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SARS-CoV-2 transmission chains from genetic data: a Danish case study
bioRxiv - Genomics Pub Date : 2020-07-05 , DOI: 10.1101/2020.05.29.123612 Andreas Bluhm , Matthias Christandl , Fulvio Gesmundo , Frederik Ravn Klausen , Laura Mančinska , Vincent Steffan , Daniel Stilck França , Albert H. Werner
bioRxiv - Genomics Pub Date : 2020-07-05 , DOI: 10.1101/2020.05.29.123612 Andreas Bluhm , Matthias Christandl , Fulvio Gesmundo , Frederik Ravn Klausen , Laura Mančinska , Vincent Steffan , Daniel Stilck França , Albert H. Werner
Background: The COVID-19 pandemic caused by the SARS-CoV-2 virus started in China in December 2019 and has since spread globally. Information about the spread of the virus in a country can inform the gradual reopening of a country and help to avoid a second wave of infections. Denmark is currently opening up after a lockdown in mid-March. The COVID-19 pandemic caused by the SARS-CoV-2 virus started in China in December 2019 and has since spread globally. Many countries have instated measures to slow the spread of the virus. Information about the introduction of the virus to a country and its further spread can inform the gradual opening of a country and help to avoid a second wave of infections. Denmark saw its first cases in late February and is currently opening up after a lockdown in mid-March. Methods: We perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries.
Results: Our findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark and in at least one case find evidence that the virus spread from Denmark to other countries. A number of the mutations found in Denmark are non-synonymous, and in general there is a considerable variety of strains. The proportions of the most common haplotypes is stable after lockdown.
Conclusion: Our work shows how genetic data can be used to identify routes of introduction of a virus into a region and provide alternative means for verifying existing assumptions. For example, our analysis supports the hypothesis that the virus was brought to Denmark by skiers returning from Ischgl. On the other hand, we identify transmission chains suggesting that Denmark was part of a network of countries among which the virus was being transmitted; thus challenging the common narrative that Denmark only got infected from abroad. Our analysis does not indicate that the major haplotypes appearing in Denmark have a different degree of virality. Our methods can be applied to other countries, regions or even highly localised outbreaks. When used in real-time, we believe they can serve to identify transmission events and supplement traditional methods such as contact tracing.
更新日期：2020-07-05
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