CoV-2 temporal signal (29), the Skygrid model (30) with 61 grid points and a Laplace root-height prior with mean equal to the dated-ML tree estimated by IQ-TREE (v.2) (26) and scale is set to 20% of mean.	IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   For all samples of HK-wave3 and HK-wave4A, we used the birth-death skyline serial (BDSS) model (14) implemented in BEAST (v.2.6.3) (33) to infer the time of origin (tOrigin), time of most recent common ancestor (tMRCA) and temporal variations (piecewise fashion over 12-15 equidistant intervals) in the effective reproductive number denoted as Rt.	BEAST suggested: (BEAST, RRID:SCR_010228)
   Mixing of the MCMC chain was inspected using Tracer (v1.7.1) (35) to ensure an effective sample size (ESS) of >200 for each parameter.	Tracer suggested: (Tracer, RRID:SCR_019121)
   This assumption was incorporated in the default birth-death model using the package TreeSlicer in BEAST2.	BEAST2 suggested: (BEAST2, RRID:SCR_017307)
   Single nucleotide variants (SNVs) in deep-sequence data were identified using three different variant callers, freebayes (v.1.3.2) (36), VarDict (v.1.82) (37) and LoFreq (v.2.15) (38).	LoFreq suggested: (LoFreq, RRID:SCR_013054)

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   Results from OddPub: Thank you for sharing your code and 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 10.1101/2021.06.19.21259169v1 on medRxiv

   Jun 23, 2021