Open AccessCharacterization 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
Author(s) -
Andreas Walker,
Torsten Houwaart,
Patrick Finzer,
Lutz Ehlkes,
Alona Tyshaieva,
Maximilian Damagnez,
Daniel Strelow,
Ashley Duplessis,
Jessica Nicolai,
Tobias Wienemann,
Teresa Tamayo,
Malte Kohns Vasconcelos,
Lisanna Hülse,
Katrin Hoffmann,
Nadine Lübke,
Sandra Hauka,
Marcel Andrée,
Martin Däumer,
Alexander Thielen,
Susanne Kolbe-Busch,
K Göbels,
Rainer B. Zotz,
Klaus Pfeffer,
Jörg Timm,
Alexander Dilthey,
Janine Altmüller,
Angel Angelov,
Anna C. Aschenbrenner,
Robert Bals,
Alexander Bartholomäus,
Anke Becker,
Daniela Bezdan,
Michael Bitzer,
Helmut Blum,
Ezio Bonifacio,
Peer Bork,
Nicolas Casadei,
Thomas Clavel,
Maria Colomé-Tatché,
Inti Alberto De La Rosa Velázquez,
Andreas Diefenbach,
Alexander Dilthey,
Nicole Fischer,
Konrad U. Förstner,
Sören Franzenburg,
Julia-Stefanie Frick,
Gisela Gabernet,
Julien Gagneur,
Tina Ganzenmüller,
Marie Gauder,
Alexander Goesmann,
Siri Göpel,
Adam Grundhoff,
Hajo Grundmann,
Torsten Hain,
André Heimbach,
Michael Hummel,
Thomas Iftner,
Angelika Iftner,
Stefan Janssen,
Jörn Kalinowski,
René Kallies,
Birte Kehr,
Andreas Keller,
Oliver T. Keppler,
Sarah Kim-Hellmuth,
Christoph Klein,
Michael Knop,
Oliver Kohlbacher,
Karl Köhrer,
Jan O. Korbel,
Peter G. Kremsner,
Denise Kühnert,
Ingo Kurth,
Markus Landthaler,
Li Yang,
Kerstin U. Ludwig,
Oliwia Makarewicz,
Manja Marz,
Alice C. McHardy,
Christian Mertes,
Maximilian Münchhoff,
Sven Nahnsen,
Markus M. Nöthen,
Francine Ntoumi,
Peter J. Nürnberg,
Uwe Ohler,
Stephan Ossowski,
Jörg Overmann,
Silke Peter,
Klaus Pfeffer,
Anna R. Poetsch,
Ulrike Protzer,
Alfred Pühler,
Nikolaus Rajewsky,
Markus Ralser,
Olaf Rieß,
Stephan Ripke,
Ulisses Nunes da Rocha,
Philip Rosenstiel,
Emmanuel Saliba,
Leif Erik Sander,
Birgit Sawitzki,
Simone Scheithauer,
Philipp Schiffer,
Jonathan L. Schmid-Burgk,
Wulf Schneider,
Eva-Christina Schulte,
Joachim L. Schultze,
Alexander Sczyrba,
Mariam L Sharaf,
Yogesh Preet Singh,
Michael Sonnabend,
Oliver Stegle,
Jens Stoye,
Fabian J. Theis,
Janne Vehreschild,
Thirumalaisamy P. Velavan,
Jörg Vogel,
Max von Kleist,
Andreas Walker,
J.D. Walter,
Dagmar Wieczorek,
Sylke Winkler,
John Ziebuhr
Publication year - 2021
Publication title -
clinical infectious diseases/clinical infectious diseases (online. university of chicago. press)
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.44
H-Index - 336
eISSN - 1537-6591
pISSN - 1058-4838
DOI - 10.1093/cid/ciab588
Subject(s) - contact tracing , medicine , population , transmission (telecommunications) , public health , outbreak , middle east respiratory syndrome coronavirus , infection control , virology , environmental health , infectious disease (medical specialty) , intensive care medicine , disease , covid-19 , pathology , computer science , telecommunications
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.