Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2

Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2

Abstract

Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections 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 SARS-CoV-2 mutational dynamics, including the observation of low-frequency mutations that progressed to fixation within the infection chain. Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and 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.

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Authors
  • Popa, Alexandra
  • Genger, Jakob-Wendelin
  • Nicholson, Michael D.
  • Penz, Thomas
  • Schmid, Daniela
  • Aberle, Stephan W.
  • Agerer, Benedikt
  • Lercher, Alexander
  • Endler, Lukas
  • Colaço, Henrique
  • Smyth, Mark
  • Schuster, Michael
  • Grau, Miguel L.
  • Martínez-Jiménez, 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
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Shortfacts
Category
Journal Paper
Divisions
Bioinformatics and Computational Biology
Journal or Publication Title
Science Translational Medicine
ISSN
1646-6234
Page Range
eabe2555
Number
573
Volume
12
Date
9 December 2020
Official URL
http://dx.doi.org/10.1126/scitranslmed.abe2555
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