Swiss SARS-CoV-2 Sequencing Consortium (S3C)
We led the Swiss SARS-CoV-2 Sequencing Consortium (S3C), the largest SARS-CoV-2 sequencing effort in Switzerland from the start of the COVID-19 pandemic until the end of 2022.
Together with diagnostic laboratories we collated SARS-CoV-2 samples from across Switzerland for high-throughput genome sequencing. Each sample is associated with publicly available metadata and we released consensus genomes and raw data on external page GISAID, external page Genbank and external page ENA (project PRJEB43828) with the help of the external page Swiss Pathogen Surveillance Program (SPSP).
The consortium was the only Swiss effort to do weekly sequencing throughout 2020 and we sequenced more than 75% of all Swiss SARS-CoV-2 genomes dating from 2020. In total, we contributed 76’905 SARS-CoV-2 genomes, representing nearly half of all Swiss SARS-CoV-2 genomes sequenced until the end of 2022.
This effort led to the first identification in Switzerland of 3 out of the 5 Variants of Concern (VOCs) declared by the external page WHO. We first identified Beta (B.1.351; Dec. 26, 2020, reported external page here), Gamma (P.1; Feb. 8, 2021, featured external page here), and Delta (B.1.617.2; featured external page here). Throughout we sequenced a random sample of confirmed cases each week, allowing us to track the spread of VOCs in Switzerland. For regular updates see external page CoV-Spectrum.
Our consortium infrastructure is described external page here and external page here. A list of consortium publications and preprints appears at the bottom of this page. More recently, we have been contributing to analyzing SARS-CoV-2 wastewater sequencing data (project lead by Prof. Niko Beerenwinkel, Computational Biology, ETHZ).
Sequencing data
Click Download here (XZ, 4.2 MB) to download a fasta file of 76'905 SARS-CoV-2 consensus genomes sequenced by the S3C (compressed using xz). These genomes are also available on external page GISAID and external page Genbank, and raw sequencing data are available on external page ENA (project PRJEB43828)
Consortium members
(from 2022.04-2022.12)
Lead
- Tanja Stadler (Computational Evolution, D-BSSE, ETHZ)
Coordination
- Louis du Plessis (Computational Evolution, D-BSSE, ETHZ)
- Franziska Singer (NEXUS, ETHZ)
- Matteo Carrara and Shuqing Yu (NEXUS, ETHZ)
- Uwe Schmitt and John Hennig (SIS, ETHZ)
- Ivan Topolsky and Niko Beerenwinkel (Computational Biology, D-BSSE, ETHZ).
- Chaoran Chen (Computational Evolution, D-BSSE, ETHZ)
- external page Violler AG: Andrea Salzmann, Sebastian Kurscheid, Henriette Kurth, Christiane Beckmann, Maurice Redondo, Olivier Kobel, Christoph Noppen.
- external page labor team w AG: Rebekka Pohl, Monika Bucher, Andreas Lindauer, Andreas Grutsch.
- external page Ospedale Regionale di Bellinzona e Valli (EOC): Gladys Martinetti-Lucchini, Valeria Romina Spina, Gloria Gaudio, Chiara Refaldi.
- external page Institute of Medical Virology (IMV), University of Zurich: Michael Huber, Maryam Zaheri, Stefan Schmutz, Verena Kufner, Kevin Steiner.
- external page University Hospital Basel: Tim Roloff, Adrian Egli, Fanny Wegner, Katharina Rentsch, Pascal Schlaepfer.
- Genomics Facility Basel (GFB), ETHZ: Christian Beisel, Rebecca Denes, Mirjam Feldkamp, Ina Nissen, Natascha Santacroce, Elodie Burcklen.
Sarah Nadeau, Kim Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Katharina Jahn, Pedro Ferreira, Sophie Seidel, Noemie Santamaria de Souza, Susana Posada-Céspedes, Tobias Schär, Emmanouil Dermitzakis.
- external page Functional Genomic Center Zurich (FGCZ), ETHZ: Catharine Aquino, Andreia Cabral de Gouvea, Maria Domenica Moccia, Simon Grüter, Timothy Sykes, Lennart Opitz, Griffin White, Laura Neff, Doris Popovic, Andrea Patrignani, Jay Tracy, Ralph Schlapbach.
- external page Health 2030 Genome Center, Geneva: Keith Harshman, Ioannis Xenarios, Henri Pegeot, Lorenzo Cerutti, Deborah Penet.