Genome Characterization and Evolutionary Study of SARS-CoV-2 Variants of Interest and Concern

Juhari, Nazwin Shahirah (2022) Genome Characterization and Evolutionary Study of SARS-CoV-2 Variants of Interest and Concern. [Project Paper] (Submitted)

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Abstract

COVID-19 is an infectious disease caused by SARS-CoV-2 virus. Different SARS-CoV-2 variants have emerged as a result of the virus's ongoing mutations. In December 2021, the World Health Organization declared two variants of interest (VOIs) (Lambda and Mu), and five variants of concern (VOCs) (Alpha, Beta, Delta, Lambda, and Omicron) as disease-threatening strains. Many studies describe VOIs and VOCs harboring multiple mutations, however, their virological characteristics and evolutionary traits to disease severity remain unclear. Objective: This study aims to investigate the genome characterization and evolution of SARS-CoV-2 VOIs and VOCs dispersed in different regions. Method: One hundred SARS-CoV-2 genome sequences from each VOI and VOC were obtained from the GISAID database; multiple sequence alignment was carried out using the Clustal Omega v2.11.2 tool, and phylogenetic analysis was carried out to determine the virus' evolution. A phylogenetic tree was constructed using maximum likelihood method with 1,000 bootstrap replicates in the IQ-TREE webserver with Wuhan reference sequence (EPI_ISL_402124) as an outgroup. Mining of mutations was done using the GISAID-CoVSurver application. Results: The phylogenetic analysis revealed that Delta variant was distinct from the other regions, and the African sequence differed from the other regions in the Delta, Lambda, and Gamma clades. Also, sister taxa patterns of closely related European, North American, and South American sequences appeared similar in the Delta, Alpha, Lambda, and Beta clades. Mutational analysis revealed that spike protein (S), non-structural 3 protein (nsp3), and nucleocapsid protein (N) had the most mutations, with 82, 23, and 15, respectively. Among the variants, Omicron had the most mutations (38 in S, 4 in nsp3, and 6 in N protein), while Beta had the fewest (13 in S, 2 in nsp3, and 1 in N protein). Comparative analyses of the spike protein revealed D614G as a common mutation associated with enhanced viral transmission. The L452R and T478K were discovered specific to the Delta variant, which impairs antibody neutralization, and 246-253del in the Lambda variant, which may account for immune escape. Conclusion: These emerging variants may potentially impact disease outcomes, hence this study has the potential to contribute to our understanding of the evolution of SARS-CoV-2. (350 words)

Item Type:	Project Paper
Faculty:	Faculty of Medicine and Health Science
Depositing User:	Ms. Nor Safa'aton Saidin
Date Deposited:	22 Aug 2023 06:34
Last Modified:	22 Aug 2023 06:34
URI:	http://psaspb.upm.edu.my/id/eprint/1397

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