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Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic.
Viruses. 2020 09 14; 12(9)V

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 × 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+Show Affiliations

Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden.Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden.Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden. Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden.School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden. International Livestock Research Institute, Nairobi 00100, Kenya. Swedish University of Agricultural Research, SE-750 07 Uppsala, Sweden.Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden.Zoonosis Science Center, Department of Medical Sciences, Uppsala University, SE-751 23 Uppsala, Sweden.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32937868

Citation

Ling, Jiaxin, et al. "Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 During the Early Pandemic." Viruses, vol. 12, no. 9, 2020.
Ling J, Hickman RA, Li J, et al. Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Viruses. 2020;12(9).
Ling, J., Hickman, R. A., Li, J., Lu, X., Lindahl, J. F., Lundkvist, Å., & Järhult, J. D. (2020). Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Viruses, 12(9). https://doi.org/10.3390/v12091026
Ling J, et al. Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 During the Early Pandemic. Viruses. 2020 09 14;12(9) PubMed PMID: 32937868.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. AU - Ling,Jiaxin, AU - Hickman,Rachel A, AU - Li,Jinlin, AU - Lu,Xi, AU - Lindahl,Johanna F, AU - Lundkvist,Åke, AU - Järhult,Josef D, Y1 - 2020/09/14/ PY - 2020/08/26/received PY - 2020/09/11/revised PY - 2020/09/12/accepted PY - 2020/9/17/entrez PY - 2020/9/18/pubmed PY - 2020/9/29/medline KW - SARS-CoV-2 KW - evolution KW - mutation KW - spike protein JF - Viruses JO - Viruses VL - 12 IS - 9 N2 - 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. SN - 1999-4915 UR - https://www.unboundmedicine.com/medline/citation/32937868/Spatio_Temporal_Mutational_Profile_Appearances_of_Swedish_SARS_CoV_2_during_the_Early_Pandemic_ L2 - https://www.mdpi.com/resolver?pii=v12091026 DB - PRIME DP - Unbound Medicine ER -