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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...

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Autores principales: Ling, Jiaxin, Hickman, Rachel A., Li, Jinlin, Lu, Xi, Lindahl, Johanna F., Lundkvist, Åke, Järhult, Josef D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551444/
https://www.ncbi.nlm.nih.gov/pubmed/32937868
http://dx.doi.org/10.3390/v12091026
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author Ling, Jiaxin
Hickman, Rachel A.
Li, Jinlin
Lu, Xi
Lindahl, Johanna F.
Lundkvist, Åke
Järhult, Josef D.
author_facet Ling, Jiaxin
Hickman, Rachel A.
Li, Jinlin
Lu, Xi
Lindahl, Johanna F.
Lundkvist, Åke
Järhult, Josef D.
author_sort Ling, Jiaxin
collection PubMed
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.
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spelling pubmed-75514442020-10-14 Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic Ling, Jiaxin Hickman, Rachel A. Li, Jinlin Lu, Xi Lindahl, Johanna F. Lundkvist, Åke Järhult, Josef D. Viruses Article 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. MDPI 2020-09-14 /pmc/articles/PMC7551444/ /pubmed/32937868 http://dx.doi.org/10.3390/v12091026 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ling, Jiaxin
Hickman, Rachel A.
Li, Jinlin
Lu, Xi
Lindahl, Johanna F.
Lundkvist, Åke
Järhult, Josef 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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7551444/
https://www.ncbi.nlm.nih.gov/pubmed/32937868
http://dx.doi.org/10.3390/v12091026
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