Abstract
BackgroundThe first cases of COVID-19 caused by the SARS-CoV-2 virus were reported in China in December 2019. The disease has since spread globally. Many countries have instated measures to slow the spread of the virus. 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. Our study focuses on Denmark, which is opening up when this study is performed (end-May 2020) after a lockdown in mid-March.MethodsWe perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries.ResultsOur findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark. In at least one case we 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 remain stable after lockdown.ConclusionEmploying phylogenetic methods on Danish genome sequences of SARS-CoV-2, we exemplify how genetic data can be used to trace the introduction of a virus to a country. This provides 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 routes which suggest that Denmark was part of a network of countries among which the virus was being transmitted. This challenges the common narrative that Denmark only got infected from abroad. Our analysis concerning the ratio of haplotypes does not indicate that the major haplotypes appearing in Denmark have a different degree of virality.
Highlights
Employing phylogenetic methods on Danish genome sequences of SARS-CoV-2, we exemplify how genetic data can be used to trace the introduction of a virus to a country
We identify transmission routes which suggest that Denmark was part of a network of countries among which the virus was being transmitted
According to peer-reviewed studies, the first cases of COVID-19 were reported in the city of Wuhan (China) at the first of December 2019 and a new virus, named SARS-CoV-2, was later identified as its origin [1]
Summary
According to peer-reviewed studies, the first cases of COVID-19 were reported in the city of Wuhan (China) at the first of December 2019 and a new virus, named SARS-CoV-2, was later identified as its origin [1]. In March, Europe was the center of the global pandemic with many European countries introducing lockdown measures and travel restrictions. Distribution of haplotypes across different countries, by utilizing date information, and, for some international sequences, location data as well as travel histories, we conclude that the majority of the Danish sequences with A2a2a originate directly or indirectly from Ischgl. This is illustrated with examples of specific chains of mutations from Ischgl. Our study focuses on Denmark, which is opening up when this study is performed (end-May 2020) after a lockdown in mid-March
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