Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection
| dc.contributor.author | Okendo, Javan | |
| dc.date.accessioned | 2023-10-04T14:59:37Z | |
| dc.date.available | 2023-10-04T14:59:37Z | |
| dc.date.issued | 2022-08-03 | |
| dc.date.updated | 2022-08-07T03:11:20Z | |
| dc.description.abstract | Background Since the COVID-19 outbreak emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. Although intensive research is ongoing worldwide to understand the emergence of SARS-CoV-2 variants, there is a lack of information on what constitutes the expressed RNA variants in critical and non-critical comorbidity-free young patients. The study sought to characterize the expressed RNA variants from young patients with critical and non-critical forms of SARS-CoV-2 infection. Methodology The bulk ribonucleic acid (RNA) sequencing data with the identifier GSE172114 were downloaded from the Gene Expression Omnibus (GEO) database. The study participants were divided into critical, nā=ā46, and non-critical, nā=ā23. FastQC version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. Spliced Transcripts Alignment to a Reference (STAR) version 2.7.10a was used to align reads to the human (hg38) reference genome. Genome Analysis Tool Kit (GATK) best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines. Results Our research demonstrates that critical and non-critical SARS-CoV-2-infected individuals are characterized by a unique set of expressed RNA variants. The expressed gene variants are enriched on the innate immune response, specifically neutrophil-mediated immune response. On the other hand, the expressed gene variants are involved in both innate and cellular immune responses. Conclusion Deeply phenotyped comorbidity-free young patients with critical and non-critical SARS-CoV-2 infection are characterized by a unique set of expressed RNA variants. The findings in this study can inform the patient classification process in health facilities globally when admitting young patients infected with SARS-CoV-2. | en_US |
| dc.identifier.apacitation | Okendo, J. (2022). Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection. <i>Egyptian Journal of Medical Human Genetics</i>, 23(1), 115. http://hdl.handle.net/11427/39029 | en_ZA |
| dc.identifier.chicagocitation | Okendo, Javan "Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection." <i>Egyptian Journal of Medical Human Genetics</i> 23, 1. (2022): 115. http://hdl.handle.net/11427/39029 | en_ZA |
| dc.identifier.citation | Okendo, J. 2022. Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection. <i>Egyptian Journal of Medical Human Genetics.</i> 23(1):115. http://hdl.handle.net/11427/39029 | en_ZA |
| dc.identifier.ris | TY - Journal Article AU - Okendo, Javan AB - Background Since the COVID-19 outbreak emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved into variants with underlying mutations associated with increased transmissibility, potential escape from neutralizing antibodies, and disease severity. Although intensive research is ongoing worldwide to understand the emergence of SARS-CoV-2 variants, there is a lack of information on what constitutes the expressed RNA variants in critical and non-critical comorbidity-free young patients. The study sought to characterize the expressed RNA variants from young patients with critical and non-critical forms of SARS-CoV-2 infection. Methodology The bulk ribonucleic acid (RNA) sequencing data with the identifier GSE172114 were downloaded from the Gene Expression Omnibus (GEO) database. The study participants were divided into critical, nā=ā46, and non-critical, nā=ā23. FastQC version 0.11.9 and Cutadapt version 3.7 were used to assess the read quality and perform adapter trimming, respectively. Spliced Transcripts Alignment to a Reference (STAR) version 2.7.10a was used to align reads to the human (hg38) reference genome. Genome Analysis Tool Kit (GATK) best practice was followed to call variants using the rnavar pipeline, part of the nf-core pipelines. Results Our research demonstrates that critical and non-critical SARS-CoV-2-infected individuals are characterized by a unique set of expressed RNA variants. The expressed gene variants are enriched on the innate immune response, specifically neutrophil-mediated immune response. On the other hand, the expressed gene variants are involved in both innate and cellular immune responses. Conclusion Deeply phenotyped comorbidity-free young patients with critical and non-critical SARS-CoV-2 infection are characterized by a unique set of expressed RNA variants. The findings in this study can inform the patient classification process in health facilities globally when admitting young patients infected with SARS-CoV-2. DA - 2022-08-03 DB - OpenUCT DP - University of Cape Town IS - 1 J1 - Egyptian Journal of Medical Human Genetics LK - https://open.uct.ac.za PY - 2022 T1 - Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection TI - Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection UR - http://hdl.handle.net/11427/39029 ER - | en_ZA |
| dc.identifier.uri | https://doi.org/10.1186/s43042-022-00327-4 | |
| dc.identifier.uri | http://hdl.handle.net/11427/39029 | |
| dc.identifier.vancouvercitation | Okendo J. Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection. Egyptian Journal of Medical Human Genetics. 2022;23(1):115. http://hdl.handle.net/11427/39029. | en_ZA |
| dc.language.iso | en | en_US |
| dc.language.rfc3066 | en | |
| dc.rights.holder | The Author(s) | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_US |
| dc.source | Egyptian Journal of Medical Human Genetics | en_US |
| dc.source.journalissue | 1 | en_US |
| dc.source.journalvolume | 23 | en_US |
| dc.source.pagination | 115 | en_US |
| dc.title | Characterization of the expressed RNA variants from young patients with critical and non-critical SARS-CoV-2 infection | en_US |
| dc.type | Journal Article | en_US |