Eurosurv. Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020

[tetano]

• Maximilian Muenchhoff[SUP]1,2,3,*[/SUP] , Alexander Graf[SUP]4,*[/SUP] , Stefan Krebs[SUP]4[/SUP] , Caroline Quartucci[SUP]5,6[/SUP] , Sandra Hasmann[SUP]3,7[/SUP] , Johannes Hellmuth[SUP]3,8,9[/SUP] , Clemens Scherer[SUP]3,10,11[/SUP] , Andreas Osterman[SUP]1[/SUP] , Stephan Boehm[SUP]1[/SUP] , Christopher Mandel[SUP]3,7[/SUP] , Andrea Becker-Pennrich[SUP]12[/SUP] , Michael Zoller[SUP]3,12[/SUP] , Hans Christian Stubbe[SUP]3,13[/SUP] , Stefan Munker[SUP]3,13[/SUP] , Dieter Munker[SUP]3,6[/SUP] , Katrin Milger-Kneidinger[SUP]3,6[/SUP] , Madeleine Gapp[SUP]1[/SUP] , Stephanie Schneider[SUP]1[/SUP] , Adrian Ruhle[SUP]1[/SUP] , Linda Jocham[SUP]1[/SUP] , Leo Nicolai[SUP]3,10,11[/SUP] , Kami Pekayvaz[SUP]3,10,11[/SUP] , Tobias Weinberger[SUP]3,10,11[/SUP] , Helga Mairhofer[SUP]1[/SUP] , Elham Khatamzas[SUP]3,8,9[/SUP] , Katharina Hofmann[SUP]1[/SUP] , Patricia Spaeth[SUP]1[/SUP] , Sabine Bender[SUP]1[/SUP] , Stefan Kääb[SUP]3,10,11[/SUP] , Bernhard Zwißler[SUP]3,6,12[/SUP] , Julia Mayerle[SUP]3,13[/SUP] , Juergen Behr[SUP]6[/SUP] , Michael von Bergwelt-Baildon[SUP]3,8,9[/SUP] , Martin Reincke[SUP]3,7[/SUP] , Beatrice Grabein[SUP]14[/SUP] , Christian Ludwig Hinske[SUP]12[/SUP] , Helmut Blum[SUP]4[/SUP] , Oliver T Keppler[SUP]1,2,3[/SUP]

Background

In the SARS-CoV-2 pandemic, viral genomes are available at unprecedented speed, but spatio-temporal bias in genome sequence sampling precludes phylogeographical inference without additional contextual data.

Aim

We applied genomic epidemiology to trace SARS-CoV-2 spread on an international, national and local level, to illustrate how transmission chains can be resolved to the level of a single event and single person using integrated sequence data and spatio-temporal metadata.

Methods

We investigated 289 COVID-19 cases at a university hospital in Munich, Germany, between 29 February and 27 May 2020. Using the ARTIC protocol, we obtained near full-length viral genomes from 174 SARS-CoV-2-positive respiratory samples. Phylogenetic analyses using the Auspice software were employed in combination with anamnestic reporting of travel history, interpersonal interactions and perceived high-risk exposures among patients and healthcare workers to characterise cluster outbreaks and establish likely scenarios and timelines of transmission.

Results

We identified multiple independent introductions in the Munich Metropolitan Region during the first weeks of the first pandemic wave, mainly by travellers returning from popular skiing areas in the Alps. In these early weeks, the rate of presumable hospital-acquired infections among patients and in particular healthcare workers was high (9.6% and 54%, respectively) and we illustrated how transmission chains can be dissected at high resolution combining virus sequences and spatio-temporal networks of human interactions.

Conclusions

Early spread of SARS-CoV-2 in Europe was catalysed by superspreading events and regional hotspots during the winter holiday season. Genomic epidemiology can be employed to trace viral spread and inform effective containment strategies.


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