Genomic epidemiology of superspreading events reveals mutational dynamics and transmission properties of SARS-CoV-2
Study overview
Superspreading events shape the COVID-19 pandemic. Their rapid identification and containment are essential for disease control. Here we provide a national-scale analysis of SARS-CoV-2 superspreading in Austria, a country that played a major role in initial virus transmissions in Europe. Capitalizing on Austria’s well-developed epidemiological surveillance system, we identified major SARS-CoV-2 clusters during the first wave of infections and performed deep whole-genome sequencing of more than 500 virus samples. Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020. Moreover, we exploited epidemiologically well-defined clusters to quantify the mutational dynamics, including the observation of a low-frequency mutation that progressed to fixation within the infection chain. Time-resolved virus sequencing unveiled viral mutation dynamics within individual COVID-19 patients, while epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 103 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2, and to gain fundamental insights into mutational dynamics and transmission properties.
Phylogenetic-epidemiological analyses reveal clusters of infection
Scripts for the reconstruction of global phylogeny (Global), phylogeny of Austrian strains (OnlyAustrian) and phylogeny of early European strains (EarlyEuropean).
Input data, R markdown script and output data for sample characteristics figures and all the analyses concerning low frequency variants across samples.
The scripts for computing bottleneck sizes between infector-infectee pairs.
Citation
Alexandra Popa†, Jakob-Wendelin Genger†, Michael D. Nicholson‡, Thomas Penz‡, Daniela Schmid‡, Stephan W. Aberle‡, Benedikt Agerer‡, Alexander Lercher‡, Lukas Endler, Henrique Colaço, Mark Smyth, Michael Schuster, Miguel L. Grau, Francisco Martínez-Jiménez, Oriol Pich, Wegene Borena, Erich Pawelka, Zsofia Keszei, Martin Senekowitsch, Jan Laine, Judith H. Aberle, Monika Redlberger-Fritz, Mario Karolyi, Alexander Zoufaly, Sabine Maritschnik, Martin Borkovec, Peter Hufnagl, Manfred Nairz, Günter Weiss, Michael T. Wolfinger, Dorothee von Laer, Giulio Superti-Furga, Nuria Lopez-Bigas, Elisabeth Puchhammer-Stöckl, Franz Allerberger, Franziska Michor, Christoph Bock, Andreas Bergthaler*
Genomic epidemiology of superspreading events reveals mutational dynamics and transmission properties of SARS-CoV-2