CovProfile: profiling the viral genome and gene expressions of SARS-COV-2
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Abstract
The SARS-CoV-2 virus has infected more than one million people worldwide to date. Knowing its genome and gene expressions is essential to understand the virus’ mechanism. Here, we propose a computational tool CovProfile to detect the viral genomic variations as well as viral gene expressions from the sequences obtained from Nanopore devices. We applied CovProfile to 11 samples, each from a terminally ill patient, and discovered that all the patients are infected by multiple viral strains, which might affect the reliability of phylogenetic analysis. Moreover, the expression of viral genes ORF1ab gene, S gene, M gene, and N gene are high among most of the samples. While performing the tests, we noticed a consistent abundance of transcript segments of MUC5B, presumably from the host, across all the samples.
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SciScore for 10.1101/2020.04.05.026146: (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 Then, the library was built by Nanopore library construction kit (EXP-FLP002-XL, Flow Cell Priming Kit XL, YILIMART, China), while the adapter and barcode sequences were also added to the samples. Nanoporesuggested: NoneThe samples were sequenced on the Oxford Nanopore MinIon. MinIonsuggested: (MinION, RRID:SCR_017985)By applying NanoFilt (version 1.7.0) [26], we performed data filtration on the raw fastq data with the following criteria: read lengths should be longer than 100 bp after the removal of the adapter sequences, with an overall quality higher than 10. NanoFiltsuggested: (NanoFilt, …SciScore for 10.1101/2020.04.05.026146: (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 Then, the library was built by Nanopore library construction kit (EXP-FLP002-XL, Flow Cell Priming Kit XL, YILIMART, China), while the adapter and barcode sequences were also added to the samples. Nanoporesuggested: NoneThe samples were sequenced on the Oxford Nanopore MinIon. MinIonsuggested: (MinION, RRID:SCR_017985)By applying NanoFilt (version 1.7.0) [26], we performed data filtration on the raw fastq data with the following criteria: read lengths should be longer than 100 bp after the removal of the adapter sequences, with an overall quality higher than 10. NanoFiltsuggested: (NanoFilt, RRID:SCR_016966)Primer alignment were performed with BLAT [27]. BLATsuggested: (BLAT, RRID:SCR_011919)Results from OddPub: Thank you for sharing your data.
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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