Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea

Atanas V Demirev; Kyuyoung Lee; Joon-Yong Bae; Heedo Park; Sejik Park; Hyunbeen Kim; Jungmin Lee; Junhyung Cho; Jeong-Sun Yang; Kyung-Chang Kim; Joo-Yeon Lee; Kisoon Kim; Philippe Lemey; Man-Seong Park; Jin Il Kim

doi:10.1016/j.isci.2023.107689

Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea

iScience. 2023 Aug 22;26(9):107689. doi: 10.1016/j.isci.2023.107689. eCollection 2023 Sep 15.

Authors

Atanas V Demirev¹, Kyuyoung Lee¹, Joon-Yong Bae¹, Heedo Park¹, Sejik Park¹, Hyunbeen Kim¹, Jungmin Lee¹, Junhyung Cho², Jeong-Sun Yang², Kyung-Chang Kim², Joo-Yeon Lee³, Kisoon Kim^{1

4}, Philippe Lemey⁵, Man-Seong Park^{1

4

6}, Jin Il Kim^{1

4

6}

Affiliations

¹ Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea.
² Division of Emerging Viral Diseases and Vector Research, Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea.
³ Center for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of Korea.
⁴ Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea.
⁵ Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
⁶ Biosafety Center, Korea University College of Medicine, Seoul, Republic of Korea.

Abstract

SARS-CoV-2 variants have continuously emerged globally, including in South Korea. To characterize the molecular evolution of SARS-CoV-2 in South Korea, we performed phylogenetic and genomic recombination analyses using more than 12,000 complete genome sequences collected until October 2022. The variants in South Korea originated from globally identified variants of concern and harbored genetic clade-common and clade-specific amino acid mutations mainly around the N-terminal domain (NTD) or receptor binding domain (RBD) in the spike protein. Several point mutation residues in key antigenic sites were under positive selection persistently with changing genetic clades of SARS-CoV-2. Furthermore, we detected 17 potential genomic recombinants and 76.4% (13/17) retained the mosaic NTD or RBD genome. Our results suggest that point mutations and genomic recombination in the spike contributed to the molecular evolution of SARS-CoV-2 in South Korea, which will form an integral part of global prevention and control measures against SARS-CoV-2.

Keywords: Phylogenetics; Virology.