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SARS-CoV-2 transmission routes from genetic data: A Danish case study
Andreas Bluhm1, Matthias Christandl1, Fulvio Gesmundo1
1Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark.
Plos One
|October 29, 2020
Summary
Phylogenetic analysis of SARS-CoV-2 genomes in Denmark reveals multiple virus introductions and transmission chains within the country. This genetic data helps trace viral spread and challenges the narrative of solely external infections, informing public health strategies during reopening.
Area of Science:
- Genomics
- Epidemiology
- Viral Evolution
Background:
- The first cases of COVID-19 (caused by SARS-CoV-2) emerged in China in December 2019, leading to a global pandemic.
- Understanding viral spread within a country is crucial for managing reopening strategies and preventing subsequent infection waves.
- This study focuses on Denmark, which began reopening in late May 2020 following a mid-March lockdown.
Purpose of the Study:
- To analyze the phylogenetic relationships of SARS-CoV-2 genomes within Denmark.
- To trace the introduction and transmission routes of SARS-CoV-2 in Denmark using genetic data.
- To provide insights into viral diversity and evolution within the Danish population during the pandemic.
Main Methods:
- Phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences.
- Comparative analysis with international SARS-CoV-2 genome sequences to contextualize findings.
- Identification of mutation chains and haplotype proportions within the Danish viral population.
Main Results:
- Evidence of multiple independent introductions of SARS-CoV-2 into Denmark from various sources.
- Identification of distinct SARS-CoV-2 mutation chains originating within Denmark.
- Detection of viral spread from Denmark to other countries, indicating its role in international transmission networks.
- Significant genetic diversity of SARS-CoV-2 strains observed in Denmark, with stable proportions of common haplotypes post-lockdown.
Conclusions:
- Phylogenetic analysis of SARS-CoV-2 genomes effectively traces virus introduction and spread, complementing existing epidemiological data.
- The study supports the hypothesis of SARS-CoV-2 introduction via travelers (e.g., skiers from Ischgl) but also highlights Denmark's participation in a broader international transmission network.
- Analysis of haplotype ratios suggests no significant difference in the virality of major SARS-CoV-2 strains circulating in Denmark.
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