PT  - JOURNAL ARTICLE
AU  - Andreas Bluhm
AU  - Matthias Christandl
AU  - Fulvio Gesmundo
AU  - Frederik Ravn Klausen
AU  - Laura Mančinska
AU  - Vincent Steffan
AU  - Daniel Stilck França
AU  - Albert H. Werner
TI  - SARS-CoV-2 Transmission Chains from Genetic Data: A Danish Case Study
AID  - 10.1101/2020.05.29.123612
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.05.29.123612
4099  - http://biorxiv.org/content/early/2020/05/29/2020.05.29.123612.short
4100  - http://biorxiv.org/content/early/2020/05/29/2020.05.29.123612.full
AB  - Background The Covid-19 pandemic caused by the SARS-CoV-2 virus started in China in December 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 the avoidance of a second wave of infections. Denmark has seen first cases in late February and is currently opening up.Methods Sequenced virus genome can be used to reconstruct transmission events. We perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 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, the majority from a ski area in Austria. We identify several chains of mutations that occurred in Denmark and in at least one case find evidence that it spread from Denmark to other countries. There is a number of the Danish mutations that are non-synonymous, and in general there is a considerable variety of strains circulating in Denmark.Conclusion The introduction of the virus from the Austrian ski area happened after Iceland had declared this area high-risk, thereby giving an independent assessment of the effectiveness of the early identification of high-risk areas. The likely further spread of the virus from Denmark challenges the common narrative that Denmark only got infected from abroad, highlighting that Denmark was part of a network of countries among which the virus was being transmitted. Furthermore, our broad analysis of the mutations does not indicate that the virus underwent a systematic change in virulence in Denmark. We believe that the methods used can be a valuable tool to identifying and validating transmission chains during the reopening.Competing Interest StatementThe authors have declared no competing interest.