National SARS-CoV-2 sequencing program

The Swiss Federal Office of Public Health has mandated CRIVE-HUG to coordinate the national SARS-CoV-2 genomic surveillance program from March 1, 2021. The aim is to detect clinically relevant variants, in particular to identify those that are better transmitted, to assess their relative prevalence, and to monitor the emergence of mutations that could influence the clinical management of Covid-19.

In its first year, by bringing together 3 sequencing platforms in Switzerland and up to 11 laboratories in Switzerland, the project enabled the weekly sequencing of around 2000 complete SARS-CoV-2 genomes. Sequences were systematically deposited in both the GISAID platform and the Swiss Pathogen Surveillance Platform (SPSP). This enabled sufficient positive samples to be analyzed to provide a representative picture of the situation in Switzerland. A basic immunological characterization of the significant variants circulating in Switzerland (VOCs and VOIs) was also carried out as part of the program.

The virology laboratory at Geneva University Hospital was one of two laboratories involved in enhanced surveillance, contributing up to 350 sequences per week.

Since January 1, 2023, the genomic surveillance program has focused primarily on virus variants that cause severe disease progression and hospitalization, while continuing to monitor community transmission through samples obtained by the Swiss Sentinella surveillance system. The current mandate has reduced weekly sequencing to around 200 complete SARS-CoV-2 genomes per week for the whole of Switzerland (all sequencing is carried out at the Health 2030 genome center).

Centralized analysis of this national surveillance is carried out in collaboration with the groups led by Prof. Neher, Prof. Stadler and Dr. Althaus. Variant epidemiology is accessible via Nextstrain, Covariant and Cov-Spectrum. A report is published monthly, coordinated by the Center for Emerging Viral Diseases (see below).

This work is carried out in close collaboration with the Swiss national scientific working group COVID-19 and the Swiss Institute of Bioinformatics (SIB).