Unmasking the Global Journey: Investigation of SARS-CoV-2 Variants of Interest from Various Region through Whole-Genome Analysis and Phylogenetic Analysis

authors:

avatar Yocyny Surendran 1 , avatar Parameswaran Vityashri 1 , avatar NAZWIN SHAHIRAH BINTI JUHARI 1 , avatar Karuppiah Thilakavathy 1 , avatar Xiong Chenglong 2 , avatar Narcisse Joseph 1 , *

Faculty of Medicine and Health Sciences, Universiti Putra Malaysia
Department of Public Health Microbiology, School of Public Health, Fudan University, Shanghai, China
Jundishapur Journal of Microbiology: Vol.17, issue 9; e143544
article type: Research Article
revised: July 24, 2024

how to cite: Surendran Y, Vityashri P, BINTI JUHARI N S, Thilakavathy K, Chenglong X, et al. Unmasking the Global Journey: Investigation of SARS-CoV-2 Variants of Interest from Various Region through Whole-Genome Analysis and Phylogenetic Analysis. Jundishapur J Microbiol. 2024;17(9):e143544. 

Abstract

Background: The prolonged course of the Coronavirus Disease 2019 (Covid-19) pandemic and the virus's high susceptibility to mutations have sparked widespread interest in studying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in depth. Studies have reported that SARS-CoV-2 has evolved into numerous variants since its discovery. 
Objectives: This study aimed to study the differences in SARS-CoV-2's Variants of Interest and Concern from different geographical regions via phylogenetic construction and mutational analysis. 
Methods: A total of 700 SARS-CoV-2 virus whole genome sequences have been retrieved from the GISAID database from the 1st of January 2021 to the 31st of December 2021 and aligned with the reference sequence (NC_045512) using Clustal Omega version 1.2.4. A phylogenetic tree was constructed using the IQ-TREE web server and viewed using ItoL. 
Results: The results showed a fully resolved tree of maximum likelihood analysis with statistical support of bootstrap value. The analyses show that Delta sequences clustered separately from other VOIs, VOCs, and outgroups. The shorter topology of the Delta variant depicts Africa branched away, similar to the Lambda and Gamma variants. Next, the structural analysis showed three mainly uniform clusters in Europe, North and South America that were congruent in sister relationships observed in Clade 1, 2, and 7 topologies. These evolutionary trees were later linked to mutations in spike, nucleocapsid, and nsp3 proteins, which showed a high number of mutations. 
Conclusions: Overall, this study provides new information on SARS-CoV-2 VOIs and VOCs evolving mutations in terms of differences between regions around the world with implications to understand viral pathogenicity.