Investigation of target sequencing of SARS-CoV-2 and immunogenic GWAS profiling in host cells of COVID-19 in Vietnam

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.

Clinical characteristics and mortality risk among critically ill patients with COVID-19 owing to the B.1.617.2 (Delta) variant in Vietnam: A retrospective observational study

“…We conducted the present study during the Delta variant epidemic in Vietnam; however, no included patients with COVID-19 underwent genomic analysis to confirm infection with a SARS-CoV-2 mutant virus strain. However, according to sequencing data at the time of the study period in Ho Chi Minh City, COVID-19 was almost entirely caused by one PLOS ONE lineage of the delta variant (AY.57) [25]. In that sense, we evaluated a relatively homogeneous patient population in virologically.…”

Predictive validity of the simplified Radiographic Assessment of Lung Edema score for the mortality in critically ill COVID-19 patients with the B.1.617.2 (Delta) variant in Vietnam: a single-centre, cross-sectional study

“…However, according to sequencing data at the time of the study period in Ho Chi Minh City, COVID-19 was almost entirely caused by one lineage of the Delta variant (AY.57). (60) In that sense, we evaluated a relatively homogeneous patient population in virologically. Finally , although the sample size was large enough, the confidence interval was wide (±8.02%), which might influence the normal distribution of the collected sample.…”

“…Secondly, we conducted the present study during the Delta variant epidemic in Vietnam; however, no included patients with COVID-19 underwent genomic analysis to confirm infection with a SARS-CoV-2 mutant virus strain. However, according to sequencing data at the time of the study period in Ho Chi Minh City, COVID-19 was almost entirely caused by one lineage of the Delta variant (AY.57) (60). In that sense, we evaluated a relatively homogeneous patient population in virologically.…”

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19

“…It was used to identify the first VOCs B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) and those that emerged later on, such as B.1.617.2 (Delta) and Omicron BA.1 and BA.2 lineages associated with enhanced viral transmission and pathogenicity, and immune escape (Akilesh et al, 2021;Alcoba-Florez et al, 2021;Altmann et al, 2021;Hirotsu and Omata, 2021;Nakamichi et al, 2021;Alsafar et al, 2022;Ciuffreda et al, 2022;Harrigan et al, 2022;Lyngse et al, 2022;Wawina-Bokalanga et al, 2022). In fact, the viral WGS is appropriated for the identification of the viral genomic variants that are associated with severe disease patterns (Hoffmann et al, 2021;Hoang et al, 2022;Overton et al, 2022;von Wintersdorff et al, 2022).…”