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 pageGISAIDcall_made, external pageGenbankcall_made and external pageENAcall_made (project PRJEB43828) with the help of the external pageSwiss Pathogen Surveillance Programcall_made (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 pageWHOcall_made. We first identified Beta (B.1.351; Dec. 26, 2020, reported external pageherecall_made), Gamma (P.1; Feb. 8, 2021, featured external pageherecall_made), and Delta (B.1.617.2; featured external pageherecall_made). 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 pageCoV-Spectrumcall_made.
Our consortium infrastructure is described external pageherecall_made and external pageherecall_made. 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 Downloadhere (XZ, 4.2 MB)vertical_align_bottom 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 pageGISAIDcall_made and external pageGenbankcall_made, and raw sequencing data are available on external pageENAcall_made (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 pageVioller AGcall_made: Andrea Salzmann, Sebastian Kurscheid, Henriette Kurth, Christiane Beckmann, Maurice Redondo, Olivier Kobel, Christoph Noppen.
- external pagelabor team w AGcall_made: Rebekka Pohl, Monika Bucher, Andreas Lindauer, Andreas Grutsch.
- external pageOspedale Regionale di Bellinzona e Vallicall_made (EOC): Gladys Martinetti-Lucchini, Valeria Romina Spina, Gloria Gaudio, Chiara Refaldi.
- external pageInstitute of Medical Virologycall_made (IMV), University of Zurich: Michael Huber, Maryam Zaheri, Stefan Schmutz, Verena Kufner, Kevin Steiner.
- external pageUniversity Hospital Baselcall_made: 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 pageFunctional Genomic Center Zurichcall_made (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 pageHealth 2030 Genome Centercall_made, Geneva: Keith Harshman, Ioannis Xenarios, Henri Pegeot, Lorenzo Cerutti, Deborah Penet.