Conserved Genomic Terminals of SARS-CoV-2 as Coevolving Functional Elements and Potential Therapeutic Targets
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Abstract
The CoV disease 2019 (COVID-19) infectious disease outbreak is having a dramatic global effect on public health and the economy. As of October 2020, SARS-CoV-2 has been detected in over 189 countries, has infected over 40 million people, and is responsible for more than 1 million deaths.
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SciScore for 10.1101/2020.07.06.190207: (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 family sequence conservation analysis: The SARS-CoV-2 NCBI RefSeq genome (NC_045512.2) was used as the reference. RefSeqsuggested: (RefSeq, RRID:SCR_003496), processed peptides, and UTRs) of SARS-CoV-2 was searched against the 109 representative CoV genomes collected from four genera (alpha, beta, gamma, and delta) (Table S1) using NCBI BLAST+ NCBIsuggested: (NCBI, RRID:SCR_006472)The maximum likelihood phylogeny tree was constructed using RAxML (v8.2.11) with 100 bootstraps under the GTRGAMMA model (48). RAxMLsuggested: (RAxML, RRID:SCR_006086)An MSA was performed on the … SciScore for 10.1101/2020.07.06.190207: (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 family sequence conservation analysis: The SARS-CoV-2 NCBI RefSeq genome (NC_045512.2) was used as the reference. RefSeqsuggested: (RefSeq, RRID:SCR_003496), processed peptides, and UTRs) of SARS-CoV-2 was searched against the 109 representative CoV genomes collected from four genera (alpha, beta, gamma, and delta) (Table S1) using NCBI BLAST+ NCBIsuggested: (NCBI, RRID:SCR_006472)The maximum likelihood phylogeny tree was constructed using RAxML (v8.2.11) with 100 bootstraps under the GTRGAMMA model (48). RAxMLsuggested: (RAxML, RRID:SCR_006086)An MSA was performed on the collected 693 genome sequences including SARS-CoV-2 reference genome using Clustal Omega (v1.2.4). Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)In addition, an MSA of the 18,599 genomes was built using MAFFT (v6.861b), which was used for independent validations of major mutation positions (51). MAFFTsuggested: (MAFFT, RRID:SCR_011811)The functional impact of amino acid substitutions and indels were predicted using PROVEAN (26). PROVEANsuggested: (PROVEAN, RRID:SCR_002182)Linkage disequilibrium (LD) analysis was performed to identify co-evolving variants among SNVs with frequency of 0.1% or higher using Tagger implemented in Haploview (v4.2) (52). Haploviewsuggested: (Haploview, RRID:SCR_003076)Identification of putatively interacting human microRNAs: The UTR sequences of SARS-CoV-2 and SARS-CoV were used to search against the miRBase mature RNA sequences (Release 22.1) (31) using blastn with the following parameters set for short sequences: “-penalty −4 -reward 5 -gapopen 25 -gapextend 10 -dust no -soft_masking false.” For cross-species conservation analysis in other organisms, we searched the miRBase database requiring 18 or more bases matched with 100% sequence identity. blastnsuggested: (BLASTN, RRID:SCR_001598)miRBasesuggested: (miRBase, RRID:SCR_017497)A SARS-CoV-2 gene-by-gene BLAST analysis was performed against the CoV family genomes at nucleotide and amino acid sequence levels. BLASTsuggested: (BLASTX, RRID:SCR_001653)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).
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.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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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