Genetic Diversity Among SARS-CoV2 Strains in South America may Impact Performance of Molecular Detection

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1. Version published to 10.3390/pathogens9070580

   Jul 17, 2020
2. 

   ScreenIT

   Jun 22, 2020

   SciScore for 10.1101/2020.06.18.20134759: (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 complete set of sequences was aligned using MAFFT v7.407 with FFT-NS-2 algorithm and default parameter settings [17,18].	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Each sub-alignment was manually verified to remove sequences with Ns, not identified positions (denoted with IUPAC code) and gaps.	IUPAC suggested: (IUPAC, RRID:SCR_005084)
   The “good-sequence” alignment by gene (N, E and RdRp) was used to identify nucleotide and haplotype diversity using DnaSP 5.10 software [20].	DnaSP suggested: (DnaSP, RRID:SCR_003067)
   A representative sequence by haplotype was used to construct a haplotype …

   SciScore for 10.1101/2020.06.18.20134759: (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 complete set of sequences was aligned using MAFFT v7.407 with FFT-NS-2 algorithm and default parameter settings [17,18].	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Each sub-alignment was manually verified to remove sequences with Ns, not identified positions (denoted with IUPAC code) and gaps.	IUPAC suggested: (IUPAC, RRID:SCR_005084)
   The “good-sequence” alignment by gene (N, E and RdRp) was used to identify nucleotide and haplotype diversity using DnaSP 5.10 software [20].	DnaSP suggested: (DnaSP, RRID:SCR_003067)
   A representative sequence by haplotype was used to construct a haplotype alignment and then trees were generated using FastTree double precision version 2.1.10 [21] and visualized in the interactive tool Tree Of Life V4 (http://itol.embl.de) [22].	FastTree suggested: (FastTree, RRID:SCR_015501)

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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:

   Despite no present evidence on false negative results for RdRp gene based assays, its inherent mutation rate (due to environmental pressure and its role as a virulence factor) and having account this gene showed low sensitivity [41] is an aspect that deserves further investigation It is important to note some limitations in the interpretations of our data. First, because all sequences were retrieved from public databases the accuracy of these sequences could not be entirely verified. In addition, given the most recent emergence of the virus in South America, it is possible that our analysis may represent a snapshot of the most recent evolutionary episodes and does not represent the entire developmental history of the different lineages since introduction. Further studies will be needed to expand our ability to characterize the complete and evolving evolutionary track of the virus. In summary, this preliminary analysis based on the genomic diversity of SARS-CoV-2 in South America demonstrates how the presence of changes in suggested target regions for primer annealing sites may preclude accurate molecular diagnosis of SARS-CoV-2 when targeting locations within the N-gene region. Our results, confirm the relatively conserved fitness of the E-gene region where no mutations were found, thus making it an ideal candidate for first-line screening in the South America. Due to the lack of resources and unavailability to acquire reagents and consumables for molecular diagnosis in many ...

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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 10.1101/2020.06.18.20134759v1 on medRxiv

   Jun 22, 2020