An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets

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1. Version published to 10.1186/s13073-020-00822-6

   Jan 7, 2021
2. 

   ScreenIT

   Jun 8, 2020

   SciScore for 10.1101/2020.05.11.089409: (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
   Whole genome sequence data analysis: SARS-CoV-2 nucleotide sequences were downloaded from NCBI (https://www.ncbi.nlm.nih.gov) and GISAID (https://www.gisaid.org).	https://www.ncbi.nlm.nih.gov suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)
   As a part of an automated in-house pipeline, sequences were aligned using MAFFT software (v7.2) [12] and trimmed to the beginning of the first reading frame (orf1ab-nsp1).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Using data available from the NCBI COVID-19 resource, a modified annotation (GFF) file was generated and open …

   SciScore for 10.1101/2020.05.11.089409: (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
   Whole genome sequence data analysis: SARS-CoV-2 nucleotide sequences were downloaded from NCBI (https://www.ncbi.nlm.nih.gov) and GISAID (https://www.gisaid.org).	https://www.ncbi.nlm.nih.gov suggested: (GENSAT at NCBI - Gene Expression Nervous System Atlas, RRID:SCR_003923)
   As a part of an automated in-house pipeline, sequences were aligned using MAFFT software (v7.2) [12] and trimmed to the beginning of the first reading frame (orf1ab-nsp1).	MAFFT suggested: (MAFFT, RRID:SCR_011811)
   Using data available from the NCBI COVID-19 resource, a modified annotation (GFF) file was generated and open reading frames (ORFs) for each respective viral protein were extracted (taking in to account ribosomal slippage) using bedtools ‘getfasta’ function [13].	bedtools suggested: (BEDTools, RRID:SCR_006646)
   Each ORF was translated using EMBOSS transeq software [14] and the variants for each protein sequence were identified using an in-house script.	EMBOSS suggested: (EMBOSS, RRID:SCR_008493)
   Using BLASTp [26] we mapped short amino acid epitope sequences onto the canonical sequence of SARS-CoV-2 proteins.	BLASTp suggested: (BLASTP, RRID:SCR_001010)
   Coronavirus homology analysis: Reference proteomes for SARS, MERS, OC43, 229E, HKU1 and NL63 α and β coronavirus (-CoV) species were sourced from UniProt database.	UniProt suggested: (UniProtKB, RRID:SCR_004426)
   Homologous peptide sequences with a BLAST bitscore indicating 10 or more residues mapped to the target sequence were recorded and parsed for display on the graph.	BLAST suggested: (BLASTX, RRID:SCR_001653)
   The BioCircos.js library [10] was used to generate the interactive plot and Datatables.net libraries for the table.	BioCircos suggested: None
   For the temporal/geographic non-synonymous mutation plots, we partitioned the whole genome sequencing dataset by week and continent and plotted non-synonymous allele frequencies using the Google Charts JavaScript libraries.	Google suggested: (Google, RRID:SCR_017097)

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   Results from OddPub: Thank you for sharing your code and 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 10.1101/2020.05.11.089409 on bioRxiv

   May 13, 2020