Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
Sarah Nadeau; Christiane Beckmann; Ivan Topolsky; Timothy Vaughan; Emma Hodcroft; Tobias Schaer; Ina Nissen; Natascha Santacroce; Elodie Burcklen; Pedro Ferreira; Kim Philipp Jablonski; Susana Posada-Cespedes; Vincenzo Capece; Sophie Seidel; Noemi Santamaria de Souza; Julia M. Martinez-Gomez; Phil Cheng; Philipp Bosshard; Mitchell P. Levesque; Verena Kufner; Stefan Schmutz; Maryam Zaheri; Michael Huber; Alexandra Trkola; Samuel Cordey; Florian Laubscher; Ana Rita Goncalves; Karoline Leuzinger; Madlen Stange; Alfredo Mari; Tim Roloff; Helena Seth-Smith; Hans H. Hirsch; Adrian Egli; Maurice Redondo; Olivier Kobel; Christoph Noppen; Niko Beerenwinkel; Richard A. Neher; Christian Beisel; Tanja Stadler.
Preprint
en Inglés
| PREPRINT-MEDRXIV | ID: ppmedrxiv-20212621
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.
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