Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

• DOI: 10.1126/scitranslmed.abn7979
• Publication Date: 2022-11-08T15:47:48Z
• Authors: Sarah A. Nadeau; Timothy G. Vaughan; Christiane Beckmann; Ivan Topolsky; Chaoran Chen; Emma Hodcroft; Tobias Schär; Ina Nissen; Natascha Santacroce; Elodie Burcklen; Pedro Ferreira; Kim Philipp Jablo...; Susana Posada-Cés...; Vincenzo Capece; Sophie Seidel; Noemi Santamaria ...; Julia M. Martinez...; Phil Cheng; Philipp P. Bosshard; Mitchell P. Levesque; Verena Kufner; Stefan Schmutz; Maryam Zaheri; Michael Huber; Alexandra Trkola; Samuel Cordey; Florian Laubscher; Ana Rita Gonçalves; Sébastien Aeby; Trestan Pillonel; Damien Jacot; Claire Bertelli; Gilbert Greub; Karoline Leuzinger; Madlen Stange; Alfredo Mari; Tim Roloff; Helena Seth-Smith; Hans H. Hirsch; Adrian Egli; Maurice Redondo; Olivier Kobel; Christoph Noppen; Louis du Plessis; Niko Beerenwinkel; Richard A. Neher; Christian Beisel; Tanja Stadler
• Keywords: 0301 basic medicine; 0303 health sciences; SARS-CoV-2; COVID-19 / genetics; COVID-19; 610 Medicine & health; Genome, Viral / genetics; Genome, Viral; Switzerland / epidemiology; 3. Good health; 03 medical and health sciences; 360 Social problems & social services; SARS-CoV-2 / genetics; info:eu-repo/classification/ddc/616; Communicable Disease Control; Humans; Public Health; Research Articles; Switzerland; Phylogeny

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020—the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland’s border closures decoupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86 to 98% reduction in introductions during Switzerland’s strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred using a phylodynamic model. We found that transmission slowed 35 to 63% upon outbreak detection in summer 2020 but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.