Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains

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1. Version published to 10.1016/j.heliyon.2021.e07284

   Jun 1, 2021
2. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.04.08.031856: (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
   Human transcriptome: RNA products annotated on the Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13) were downloaded from NCBI FTP site (RefSeq accession: GCF_000001405.39).	RefSeq suggested: (RefSeq, RRID:SCR_003496)
   The potential pairing were computed by aligning short 15-base sequences on RNA sequences with the STAR RNA-seq aligner [35] and by retaining only perfect matches for which the short sequence was reverse complemented.	STAR suggested: (STAR, RRID:SCR_015899)
   Assesment of the scope of hybrid duplexing against other species or viruses: To assess whether the …

   SciScore for 10.1101/2020.04.08.031856: (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
   Human transcriptome: RNA products annotated on the Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13) were downloaded from NCBI FTP site (RefSeq accession: GCF_000001405.39).	RefSeq suggested: (RefSeq, RRID:SCR_003496)
   The potential pairing were computed by aligning short 15-base sequences on RNA sequences with the STAR RNA-seq aligner [35] and by retaining only perfect matches for which the short sequence was reverse complemented.	STAR suggested: (STAR, RRID:SCR_015899)
   Assesment of the scope of hybrid duplexing against other species or viruses: To assess whether the sequences identified in SARS-CoV-2 could impact other species, we used BLAST to calculate the similarities between each human sequence and the following 12 other species : Gorilla gorilla, Pan troglodytes, Pongo abelii, Papio anubis, Macaca mulatta, Sapajus apella, Mus musculus, Rattus norvegicus, Pteropus vampyrus,	BLAST suggested: (BLASTX, RRID:SCR_001653)

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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.
   • 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 10.1101/2020.04.08.031856 on bioRxiv

   Apr 9, 2020