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

Sci Transl Med. 2020 Dec 9;12(573):eabe2555. doi: 10.1126/scitranslmed.abe2555. Epub 2020 Nov 23.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Austria / epidemiology
  • Base Sequence
  • COVID-19 / epidemiology*
  • COVID-19 / genetics
  • COVID-19 / transmission*
  • COVID-19 / virology
  • Host-Pathogen Interactions / genetics
  • Humans
  • Mutation / genetics*
  • Mutation Rate
  • Phylogeny
  • SARS-CoV-2 / genetics*