Evaluation of global evolutionary variations in the early stage of SARS-CoV-2 pandemic

Sanghyun Lee; Chi-Hwan Choi; Mi-Ran Yun; Dae-Won Kim; Sung Soon Kim; Young Ki Choi; Young Sill Choi

doi:10.1016/j.heliyon.2021.e08170

Evaluation of global evolutionary variations in the early stage of SARS-CoV-2 pandemic

Heliyon. 2021 Oct;7(10):e08170. doi: 10.1016/j.heliyon.2021.e08170. Epub 2021 Oct 13.

Authors

Sanghyun Lee^{1

2

3}, Chi-Hwan Choi¹, Mi-Ran Yun¹, Dae-Won Kim¹, Sung Soon Kim⁴, Young Ki Choi³, Young Sill Choi¹

Affiliations

¹ Division of Pathogen Resource Management, Center for Public Vaccine Development and Support, National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si, Republic of Korea.
² Division of Bio Bigdata, Department of Precision Medicine, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si, Republic of Korea.
³ Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea.
⁴ Center for Public Vaccine Development and Support, National Institute of Infectious Diseases, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si, Republic of Korea.

Abstract

To understand the origin of variants and their evolutionary history in the early stage of the COVID-19 pandemic, time-scaled phylogenetic and gene variation analyses were performed. The mutation patterns and evolution characteristics were examined using the Bayesian Evolutionary Analysis Sampling Trees (BEAST) with 349 whole-genome sequences available by March 2020. The results revealed five phylogenetic clusters (Groups A-E), with 408 nucleotide variants. The mutations including the deletion of three nucleotides underwent various and complicated changes in the whole genome over time, while some frequency or transient mutations were also observed. Phylogenetic analysis demonstrated that SARS-CoV-2 originated from China and was transmitted to other Asian countries, followed by North America and Europe. This study could help to comprehensively understand the evolutionary characteristics of SARS-CoV-2 with a special emphasis on its global variation patterns.

Keywords: COVID-19; Evolution; Genetic variation; Phylogeny; SARS-CoV-2.