Genomic Characterisation

Switzerland launched its National Genomic Monitoring Programme for SARS-CoV-2 in March 2021 (bag.admin). Before this, genomes were compiled at the discretion of individual laboratories (e.g. bsse.ethz and biomed.unibas and health2030). This sequencing effort allows us to monitor the evolution and epidemiology of SARS-CoV-2.

SARS-CoV-2 variants

We’ve combined the Swiss data with data from abroad and visualised them at  https://cov-spectrum.ethz.ch/ . This makes it possible to view changes in the genomic composition of the epidemic in Switzerland in almost real-time. In addition, clinical metadata are also available for a portion of the Swiss data, allowing us to show, for example, the hospitalization rate of each variant.

### B.1.1.7 in Switzerland ### B.1.351 in Switzerland ### P.1 in Switzerland ### B.1.617 (and sublineages) in Switzerland

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 nextstrain.org. We also provide a narrative explaining the analysis of the Swiss data. To explore the data in greater depth, visit nextstrain.org.

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.