Ling, Jiaxin and Hickman, Rachel A. and Li, Jinlin and Lu, Xi and Lindahl, Johanna and Lundkvist, Ake and Jarhult, Josef D.
(2020).
Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic.
Viruses. 12
, 1026
[Research article]
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Abstract
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 x 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.
Authors/Creators: | Ling, Jiaxin and Hickman, Rachel A. and Li, Jinlin and Lu, Xi and Lindahl, Johanna and Lundkvist, Ake and Jarhult, Josef D. | ||||||
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Title: | Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic | ||||||
Series Name/Journal: | Viruses | ||||||
Year of publishing : | 2020 | ||||||
Volume: | 12 | ||||||
Article number: | 1026 | ||||||
Number of Pages: | 14 | ||||||
Publisher: | MDPI | ||||||
ISSN: | 1999-4915 | ||||||
Language: | English | ||||||
Publication Type: | Research article | ||||||
Article category: | Scientific peer reviewed | ||||||
Version: | Published version | ||||||
Copyright: | Creative Commons: Attribution 4.0 | ||||||
Full Text Status: | Public | ||||||
Subjects: | (A) Swedish standard research categories 2011 > 3 Medical and Health Sciences > 301 Basic Medicine > Medical Genetics | ||||||
Keywords: | SARS-CoV-2, evolution, mutation, spike protein | ||||||
URN:NBN: | urn:nbn:se:slu:epsilon-p-108676 | ||||||
Permanent URL: | http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-108676 | ||||||
Additional ID: |
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ID Code: | 18689 | ||||||
Faculty: | VH - Faculty of Veterinary Medicine and Animal Science | ||||||
Department: | (VH) > Dept. of Clinical Sciences | ||||||
Deposited By: | SLUpub Connector | ||||||
Deposited On: | 18 Nov 2020 15:03 | ||||||
Metadata Last Modified: | 15 Jan 2021 19:26 |
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