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

Alexandra Popa(Austrian Academy of Sciences), Jakob‐Wendelin Genger(Austrian Academy of Sciences), Michael D. Nicholson(Harvard University), Thomas Penz(Austrian Academy of Sciences), Daniela Schmid(Austrian Agency for Health and Food Safety), Stephan W. Aberle(Medical University of Vienna), Benedikt Agerer(Austrian Academy of Sciences), Alexander Lercher(Austrian Academy of Sciences), Lukas Endler(University of Veterinary Medicine Vienna), Henrique G. Colaço(Austrian Academy of Sciences), Mark Smyth(Austrian Academy of Sciences), Michael Schuster(Austrian Academy of Sciences), Miguel L. Grau(Institute for Research in Biomedicine), Francisco Martı́nez(Institute for Research in Biomedicine), Oriol Pich(Institute for Research in Biomedicine), Wegene Borena(Innsbruck Medical University), Erich Pawelka(Kaiser-Franz-Josef-Spital), Zsofia Keszei(Austrian Academy of Sciences), Martin Senekowitsch(Austrian Academy of Sciences), Jan Laine(Austrian Academy of Sciences), Judith H. Aberle(Medical University of Vienna), Monika Redlberger‐Fritz(Medical University of Vienna), Mario Karolyi(Kaiser-Franz-Josef-Spital), Alexander Zoufaly(Kaiser-Franz-Josef-Spital), Sabine Maritschnik(Austrian Agency for Health and Food Safety), Martin Borkovec(Austrian Agency for Health and Food Safety), Peter Hufnagl(Austrian Agency for Health and Food Safety), Manfred Nairz(Innsbruck Medical University), Günter Weiß(Innsbruck Medical University), Michael T. Wolfinger(University of Vienna), Dorotheé von Laer(Innsbruck Medical University), Giulio Superti‐Furga(Austrian Academy of Sciences), Núria López-Bigas(Institució Catalana de Recerca i Estudis Avançats), Elisabeth Puchhammer‐Stöckl(Medical University of Vienna), Franz Allerberger(Austrian Agency for Health and Food Safety), Franziska Michor(Broad Institute), Christoph Bock(Austrian Academy of Sciences), Andreas Bergthaler(Austrian Academy of Sciences)
bioRxiv (Cold Spring Harbor Laboratory)
July 17, 2020
10.1101/2020.07.15.204339
Cited by 14Open Access
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Abstract

Abstract 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

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