Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea
Summary: 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....
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| Format: | Article |
| Language: | English |
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Elsevier
2023-09-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223017662 |
| _version_ | 1827856120099635200 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Atanas V. Demirev |
| collection | DOAJ |
| description | Summary: 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. |
| first_indexed | 2024-03-12T12:20:09Z |
| format | Article |
| id | doaj.art-ef10938a432545669ea225cd62b689f1 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-12T12:20:09Z |
| publishDate | 2023-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-ef10938a432545669ea225cd62b689f12023-08-30T05:54:37ZengElsevieriScience2589-00422023-09-01269107689Molecular evolution and targeted recombination of SARS-CoV-2 in South KoreaAtanas V. Demirev0Kyuyoung Lee1Joon-Yong Bae2Heedo Park3Sejik Park4Hyunbeen Kim5Jungmin Lee6Junhyung Cho7Jeong-Sun Yang8Kyung-Chang Kim9Joo-Yeon Lee10Kisoon Kim11Philippe Lemey12Man-Seong Park13Jin Il Kim14Department of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of KoreaDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of KoreaDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of KoreaDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of KoreaDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of KoreaDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of KoreaDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of KoreaDivision 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 KoreaDivision 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 KoreaDivision 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 KoreaCenter for Infectious Diseases Research, National Institute of Infectious Diseases, Korea National Institute of Health, Osong, Republic of KoreaDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea; Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of KoreaDepartment of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, BelgiumDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea; Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea; Biosafety Center, Korea University College of Medicine, Seoul, Republic of Korea; Corresponding authorDepartment of Microbiology, Institute for Viral Diseases, Korea University College of Medicine, Seoul, Republic of Korea; Vaccine Innovation Center, Korea University College of Medicine, Seoul, Republic of Korea; Biosafety Center, Korea University College of Medicine, Seoul, Republic of Korea; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2589004223017662VirologyPhylogenetics |
| spellingShingle | 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 Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea iScience Virology Phylogenetics |
| title | Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea |
| title_full | Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea |
| title_fullStr | Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea |
| title_full_unstemmed | Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea |
| title_short | Molecular evolution and targeted recombination of SARS-CoV-2 in South Korea |
| title_sort | molecular evolution and targeted recombination of sars cov 2 in south korea |
| topic | Virology Phylogenetics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223017662 |
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