Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic
Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 1...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2020
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/109753 |
| _version_ | 1855542650195673088 |
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| author | Ling, J. Hickman, R.A. Li, J. Lu, X. Lindahl, Johanna F. Lundkvist, Å. Järhult, J.D. |
| author_browse | Hickman, R.A. Järhult, J.D. Li, J. Lindahl, Johanna F. Ling, J. Lu, X. Lundkvist, Å. |
| author_facet | Ling, J. Hickman, R.A. Li, J. Lu, X. Lindahl, Johanna F. Lundkvist, Å. Järhult, J.D. |
| author_sort | Ling, J. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. Results: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10−3 substitutions per year. Conclusions: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches. |
| format | Journal Article |
| id | CGSpace109753 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1097532025-12-08T09:54:28Z Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic Ling, J. Hickman, R.A. Li, J. Lu, X. Lindahl, Johanna F. Lundkvist, Å. Järhult, J.D. covid-19 health epidemiology zoonoses Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. Results: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10−3 substitutions per year. Conclusions: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches. 2020-09-14 2020-10-07T10:02:45Z 2020-10-07T10:02:45Z Journal Article https://hdl.handle.net/10568/109753 en Open Access MDPI Ling, J., Hickman, R.A., Li, J., Lu, X., Lindahl, J.F., Lundkvist, Å. and Järhult, J.D. 2020. Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic. Viruses 12(9): 1026. |
| spellingShingle | covid-19 health epidemiology zoonoses Ling, J. Hickman, R.A. Li, J. Lu, X. Lindahl, Johanna F. Lundkvist, Å. Järhult, J.D. Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic |
| title | Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic |
| title_full | Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic |
| title_fullStr | Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic |
| title_full_unstemmed | Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic |
| title_short | Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic |
| title_sort | spatio temporal mutational profile appearances of swedish sars cov 2 during the early pandemic |
| topic | covid-19 health epidemiology zoonoses |
| url | https://hdl.handle.net/10568/109753 |
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