Genomic Characterisation

Since March, numerous efforts were put in place to characterize the SARS-CoV-2 genomes circulating in Switzerland. This allows us to monitor the evolution and epidemiology of SARS-CoV-2. In the following, we show figures monitoring the percentage of the variants B.1.1.7 and 501Y.V2 in Switzerland. Second, we show the phylogenetic tree displaying the overall evolution of this virus since March.

SARS-CoV-2 Variants of Concern in Switzerland

Different labs across Switzerland perform a genetic characterization of randomly chosen SARS-CoV-2 samples. All these samples stem from swabs of infected people. The goal is to estimate the frequency of the new variants B.1.1.7 (described first in the UK) and 501Y.V2 (described first in South Africa). In each week, the labs report to us the number of considered random samples and the number of identified B.1.1.7 strains and the number of 501Y.V2 strains. We then employ a binomial distribution and Wilson uncertainty intervals in order to estimate the frequency of the variants. Given the delay between infection and swab collection, the frequency estimates for a particular week reflect the epidemic situation around 1-2 weeks earlier. The data is available on Github.


Viollier: Samples are provided by Viollier AG. Whole genome sequenicing is performed through the Swiss Viollier Sequencing Consortium lead by ETH Zürich.

Risch: Samples are provided and screened by Labor Risch.

Genomic characterization is performed by Labor Risch, the University Hospital Basel (Clinical Microbiology) and the University Hospitals of Geneva (Group Eckerle and Group Kaiser).

Phylogenetic Tree

In the following we display the phylogenetic tree of Swiss SARS-CoV-2 samples. This tree allows to visually inspect the evolution and epidemic spread of the virus. For exploring the Swiss sequences further, please go to link.

This phylogeny shows evolutionary relationships of SARS-CoV-2 viruses from the ongoing novel coronavirus COVID-19 pandemic with a particular focus on Switzerland. We aim to include as many genomes from Switzerland as possible. In addition, we include virus genomes from other European countries and to lesser extent from the rest of the world to provide phylogenetic context. This context is important to understand how different outbreaks are connected and how the virus might have spread around the globe. We note, however, that direct linkage on the tree does not necessarily mean there exists a direct epidemiological link. Sampling of viral genomes is very incomplete and heterogeneous and mutations occur on average only every two weeks. Extended periods without mutations are therefore not uncommon and direct links or directionality cannot be inferred from the tree alone.

For background on genomic epidemiology, have a look at the introductory material on We also provide a narrative explaining the analysis of the Swiss data. To explore the data in greater depth, visit

The data from Switzerland was contributed by the following groups:

  • Swiss Viollier Sequencing Consortium
  • University Hospital Basel, Clinical Virology and Clinical Microbiology.
  • Laboratory of Virology (University Hospitals of Geneva (HUG). Samples were collected from different cantons in Switzerland, sequenced on Illumina HiSeq4000 instrument by the iGE3 Genomics Platform from the University of Geneva (lead M.Docquier) and processes by the Laboratory of Virology from HUG (Florian Laubscher, Samuel Cordey and Laurent Kaiser).
  • Institute of Medical Virology at University of Zurich. Samples were provided by University Hospital Zurich, Triemli Hospital Zurich and Klinik Hirslanden Zurich, sequenced on Illumina technology and processed with VirMet viral metagenomic pipeline (Stefan Schmutz, Maryam Zaheri, Verena Kufner, Gabriela Ziltener, Jürg Böni, Michael Huber, Alexandra Trkola)

All data we use (Swiss and international) are deposited in GISAID.

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based.