A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

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1. Version published to 10.1093/ofid/ofaa434

   Sep 18, 2020
2. 

   ScreenIT

   Jun 9, 2020

   SciScore for 10.1101/2020.05.31.126136: (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
   Following rRNA depletion and fragmentation, RNA was converted to cDNA and processed for NGS library prep using TruSeq Stranded Total RNA library prep kit (	NGS suggested: (PM4NGS, RRID:SCR_019164)
   Assembly of sequencing data: Raw image data was basecalled using bcl2fastq v2.20 with --no-lane-splitting option enabled.	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   QC of the FASTQ files was performed using FastQC v0.11.7, and adaptors/poor quality bases were trimmed using Trimmomatic.6,7 Reads were aligned to the reference genome MN908947.3 using hisat2.8 Consensus sequence from the bam file …

   SciScore for 10.1101/2020.05.31.126136: (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
   Following rRNA depletion and fragmentation, RNA was converted to cDNA and processed for NGS library prep using TruSeq Stranded Total RNA library prep kit (	NGS suggested: (PM4NGS, RRID:SCR_019164)
   Assembly of sequencing data: Raw image data was basecalled using bcl2fastq v2.20 with --no-lane-splitting option enabled.	bcl2fastq suggested: (bcl2fastq , RRID:SCR_015058)
   QC of the FASTQ files was performed using FastQC v0.11.7, and adaptors/poor quality bases were trimmed using Trimmomatic.6,7 Reads were aligned to the reference genome MN908947.3 using hisat2.8 Consensus sequence from the bam file was derived using seqtk and bcftools.	FastQC suggested: (FastQC, RRID:SCR_014583)
   9 Samtools depth command was used to calculate the coverage across the genome, with the options -a and -d 50000.10 The sequences were deposited in GISAID.	Samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   For this, the individual samples were systematically aligned to the Wuhan-Hu-1 reference genome (NC_045512) using EMBOSS needle.	EMBOSS suggested: (EMBOSS, RRID:SCR_008493)
   15 The sequences were aligned against the WH1 reference genome using MAFFT and spurious variant positions were masked from the alignment.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Divergence estimates and most recent common ancestor: The substitution rate of nCoV-2 was estimated using BEAST v1.10.4 following a methodology described previously.18,19 The masked alignment file was used as input to estimate a strict molecular clock and a coalescent growth rate model (exponential growth).	BEAST suggested: (BEAST, RRID:SCR_010228)
   The log output of each MCMC run was analysed in Tracer v1.7.1.20 The priors used for each parameter in the analysis are given in Supplementary Data 4.	Tracer suggested: (Tracer, RRID:SCR_019121)
   Functional evaluation of variants: The variants were also evaluated for the functional consequences using the Sorting Intolerant from Tolerant (SIFT).	SIFT suggested: (SIFT, RRID:SCR_012813)
   The functional effects of protein variants identified in the clades were assessed using the PROVEAN web server, using the protein sequences of the Wuhan-Hu-1 genome as reference and a default threshold value of −2.5.22 Additionally, PhyloP conservation scores and base-wise GERP Rejected Substitutions scores (RS scores) for the variants were also computed.	PROVEAN suggested: (PROVEAN, RRID:SCR_002182)
   The variants were also checked for overlaps with immune epitope predictions as given on UCSC Genome Browser for SARS-CoV-2.	UCSC Genome Browser suggested: (UCSC Genome Browser, RRID:SCR_005780)

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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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3. 

   Version published to 10.1101/2020.05.31.126136v1 on bioRxiv

   May 31, 2020