Phylogenomics reveals multiple introductions and early spread of SARS-CoV-2 into Peru

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1. 

   ScreenIT

   Sep 16, 2020

   SciScore for 10.1101/2020.09.14.296814: (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
   Filtered reads were mapped against SARS‐CoV‐2 reference (NC_045512) using Burrows‐ Wheeler Aligner MEM algorithm BWA‐MEM v0.7.7 (arXiv:1303.3997v2).	BWA‐MEM suggested: (Sniffles, RRID:SCR_017619)
   SAMtools and Geneious Prime were used to sort BAM files, to generate alignment statistics and to obtain consensus sequence.	SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Phylogenetic analysis of SARS-CoV in Peru: The full genomic dataset (n=3472) was aligned using MAFFT v 7.1 (10.1093/nar/gkf436) with default parameters.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   We estimate a maximum likelihood tree of …

   SciScore for 10.1101/2020.09.14.296814: (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
   Filtered reads were mapped against SARS‐CoV‐2 reference (NC_045512) using Burrows‐ Wheeler Aligner MEM algorithm BWA‐MEM v0.7.7 (arXiv:1303.3997v2).	BWA‐MEM suggested: (Sniffles, RRID:SCR_017619)
   SAMtools and Geneious Prime were used to sort BAM files, to generate alignment statistics and to obtain consensus sequence.	SAMtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Phylogenetic analysis of SARS-CoV in Peru: The full genomic dataset (n=3472) was aligned using MAFFT v 7.1 (10.1093/nar/gkf436) with default parameters.	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   We estimate a maximum likelihood tree of 3472 aligned sequences using IQ-tree v 1.6 (17) under a HKY nucleotide substitution model, with gamma distribution of among site rate variation (HKY+G+I) as selected by ModelFinder (18) and using the EPI_ISL_406801 sequence (GISAID) to root the tree.	IQ-tree suggested: (IQ-TREE, RRID:SCR_017254)
   TempEst v1.5.1 (19) was used to assess the strength of temporal signal and inspect for outliers in the dataset by a root-to-tip regression of genetic distance against sampling date.	TempEst suggested: (TempEst, RRID:SCR_017304)

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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: We detected the following sentences addressing limitations in the study:

   One of the limitations of this study are the differences between the number of Peruvian isolates from cases identified within Peru regions. Specifically, there were more SARS-CoV-2 representatives’ sequences in Lima than in any Peru departments. Thus, it means that our estimates might be biased due to them being based on available background sequences at that time. Moreover, in the absence of epidemiological information such as travel history and contacts tracking, it is hard to associate periods of untracked transmissions with any specific regions or countries.

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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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2. 

   Version published to 10.1101/2020.09.14.296814 on bioRxiv

   Sep 14, 2020