Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution

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1. Version published to 10.1128/msystems.00505-20

   Aug 25, 2020
2. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.25.006213: (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
   Selection of genomes and annotation: Sequences of different strains were downloaded from NCBI database https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/ (Table 1).	NCBI suggested: (NCBI, RRID:SCR_006472)
   Further the genomes were annotated using Prokka [22].	Prokka suggested: (Prokka, RRID:SCR_014732)
   Further the GC content information was generated using QUAST standalone tool [23].	QUAST suggested: (QUAST, RRID:SCR_001228)
   The orthologous gene clusters were aligned using MUSCLE v3.8 [24] and further processed for removing stop codons using HyPhy v2.2.4 [25].	MUSCLE suggested: (MUSCLE, RRID:SCR_01…

   SciScore for 10.1101/2020.03.25.006213: (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
   Selection of genomes and annotation: Sequences of different strains were downloaded from NCBI database https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/ (Table 1).	NCBI suggested: (NCBI, RRID:SCR_006472)
   Further the genomes were annotated using Prokka [22].	Prokka suggested: (Prokka, RRID:SCR_014732)
   Further the GC content information was generated using QUAST standalone tool [23].	QUAST suggested: (QUAST, RRID:SCR_001228)
   The orthologous gene clusters were aligned using MUSCLE v3.8 [24] and further processed for removing stop codons using HyPhy v2.2.4 [25].	MUSCLE suggested: (MUSCLE, RRID:SCR_011812) HyPhy suggested: (HyPhy, RRID:SCR_016162)
   Single-Likelihood Ancestor Counting (SLAC) method in Datamonkey v2.0 [26] (http://www.datamonkey.org/slac) was used to calculate dN/dS value for each orthologous gene cluster.	Datamonkey suggested: (DataMonkey, RRID:SCR_010278)
   The dN/dS values were plotted in R (R Development Core Team, 2015).	R Development Core suggested: (R Project for Statistical Computing, RRID:SCR_001905)
   Phylogenetic analysis: To infer the phylogeny, the core gene alignment was generated using MAFFT [27] present within the Roary Package [28].	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Since, none of the SARS-CoV-2 genomes are updated in any protein database, we first annotated the genes using BLASTp tool [34].	BLASTp suggested: (BLASTP, RRID:SCR_001010)
   STRING v10.5 [36] and IntAct [37] for predicting their interaction against host proteins.	IntAct suggested: (IntAct, RRID:SCR_006944)
   Functional enrichment analysis: Next, functional studies were performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) [41, 42] and Gene Ontology (GO) enrichment analyses using UniProt database [43] to evaluate the biological relevance and functional pathways of the HCoV-associated proteins.	KEGG suggested: (KEGG, RRID:SCR_012773) UniProt suggested: (UniProtKB, RRID:SCR_004426)
   All functional analyses were performed using STRING enrichment and STRINGify, plugin of Cytoscape v.	STRING suggested: (STRING, RRID:SCR_005223) Cytoscape suggested: (Cytoscape, RRID:SCR_003032)

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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:

   • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
   • No funding statement was detected.
   • No protocol registration statement was detected.

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3. 

   Version published to 10.1101/2020.03.25.006213v2 on bioRxiv

   Apr 16, 2020
4. 

   Version published to 10.1101/2020.03.25.006213v1 on bioRxiv

   Mar 30, 2020