Hunt for the genome of SARS-CoV-2 variants goes on in Switzerland

The Swiss National SARS-CoV-2 Genomic Surveillance Program introduced in May 2021 by the Federal Office of Public Health (FOPH) has been extended until December 31, 2022, with a further option for 2023. The program is coordinated by the Geneva Center for Emerging Viral Diseases and the National Reference Center for Emerging Viral Infections (CRIVE), and is integrated into the Virology Laboratory at the Geneva University Hospitals (HUG) and the Faculty of Medicine at the University of Geneva (UNIGE). The Health 2030 Genome Center, which was set up to promote genomic medicine in Switzerland, will work closely with HUG, and will be responsible for carrying out most of the sequencing. Around 500 weekly sequencings of new SARS-CoV-2 infections in Switzerland will be performed to support the Swiss public health strategy.

The Swiss National SARS-CoV-2 Genomic Surveillance Program has been active since spring 2021. It has proven to be essential for monitoring the prevalence of COVID-19 in the population and for identifying immune-resistant virus strains. The SARS-CoV-2 virus responsible for the COVID-19 pandemic is constantly evolving: mutations continually appear in its genome, producing different variants, which may have an impact on the virus’s contagiousness. This means, for instance, that it can elude acquired immunity through vaccination or prior infection. These mutations may also alter the speed at which the virus spreads, change its pathogenicity or enable it to resist to existing treatments. By monitoring variants found in Switzerland via genomic sequencing, it has been possible to introduce in the country a dynamic, tailor-made public health strategy.

This FOPH-funded national monitoring program is being extended and will be coordinated by the Geneva Center for Emerging Viral Diseases and CRIVE in collaboration with a number of partners and Swiss laboratories. The Genome Center includes the universities and university hospitals of Bern, Geneva and Lausanne (UNIBE, UNIGE, UNIL; Inselspital, HUG, CHUV) as well as the École Polytechnique Fédérale de Lausanne (EPFL). The Genome Center will now perform over half of the SARS-CoV-2 sequencing, with the remainder assigned to the Department of Biosystems Science and Engineering (D-BSSE), a Basel-based facility that is part of ETH Zürich. A dozen laboratories and platforms were initially in charge of sequencing over 100,000 SARS-CoV-2 genomes – with nearly a third carried out by the Genome Center – from March 1, 2021, to March 31, 2022. Henceforth, the mandate to identify viral sequences has been granted to these two bodies alone.

Speedy variants identification

The program’s second phase will sequence 500 SARS-CoV-2 samples a week in Switzerland, with a narrower focus on hospitalized patients. This weekly analysis should enable a speedy variants identification, especially those considered to be of concern by the World Health Organization (WHO).

The viral sequences will be shared on the GISAID platforms and the Swiss Pathogen Surveillance Platform (SPSP) developed by the Swiss Institute of Bioinformatics (SIB), while Nextstrain will analyze and screen for variants.

On the front line in the fight against COVID-19

The Geneva Center for Emerging Viral Diseases at HUG and the University of Geneva are responsible for coordinating the genomic surveillance of SARS-CoV-2 in Switzerland in close collaboration with the Health 2030 Genome Center. The Center for Emerging Viral Diseases has been on the front line in the fight against COVID-19, influenza and other emerging viruses.

As Professor Laurent Kaiser, head of the Department of Medicine and of the Infectious Diseases Service at HUG, explains: “The Lake Geneva region offers unique solutions to tackle the challenges we face with emerging viruses. Only through close collaboration between our different area of expertise, and between our institutions, will we be able to respond more effectively to the COVID-19 pandemic, and to all other viruses that threaten global health security.”

Cutting-edge platform

The fact that the National SARS-CoV-2 Genomic Surveillance Program is extended confirms the Genome Center’s position as a state-of-the-art sequencing platform in Switzerland. “As well as being equipped with the most powerful DNA and RNA sequencers, the Center has the expertise required to process substantial quantities of samples. It can generate high-quality data in a very short time, which is a prerequisite for this large-scale program with its thousands of samples,” says Marc Friedli, manager of the Health 2030 program that hosts the Genome Center.

Furthermore, in May 2021 the Swiss Accreditation Service awarded the Genome Center ISO 15189:2013 accreditation for its human genome, exome and transcriptome sequencing assays. “This accreditation, which is one-of-a-kind in Switzerland for a non-profit sequencing platform, also was a major factor in the decision of the FOPH”, points out Marc Friedli. “Even though this accreditation is not essential for a viral RNA surveillance program, it does mean we can analyze DNA and human RNA samples from hospitals and clinics in accordance with ISO standards, which is an indisputable guarantee of quality.”