Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria

Popa, Alexandra; Genger, Jakob-Wendelin; Nicholson, Michael; Penz, Thomas; Schmid, Daniela; Aberle, Stephan W.; Agerer, Benedikt; Lercher, Alexander; Endler, Lukas; Colaço, Henrique; Smyth, Mark; Schuster, Michael; Grau, Miguel; Martinez, Francisco; Pich, Oriol; Borena, Wegene; Pawelka, Erich; Keszei, Zsofia; Senekowitsch, Martin; Laine, Jan; Aberle, Judith H.; Redlberger-Fritz, Monika; Karolyi, Mario; Zoufaly, Alexander; Maritschnik, Sabine; Borkovec, Martin; Hufnagl, Peter; Nairz, Manfred; Weiss, Günter; Wolfinger, Michael T.; von Laer, Dorothee; Superti-Furga, Giulio; Lopez-Bigas, Nuria; Puchhammer-Stöckl, Elisabeth; Allerberger, Franz; Michor, Franziska; Bock, Christoph; Bergthaler, Andreas

Superspreading events shape the COVID-19 pandemic. Here we provide a national-scale analysis of SARS-CoV-2 outbreaks in Austria, a country that played a major role for virus transmission across Europe and beyond. Capitalizing on a national epidemiological surveillance system, we performed deep whole-genome sequencing of virus isolates from 576 samples to cover major Austrian SARS-CoV-2 clusters. Our data chart a map of early viral spreading in Europe, including the path from low-frequency mutations to fixation. Detailed epidemiological surveys enabled us to calculate the effective SARS-CoV-2 population bottlenecks during transmission and unveil time-resolved intra-patient viral quasispecies dynamics. This study demonstrates the power of integrating deep viral genome sequencing and epidemiological data to better understand how SARS-CoV-2 spreads through populations. Graphical Abstract