Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban Setting
Authors: Walker Andreas , Houwaart Torsten , Finzer Patrick , Ehlkes Lutz , Tyshaieva Alona , Damagnez Maximilian , Strelow Daniel , Duplessis Ashley , Nicolai Jessica , Wienemann Tobias , Tamayo Teresa , Kohns Vasconcelos Malte , Hülse Lisanna , Hoffmann Katrin , Lübke Nadine , Hauka Sandra , Andree Marcel , Däumer Martin P , Thielen Alexander , Kolbe-Busch Susanne , Göbels Klaus , Zotz Rainer , Pfeffer Klaus , Timm Jörg , Dilthey Alexander T ,   German COVID-19 OMICS Initiative (DeCOI), Altmüller Janine , Angelov Angel , Aschenbrenner Anna C , Bals Robert , Bartholomäus Alexander , Becker Anke , Bezdan Daniela , Bitzer Michael , Blum Helmut , Bonifacio Ezio , Bork Peer , Casadei Nicolas , Clavel Thomas , Colome-Tatche Maria , De La Rosa Velázquez Inti Alberto , Diefenbach Andreas , Dilthey Alexander , Fischer Nicole , Förstner Konrad , Franzenburg Sören , Frick Julia-Stefanie , Gabernet Gisela , Gagneur Julien , Ganzenmüller Tina , Gauder Marie , Goesmann Alexander , Göpel Siri , Grundhoff Adam , Grundmann Hajo , Hain Torsten , Heimbach André , Hummel Michael , Iftner Thomas , Iftner Angelika , Janssen Stefan , Kalinowski Jörn , Kallies René , Kehr Birte , Keller Andreas , Keppler Oliver , Kim-Hellmuth Sarah , Klein Christoph , Knop Michael , Kohlbacher Oliver , Köhrer Karl , Korbel Jan , Kremsner Peter G , Kühnert Denise , Kurth Ingo , Landthaler Markus , Li Yang , Ludwig Kerstin , Makarewicz Oliwia , Marz Manja , McHardy Alice , Mertes Christian , Münchhoff Maximilian , Nahnsen Sven , Nöthen Markus , Ntoumi Francine , Nürnberg Peter , Ohler Uwe , Ossowski Stephan , Overmann Jörg , Peter Silke , Pfeffer Klaus , Poetsch Anna R , Protzer Ulrike , Pühler Alfred , Rajewsky Nikolaus , Ralser Markus , Rieß Olaf , Ripke Stephan , Rocha Ulisses , Rosenstiel Philip , Saliba Emmanuel , Sander Leif Erik , Sawitzki Birgit , Scheithauer Simone , Schiffer Philipp , Schmid-Burgk Jonathan , Schneider Wulf , Schulte Eva-Christina , Schultze Joachim , Sczyrba Alexander , Sharaf Mariam L , Singh Yogesh , Sonnabend Michael , Stegle Oliver , Stoye Jens , Theis Fabian , Vehreschild Janne , Velavan Thirumalaisamy P , Vogel Jörg , von Kleist Max , Walker Andreas , Walter Jörn , Wieczorek Dagmar , Winkler Sylke , Ziebuhr John 
Published: June 2021

Abstract

Background
Tracing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction of viral transmission networks by integration of molecular epidemiology into classical contact tracing.

Methods
In collaboration with local public health authorities, we set up an integrated system of genomic surveillance in an urban setting, combining a) viral surveillance sequencing, b) genetically based identification of infection clusters in the population, c) integration of public health authority contact tracing data, and d) a user-friendly dashboard application as a central data analysis platform.

Results
Application of the integrated system from August to December 2020 enabled a characterization of viral population structure, analysis of 4 outbreaks at a maximum care hospital, and genetically based identification of 5 putative population infection clusters, all of which were confirmed by contact tracing. The system contributed to the development of improved hospital infection control and prevention measures and enabled the identification of previously unrecognized transmission chains, involving a martial arts gym and establishing a link between the hospital to the local population.

Conclusions
Integrated systems of genomic surveillance could contribute to the monitoring and, potentially, improved management of SARS-CoV-2 transmission in the population.