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Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic

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
[Journal 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.
Title:Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic
Year of publishing :2020
Volume:12
Article number:1026
Number of Pages:14
Publisher:MDPI
ISSN:1999-4915
Language:English
Publication Type:Journal 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:
Type of IDID
DOI10.3390/v12091026
Web of Science (WoS)000580804300001
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:18 Nov 2020 15:11

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