SARS‐CoV‐2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions

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1. Version published to 10.1111/tbed.14104

   May 22, 2021
2. 

   ScreenIT

   Nov 21, 2020

   SciScore for 10.1101/2020.11.16.20229047: (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
   Initially, the quality of FastQ files was assessed using the FastQC program [5] and then preprocessed using Fastp [6].	FastQC suggested: (FastQC, RRID:SCR_014583) Fastp suggested: (fastp, RRID:SCR_016962)
   The sequences were aligned to the SARS-CoV-2 reference genome (NC_045512.2) using Bowtie2 [7], keeping the reads mapped in proper pair.	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   The resultant filtered bam files were used for assembly of consensus SARS-CoV-2 sequences using samtools mpileup and bcftools[8].	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   To explore the temporal signal of the …

   SciScore for 10.1101/2020.11.16.20229047: (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
   Initially, the quality of FastQ files was assessed using the FastQC program [5] and then preprocessed using Fastp [6].	FastQC suggested: (FastQC, RRID:SCR_014583) Fastp suggested: (fastp, RRID:SCR_016962)
   The sequences were aligned to the SARS-CoV-2 reference genome (NC_045512.2) using Bowtie2 [7], keeping the reads mapped in proper pair.	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   The resultant filtered bam files were used for assembly of consensus SARS-CoV-2 sequences using samtools mpileup and bcftools[8].	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   To explore the temporal signal of the data, the remaining high quality Fasta files were aligned by MAFFT v7.407 using the FFT-NS-2 algorithm [14] and then a maximum-likelihood phylogenetic tree was built by applying IQ-TREE v2.1.1 with the GTR+gamma model [15].	MAFFT suggested: (MAFFT, RRID:SCR_011811) IQ-TREE suggested: (IQ-TREE, RRID:SCR_017254)
   The temporal signal was explored by TempEst providing a root-to-tip regression plot [16].	TempEst suggested: (TempEst, RRID:SCR_017304)
   Eventually, BEAST v1.10.4 was applied to estimate TMRCA and construct a Bayesian phylogenetic tree of the remaining 45 sequences, plus Wuhan-1 patient (EPI_ISL_402125) as an outgroup, using a simple model consisting of HKYγ codon partitioned 1 + 2, 3 substitution model, strict clock and coalescent exponential growth tree prior.	BEAST suggested: (BEAST, RRID:SCR_010228)
   Maximum clade credibility (MCC) tree was then made using TreeAnnotator with 10% burn-in from two separate Markov chain-Monte Carlo runs, explored by Tracer v1.7.1[17] and combined by LogCombiner from the BEAST package [13].	Tracer suggested: (Tracer, RRID:SCR_019121)
   To trace possible sources of SARS-CoV-2 entry into Iran, an additional phylogenetic tree was constructed based on a total of 261 samples including a list of high-quality genomes in GISAID [18] from the start of epidemic till the end of February, and random subsets of samples in GISAID during March-June interval available as of September 27 and selected using mothur [19].	mothur suggested: (mothur, RRID:SCR_011947)

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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 10.1101/2020.11.16.20229047 on medRxiv

   Nov 20, 2020