Integrative analyses of SARS-CoV-2 genomes from different geographical locations reveal unique features potentially consequential to host-virus interaction, pathogenesis and clues for novel therapies

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1. Version published to 10.1016/j.heliyon.2020.e04658

   Sep 1, 2020
2. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.21.001586: (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
   Coronavirus subtyping and Mutation Analysis: All assembled query genomes in FASTA format were analyzed using Genome Detective Coronavirus Typing Tool (version 1.1.3)(5) which allows quick identification and characterization of novel coronavirus genomes.	Mutation Analysis suggested: None
   MSA was performed using online CLUSTAL-OMEGA software.	CLUSTAL-OMEGA suggested: None
   Neighbor joining method with bootstrap value of 1000 replicates was used for the construction of consensus tree using MEGA software(6) (10.1.7 version).	MEGA suggested: (Mega BLAST, RRID:SCR_011920)
   (Figure 1(b)) To identify …

   SciScore for 10.1101/2020.03.21.001586: (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
   Coronavirus subtyping and Mutation Analysis: All assembled query genomes in FASTA format were analyzed using Genome Detective Coronavirus Typing Tool (version 1.1.3)(5) which allows quick identification and characterization of novel coronavirus genomes.	Mutation Analysis suggested: None
   MSA was performed using online CLUSTAL-OMEGA software.	CLUSTAL-OMEGA suggested: None
   Neighbor joining method with bootstrap value of 1000 replicates was used for the construction of consensus tree using MEGA software(6) (10.1.7 version).	MEGA suggested: (Mega BLAST, RRID:SCR_011920)
   (Figure 1(b)) To identify potential host microRNA target sites in the virus genome sequences, we have used miRanda (3.3 a version)(12, 13) software, with an energy threshold of −20 kcal/mol.	miRanda suggested: (miRanda, RRID:SCR_017496)
   We also used psRNATarget server to compare the predicted targets by the two methods(14).	psRNATarget suggested: (psRNATarget, RRID:SCR_013321)
   Immunogenic properties analysis: All the genes and protein sequences for SARS-CoV2 were retrieved from ViPR database.	ViPR suggested: (vipR, RRID:SCR_010685)

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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: 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:

   • No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
   • 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 10.1101/2020.03.21.001586v1 on bioRxiv

   Mar 21, 2020