Genomic characterisation of SARS-CoV-2 by whole genome sequencing and its association with disease severity

In this post-genomic era, whole genome sequencing is widely used to understand viral evolution and enhance epidemiological research. This study aims to describe the genome characterization of the SARS-CoV-2 virus and to associate the patient’s clinical data (sociodemographic and co-morbidities) with the disease severity. A cross-sectional study was conducted using archived samples of laboratory-confirmed SARS-CoV-2 infection with Ct value ≤30 stored in viral transport media (VTM) from the Hospital Al-Sultan Abdullah (HASA) for one year (June 2021 until June 2022). The clinical data were retrieved from the UNIMEDS database and documented information from the medical records. Before being subjected to whole genome sequencing, the Ct values of the archived samples were validated by RT-PCR. The whole genome sequencing was performed using the Oxford Nanopore Technology (ONT) and assembled using bioinformatic tools EPI2ME software and Minimapv2.24 with quality scores Q10. Lineage assignment was done using Pangolin and NextClade with >80% coverage. Multiple logistic regression was performed to determine the association between the variables and the disease severity. Results showed that out of 129 samples, 86 were successfully sequenced. Among these, 1/86, (1.16%) was the Beta variant (B.1.354), Delta variant was 51/86, (59.3%) comprised of sublineages AY.59, AY.76 and AY.79. The Omicron variant has 34/86, (39.53%) which include subvariants BA.1.1, BA.1.17, BA.2, BA.2.3, and BA.2.10. Omicron was the most predominant variant detected, with BA.2 (21/51, 24.4%) being the most frequent subvariant, followed by Delta sub lineage AY.59 (21/34, 24.4%). The D614G mutation, was the predominant mutation that was found in all three variants, while mutations like K417N, N501Y were present in Beta and Omicron, and G142D, T478K, and D950N were observed in Delta and Omicron. Phylogenetic analysis reveals three distinct clades (GH, GK and GRA) with seven clusters indicating possible outbreaks occur within the area. Five variables were significantly associated with the disease severity with a p-value <0.05. They were the VOC Delta (aOR = 22.354; 95% CI = 1.694, 294.921), age 49 years old (aOR = 2.143; 95% CI = 1.010, 4.546), hypertension (aOR = 33.600; 95% CI =6.595, 171.175) chronic kidney disease (aOR = 25.840; 95% CI = 1.301, 513.20), and chronic illness (aOR = 28.677; 95% CI =1.924, 427.334). At the point of the study, the Omicron variant’s continued dominance could be explained due to the acquisition of mutations from other variants owing to the dynamic nature of SARS CoV-2 evolution. For example, mutations like D614G and N501Y were linked to increased transmissibility and were also found in Beta and Alpha variants. Since its emergence, Omicron has highly diversified and transformed into other Omicron subvariants. Based on the phylogenetic tree, the gradual displacement process of each variant was like other parts of Malaysia which corresponded with the reference strain used in this study. The clinical factors including the Delta variant as well as patients’ comorbidity such as hypertension were associated with severe diseases and were consistent with other studies. Thus, the study of the SARS-CoV-2 genome and genomic surveillance will have a significant impact on viral trekking and monitoring to help in making informed decisions for public health preventive and containment strategies.