National genomic monitoring programme confirmed

Bern, 28.05.2021 - Monitoring of the variants of SARS-CoV-2 and the prevalence of the infection in the population are two important elements of efforts to combat the novel coronavirus. Monitoring enables the evolution of the different variants to be tracked and the risk of strains which circumvent the immunity conferred by the different vaccines or prior infection to be evaluated. Against this background, the Federal Office of Public Health (FOPH) has endorsed the establishment of a national genomic monitoring programme for SARS-CoV-2 in collaboration with the Centre for Emerging Viral Diseases at Geneva University Hospitals and the reference laboratory (CRIVE), the Federal Institutes of Technology, university and privately run laboratories, the NextStrain platform and the Covid-19 Scientific Task Force.

Genetic monitoring of SARS-CoV-2 is an essential component in monitoring the Covid-19 epidemic. Although most mutations have neither an epidemiological nor a clinical impact, some increase the contagiousness or the pathogenicity of the virus, or they reduce its susceptibility to the immunity induced by vaccines or prior infection. Sequencing the genome of the virus permits a fine classification of the mutations that emerge over time, enabling chains of transmission to be traced and measures to be adapted dynamically if necessary.

In early March, the FOPH expanded the arrangement by launching a national systematic genome sequencing programme.  Some 2,000 samples positive for SARS-CoV-2 are analysed every week, with the number expected to change in response to the epidemiological situation. The objective is to rapidly identify virus variants of concern, their possible significance for travellers and their distribution within the country. The strategy, which is based on the recommendations issued by the WHO, is being funded by the FOPH and coordinated by CRIVE.

The programme has been put in place gradually since the start of the year, and is now fully deployed. It is intended to run from 1 March 2021 to 31 March 2022. Sampling is performed in such a way that, among other things, a representative picture of Switzerland is obtained, covering all the geographic regions and age groups. Ten laboratories are taking part in the programme – the five university hospitals and a network of privately run laboratories. Other laboratories could join in the near future. The samples are sequenced on site or sent to one of the three high-throughput centres of sequencing excellence: the Health 2030 Genome Centre in Geneva, the Department of Biosystems Science and Engineering (D-BSSE), part of ETH Zurich based in Basel, and the Functional Genomics Centre run by ETH Zurich.

The viral sequences are stored centrally on the Swiss Pathogen Surveillance Platform and are also accessible on the international GISAID platform. The FOPH evaluates the sequences and officially publishes the data on Variants of concern are counted and screening for new variants is carried out by NextStrain (

In addition, the monitoring programme will monitor waste water and perform immunological characterisation of variants of concern to establish whether they are able to circumvent the immunity conferred by vaccines or prior infection.

Address for enquiries

Federal Office of Public Health, Communication, +41 58 462 95 05,

Centre for Emerging Viral Diseases at Geneva University Hospitals (HUG), Media Relations, +41 22 372 37 37,

Swiss Federal Institute of Technology Lausanne, Media Relations,


Federal Office of Public Health