SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design
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SciScore for 10.1101/2020.05.14.097170: (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
Experimental Models: Cell Lines Sentences Resources We used publicly available transcriptome data (PRJNA615032) of SARS-CoV-2 infection in A549 and NHBE cell lines [13]. A549suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)Software and Algorithms Sentences Resources All the available data were download from the sequence read archive of NCBI database and fastq-dump program of SRAtoolkit [14] was used to extract fastq reads. NCBIsuggested: (NCBI, RRID:SCR_006472)Quality assessment and control of RNA-seq data was performed through the FastQC version 0.11.5 [15], MultiQC version 1.8 [16] and trimmomatic version 0.39 software [17]. FastQCsuggested…SciScore for 10.1101/2020.05.14.097170: (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
Experimental Models: Cell Lines Sentences Resources We used publicly available transcriptome data (PRJNA615032) of SARS-CoV-2 infection in A549 and NHBE cell lines [13]. A549suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)Software and Algorithms Sentences Resources All the available data were download from the sequence read archive of NCBI database and fastq-dump program of SRAtoolkit [14] was used to extract fastq reads. NCBIsuggested: (NCBI, RRID:SCR_006472)Quality assessment and control of RNA-seq data was performed through the FastQC version 0.11.5 [15], MultiQC version 1.8 [16] and trimmomatic version 0.39 software [17]. FastQCsuggested: (FastQC, RRID:SCR_014583)MultiQCsuggested: (MultiQC, RRID:SCR_014982)trimmomaticsuggested: (Trimmomatic, RRID:SCR_011848)All high-quality reads were mapped over SARS-CoV-2 isolate Wuhan-Hu-1(MN908947.3) by using HISAT2 version 2.1.0 on default parameters [18]. HISAT2suggested: (HISAT2, RRID:SCR_015530)Samtools version 1.1.0 [19] and Bedtools version 2.26.0 [20] were used to extract all the mapped read from each sample and extracted reads were used to construct de novo assemblies by using the Trinity assembler version 2.5.1 [21]. Samtoolssuggested: (SAMTOOLS, RRID:SCR_002105)Bedtoolssuggested: (BEDTools, RRID:SCR_006646)Trinitysuggested: (Trinity, RRID:SCR_013048)TransDecoder program [22] was used to generate protein sequence from assembled transcriptome. TransDecodersuggested: (TransDecoder, RRID:SCR_017647)Therefore, selected epitopes were checked for similarities with the human proteome sequences (Homo sapiens: GRCh38) through standalone NCBI BLAST similarity search tool. 2.3. BLASTsuggested: (BLASTX, RRID:SCR_001653)In the sequence based approach, VaxiJen server was used to identify most antigenic proteins from translated transcriptome, and BepiPred-2.0 program [29] was used to identify B-cell epitopes from the identified antigenic proteins. VaxiJensuggested: (VaxiJen, RRID:SCR_018514)To identify the interactions between predicted T- and B-cell epitopes and protein receptors, the molecular docking studies were performed using AutoDockTools, AutoDock Vina and CABS-dock server [31–33]. AutoDockToolssuggested: NoneTherefore, initial screening of peptides for receptors were performed through Autodock, whereas CABSdocks, considered full flexibility of peptide and small fluctuation in receptor backbone, was used for final binding and compatibility analysis. Autodocksuggested: (AutoDock, RRID:SCR_012746)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Genetic diversity of MHC molecules across the various ethnic groups worldwide is another the major limitation such as different MHC class alleles form different geographical region might be presented by a particular set of epitopes only. To understand demographic coverage of epitopes, population coverage analysis was performed through selected T-cell epitopes, and analysis revealed that approximately 89.44% and 93% average coverage can be achieved for world population and population of ethnic groups respectively (Figure-2, Supplementary file1: Table – S3). In various B-cell research studies, particular antigen induces distinct class or subclass of antibodies such as schistosomiasis and filariasis induced a mixed response of IgE and IgG [57, 58]. In order to select distinct class of epitopes, sequence and structure-based dual approaches were used to identify B-cell epitope by using BepiPred-2.0 and ElliPro programs. 14 non-toxic, non cross-reactive, antigenic, and immunogenic B-cell epitopes were identified of different length (Table – 4). Predicted epitopes may or may not be a key feature of proteins because prediction methods, ignored epitope and receptor interaction, may be predicted only putative epitopes, which might lead to produce an antibody of no use. The real epitopes cannot be identified without considering the structural compatibility of complex formation [41]. Therefore, it became important to determine the structural coordinates of peptide-binding pockets to iden...
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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