tetano
Editor, Senior Moderator
BMC Infect Dis
. 2022 Jun 19;22(1):558.
doi: 10.1186/s12879-022-07415-1.
Investigation of target sequencing of SARS-CoV-2 and immunogenic GWAS profiling in host cells of COVID-19 in Vietnam
Tham H Hoang[SUP] 1 [/SUP], Giang M Vu[SUP] 2 [/SUP], Mai H Tran[SUP] 2 [/SUP], Trang T H Tran[SUP] 2 [/SUP], Quang D Le[SUP] 3 [/SUP], Khanh V Tran[SUP] 4 [/SUP], Tue T Nguyen[SUP] 4 [/SUP], Lan T N Nguyen[SUP] 4 [/SUP], Thinh H Tran[SUP] 4 [/SUP], Van T Ta[SUP] 4 [/SUP], Nam S Vo[SUP] 2 5 [/SUP]
Affiliations
Abstract
Background: A global pandemic has been declared for coronavirus disease 2019 (COVID-19), which has serious impacts on human health and healthcare systems in the affected areas, including Vietnam. None of the previous studies have a framework to provide summary statistics of the virus variants and assess the severity associated with virus proteins and host cells in COVID-19 patients in Vietnam.
Method: In this paper, we comprehensively investigated SARS-CoV-2 variants and immune responses in COVID-19 patients. We provided summary statistics of target sequences of SARS-CoV-2 in Vietnam and other countries for data scientists to use in downstream analysis for therapeutic targets. For host cells, we proposed a predictive model of the severity of COVID-19 based on public datasets of hospitalization status in Vietnam, incorporating a polygenic risk score. This score uses immunogenic SNP biomarkers as indicators of COVID-19 severity.
Result: We identified that the Delta variant of SARS-CoV-2 is most prevalent in southern areas of Vietnam and it is different from other areas in the world using various data sources. Our predictive models of COVID-19 severity had high accuracy (Random Forest AUC = 0.81, Elastic Net AUC = 0.7, and SVM AUC = 0.69) and showed that the use of polygenic risk scores increased the models' predictive capabilities.
Conclusion: We provided a comprehensive analysis for COVID-19 severity in Vietnam. This investigation is not only helpful for COVID-19 treatment in therapeutic target studies, but also could influence further research on the disease progression and personalized clinical outcomes.
Keywords: COVID-19 severity; Clade; PRS; SARS-CoV-2; Vietnam.
. 2022 Jun 19;22(1):558.
doi: 10.1186/s12879-022-07415-1.
Investigation of target sequencing of SARS-CoV-2 and immunogenic GWAS profiling in host cells of COVID-19 in Vietnam
Tham H Hoang[SUP] 1 [/SUP], Giang M Vu[SUP] 2 [/SUP], Mai H Tran[SUP] 2 [/SUP], Trang T H Tran[SUP] 2 [/SUP], Quang D Le[SUP] 3 [/SUP], Khanh V Tran[SUP] 4 [/SUP], Tue T Nguyen[SUP] 4 [/SUP], Lan T N Nguyen[SUP] 4 [/SUP], Thinh H Tran[SUP] 4 [/SUP], Van T Ta[SUP] 4 [/SUP], Nam S Vo[SUP] 2 5 [/SUP]
Affiliations
- PMID: 35718768
- DOI: 10.1186/s12879-022-07415-1
Abstract
Background: A global pandemic has been declared for coronavirus disease 2019 (COVID-19), which has serious impacts on human health and healthcare systems in the affected areas, including Vietnam. None of the previous studies have a framework to provide summary statistics of the virus variants and assess the severity associated with virus proteins and host cells in COVID-19 patients in Vietnam.
Method: In this paper, we comprehensively investigated SARS-CoV-2 variants and immune responses in COVID-19 patients. We provided summary statistics of target sequences of SARS-CoV-2 in Vietnam and other countries for data scientists to use in downstream analysis for therapeutic targets. For host cells, we proposed a predictive model of the severity of COVID-19 based on public datasets of hospitalization status in Vietnam, incorporating a polygenic risk score. This score uses immunogenic SNP biomarkers as indicators of COVID-19 severity.
Result: We identified that the Delta variant of SARS-CoV-2 is most prevalent in southern areas of Vietnam and it is different from other areas in the world using various data sources. Our predictive models of COVID-19 severity had high accuracy (Random Forest AUC = 0.81, Elastic Net AUC = 0.7, and SVM AUC = 0.69) and showed that the use of polygenic risk scores increased the models' predictive capabilities.
Conclusion: We provided a comprehensive analysis for COVID-19 severity in Vietnam. This investigation is not only helpful for COVID-19 treatment in therapeutic target studies, but also could influence further research on the disease progression and personalized clinical outcomes.
Keywords: COVID-19 severity; Clade; PRS; SARS-CoV-2; Vietnam.