Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries
A newly emerged coronavirus, SARS-CoV-2, caused severe pneumonia outbreaks in China in December 2019 and has since spread to various countries around the world. To trace the evolution route and probe the transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality geno...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2020-01-01
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| Series: | Emerging Microbes and Infections |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2020.1773745 |
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| author | Xuemei Yang Ning Dong Edward Wai-Chi Chan Sheng Chen |
| author_facet | Xuemei Yang Ning Dong Edward Wai-Chi Chan Sheng Chen |
| author_sort | Xuemei Yang |
| collection | DOAJ |
| description | A newly emerged coronavirus, SARS-CoV-2, caused severe pneumonia outbreaks in China in December 2019 and has since spread to various countries around the world. To trace the evolution route and probe the transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality genomic sequences available in the GISAID platform as of 5 March 2020. Among them, four genetic clusters, defined as super-spreaders (SSs), could be identified and were found to be responsible for the major outbreaks that subsequently occurred in various countries. SS1 was widely disseminated in Asia and the US, and mainly responsible for outbreaks in the states of Washington and California as well as South Korea, whereas SS4 contributed to the pandemic in Europe. Using the signature mutations of each SS as markers, we further analysed 1539 genome sequences reported after 29 February 2020 and found that 90% of these genomes belonged to SSs, with SS4 being the most dominant. The relative degree of contribution of each SS to the pandemic in different continents was also depicted. Identification of these super-spreaders greatly facilitates development of new strategies to control the transmission of SARS-CoV-2. |
| format | Article |
| id | doaj-art-ca91e4526ea34effbbc839c56f974bf2 |
| institution | OA Journals |
| issn | 2222-1751 |
| language | English |
| publishDate | 2020-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj-art-ca91e4526ea34effbbc839c56f974bf22025-08-20T02:15:52ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512020-01-01911287129910.1080/22221751.2020.1773745Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countriesXuemei Yang0Ning Dong1Edward Wai-Chi Chan2Sheng Chen3Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong KongDepartment of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong KongState Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong KongDepartment of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong KongA newly emerged coronavirus, SARS-CoV-2, caused severe pneumonia outbreaks in China in December 2019 and has since spread to various countries around the world. To trace the evolution route and probe the transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality genomic sequences available in the GISAID platform as of 5 March 2020. Among them, four genetic clusters, defined as super-spreaders (SSs), could be identified and were found to be responsible for the major outbreaks that subsequently occurred in various countries. SS1 was widely disseminated in Asia and the US, and mainly responsible for outbreaks in the states of Washington and California as well as South Korea, whereas SS4 contributed to the pandemic in Europe. Using the signature mutations of each SS as markers, we further analysed 1539 genome sequences reported after 29 February 2020 and found that 90% of these genomes belonged to SSs, with SS4 being the most dominant. The relative degree of contribution of each SS to the pandemic in different continents was also depicted. Identification of these super-spreaders greatly facilitates development of new strategies to control the transmission of SARS-CoV-2.https://www.tandfonline.com/doi/10.1080/22221751.2020.1773745SARS-CoV-2COVID-19transmissionphylodynamic analysissuper-spreader |
| spellingShingle | Xuemei Yang Ning Dong Edward Wai-Chi Chan Sheng Chen Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries Emerging Microbes and Infections SARS-CoV-2 COVID-19 transmission phylodynamic analysis super-spreader |
| title | Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries |
| title_full | Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries |
| title_fullStr | Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries |
| title_full_unstemmed | Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries |
| title_short | Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries |
| title_sort | genetic cluster analysis of sars cov 2 and the identification of those responsible for the major outbreaks in various countries |
| topic | SARS-CoV-2 COVID-19 transmission phylodynamic analysis super-spreader |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2020.1773745 |
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