1. Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
- Author
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Elodie Burcklen, Tanja Stadler, Verena Kufner, Alfredo Mari, Samuel Cordey, Sarah Nadeau, Mitchell P. Levesque, Tobias Schaer, Michael Huber, Susana Posada-Cespedes, Richard A. Neher, Pedro Ferreira, Julia M. Martinez-Gomez, Adrian Egli, Emma B. Hodcroft, Christoph Noppen, Alexandra Trkola, Helena M.B. Seth-Smith, Timothy G. Vaughan, Christian Beisel, Ina Nissen, Olivier Kobel, Kim Philipp Jablonski, Niko Beerenwinkel, Philipp P. Bosshard, Ivan Topolsky, Madlen Stange, Natascha Santacroce, Ana Rita Gonçalves, Christiane Beckmann, Tim Roloff, Maryam Zaheri, Hans H. Hirsch, Sophie Seidel, Phil F. Cheng, Stefan Schmutz, Karoline Leuzinger, Maurice Redondo, Vincenzo Capece, Noemi Santamaria de Souza, and Florian Laubscher
- Subjects
2019-20 coronavirus outbreak ,Transmission (mechanics) ,law ,Evolutionary biology ,Genomic data ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Lineage (evolution) ,Genomic sequencing ,Epidemic spread ,Biology ,Genome ,law.invention - Abstract
Pathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early viral introductions from Germany, France, and Italy and many recent introductions from Germany and France. Over the summer, we quantify the number of non-traceable infections stemming from introductions, quantify the effective reproductive number, and estimate the degree of undersampling. Our framework can be applied to quantify evolution and epidemiology in other locations or for other pathogens based on genomic data.One Sentence SummaryWe quantify SARS-CoV-2 spread in Switzerland based on genome sequences from our nation-wide sequencing effort.
- Published
- 2020
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