Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2
The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subt...
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MDPI AG
2022-02-01
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| Online Access: | https://www.mdpi.com/1999-4915/14/3/454 |
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| author | Binbin Xi Yuhuan Meng Dawei Jiang Yunmeng Bai Zixi Chen Yimo Qu Shuhua Li Jinfen Wei Lizhen Huang Hongli Du |
| author_facet | Binbin Xi Yuhuan Meng Dawei Jiang Yunmeng Bai Zixi Chen Yimo Qu Shuhua Li Jinfen Wei Lizhen Huang Hongli Du |
| author_sort | Binbin Xi |
| collection | DOAJ |
| description | The scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subtypes or regions based on 1.8 million high-quality SARS-CoV-2 genomic data. The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) in North America and the United States were always more than 1.0, while the Ka/Ks in other continents and countries showed a sharp decline, then a slow increase to 1.0, and a dramatic increase over time. H1 (B.1) with the highest substitution rate has become the most dominant haplotype subtype since March 2020 and has evolved into multiple haplotype subtypes with smaller substitution rates. Many evolutionary characteristics of early SARS-CoV-2, such as H3 being the only early haplotype subtype that existed for the shortest time, the global prevalence of H1 and H1-5 (B.1.1) within a month after being detected, and many high divergent genome sequences early in February 2020, indicate the missing of early SARS-CoV-2 genomic data. SARS-CoV-2 experienced dynamic selection from December 2019 to August 2021 and has been under strong positive selection since May 2021. Its transmissibility and the ability of immune escape may be greatly enhanced over time. This will bring greater challenges to the control of the pandemic. |
| first_indexed | 2024-03-09T12:19:01Z |
| format | Article |
| id | doaj.art-998551fe23ab4db6ae2754366e788d38 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T12:19:01Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-998551fe23ab4db6ae2754366e788d382023-11-30T22:43:41ZengMDPI AGViruses1999-49152022-02-0114345410.3390/v14030454Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2Binbin Xi0Yuhuan Meng1Dawei Jiang2Yunmeng Bai3Zixi Chen4Yimo Qu5Shuhua Li6Jinfen Wei7Lizhen Huang8Hongli Du9School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaGuangzhou KingMed Transformative Medicine Institute Co., Ltd., Guangzhou KingMed Center for Clinical Laboratory Co., Ltd. & Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou 510220, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaSchool of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, ChinaThe scale of SARS-CoV-2 infection and death is so enormous that further study of the molecular and evolutionary characteristics of SARS-CoV-2 will help us better understand and respond to SARS-CoV-2 outbreaks. The present study analyzed the epidemic and evolutionary characteristics of haplotype subtypes or regions based on 1.8 million high-quality SARS-CoV-2 genomic data. The estimated ratio of the rates of non-synonymous to synonymous changes (Ka/Ks) in North America and the United States were always more than 1.0, while the Ka/Ks in other continents and countries showed a sharp decline, then a slow increase to 1.0, and a dramatic increase over time. H1 (B.1) with the highest substitution rate has become the most dominant haplotype subtype since March 2020 and has evolved into multiple haplotype subtypes with smaller substitution rates. Many evolutionary characteristics of early SARS-CoV-2, such as H3 being the only early haplotype subtype that existed for the shortest time, the global prevalence of H1 and H1-5 (B.1.1) within a month after being detected, and many high divergent genome sequences early in February 2020, indicate the missing of early SARS-CoV-2 genomic data. SARS-CoV-2 experienced dynamic selection from December 2019 to August 2021 and has been under strong positive selection since May 2021. Its transmissibility and the ability of immune escape may be greatly enhanced over time. This will bring greater challenges to the control of the pandemic.https://www.mdpi.com/1999-4915/14/3/454SARS-CoV-2haplotype subtypesevolutionepidemic trendsKa/Kssubstitution rate |
| spellingShingle | Binbin Xi Yuhuan Meng Dawei Jiang Yunmeng Bai Zixi Chen Yimo Qu Shuhua Li Jinfen Wei Lizhen Huang Hongli Du Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2 Viruses SARS-CoV-2 haplotype subtypes evolution epidemic trends Ka/Ks substitution rate |
| title | Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2 |
| title_full | Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2 |
| title_fullStr | Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2 |
| title_full_unstemmed | Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2 |
| title_short | Analyses of Long-Term Epidemic Trends and Evolution Characteristics of Haplotype Subtypes Reveal the Dynamic Selection on SARS-CoV-2 |
| title_sort | analyses of long term epidemic trends and evolution characteristics of haplotype subtypes reveal the dynamic selection on sars cov 2 |
| topic | SARS-CoV-2 haplotype subtypes evolution epidemic trends Ka/Ks substitution rate |
| url | https://www.mdpi.com/1999-4915/14/3/454 |
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