Investigating expressed RNA variants that are related to disease severity in SARS-CoV-2-infected patients with mild-to-severe disease

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dc.contributor.authorOkendo, Javan
dc.contributor.authorOkanda, David
dc.date.accessioned2022-05-03T07:27:16Z
dc.date.available2022-05-03T07:27:16Z
dc.date.issued2022-04-28
dc.date.updated2022-05-01T03:17:49Z
dc.description.abstractBackground: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a significant public health challenge globally. SARS-CoV-2 is a novel virus, and the understanding of what constitutes expressed RNAseq variants in healthy, convalescent, severe, moderate, and those admitted to the intensive care unit (ICU) is yet to be presented. We characterize the different expressed RNAseq variants in healthy, severe, moderate, ICU, and convalescent individuals. Materials and methods: The bulk RNA sequencing data with identifier PRJNA639275 were downloaded from Sequence Reads Archive (SRA). The individuals were divided into: (1) healthy, n = 34, moderate, n = 8, convalescent, n = 2, severe, n = 16, and ICU, n = 8. Fastqc version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. STAR was used to align reads to the reference genome, and GATK best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines. Results: Our analysis demonstrated that different sets of unique RNAseq variants characterize convalescent, moderate, severe, and those admitted to the ICU. The data show that the individuals who recover from SARS-CoV-2 infection have the same set of expressed variants as the healthy controls. We showed that the healthy and SARS-CoV-2-infected individuals display different sets of expressed variants characteristic of the patient phenotype. Conclusion: The individuals with severe, moderate, those admitted to the ICU, and convalescent display a unique set of variants. The findings in this study will inform the test kit development and SARS-CoV-2 patients classification to enhance the management and control of SARS-CoV-2 infection in our population.en_US
dc.identifier.citationEgyptian Journal of Medical Human Genetics. 2022 Apr 28;23(1):84
dc.identifier.citationEgyptian Journal of Medical Human Genetics. 2022 Apr 28;23(1):84
dc.identifier.urihttps://doi.org/10.1186/s43042-022-00299-5
dc.identifier.urihttp://hdl.handle.net/11427/36408
dc.language.isoenen_US
dc.language.rfc3066en
dc.publisher.departmentDepartment of Integrative Biomedical Sciencesen_US
dc.publisher.facultyFaculty of Health Sciencesen_US
dc.rights.holderThe Author(s)
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourceEgyptian Journal of Medical Human Geneticsen_US
dc.source.journalissue1en_US
dc.source.journalvolume23en_US
dc.source.pagination84en_US
dc.source.urihttps://jmhg.springeropen.com/
dc.subjectRNAseqen_US
dc.subjectVariantsen_US
dc.subjectSARS-CoV-2en_US
dc.subjectSevereen_US
dc.subjectICUen_US
dc.subjectModerateen_US
dc.titleInvestigating expressed RNA variants that are related to disease severity in SARS-CoV-2-infected patients with mild-to-severe diseaseen_US
dc.typeJournal Articleen_US
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