National SARS-CoV-2 sequencing program

Starting on 1 March 2021, the CRIVE-HUG has been coordinating the national SARS-CoV-2 genomic surveillance program under a mandate from the Swiss Federal Office of Public Health. The initial aim was to detect clinically relevant variants (particularly 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. As the pandemic progressed, this mandate was renewed while reducing the overall sequencing volume multiple times. In late 2024, the decision was taken to combine surveillance of SARS-CoV-2 with surveillance of respiratory syncytial virus (RSV) and Influenza.

Currently, samples mainly originate from the Swiss Sentinella surveillance system, completed by samples originating by canotnal laboratory hospitals. All sequencing is carried out at the Health 2030 genome center. Sequences obtained through this program are systematically deposited in both the GISAID platform and the Swiss Pathogen Surveillance Platform (SPSP).This work is carried out in close collaboration with the Swiss national scientific working group COVID-19 and the Swiss Institute of Bioinformatics (SIB).

Centralized analysis of this national surveillance is carried out in collaboration with the group led by Prof. Neher. Variant epidemiology is accessible via Nextstrain, Covariant, Cov-Spectrum, and Genspectrum. A report is published after each sequencing batch (every few months), coordinated by the Center for Emerging Viral Diseases.

For these reports, as well as the reports from earlier in the program when only SARS-CoV-2 was surveilled, please see below.