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

Autor:	Muenchhoff M; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.; German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Graf A; Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany., Krebs S; Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany., Quartucci C; Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany.; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany., Hasmann S; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany., Hellmuth JC; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.; German Cancer Consortium (DKTK), Munich, Germany., Scherer C; Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Osterman A; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Boehm S; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Mandel C; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany., Becker-Pennrich AS; Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.; Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany., Zoller M; Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Stubbe HC; Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Munker S; Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Munker D; Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany., Milger K; Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany., Gapp M; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Schneider S; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Ruhle A; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Jocham L; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Nicolai L; Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Pekayvaz K; Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Weinberger T; Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Mairhofer H; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Khatamzas E; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.; German Cancer Consortium (DKTK), Munich, Germany., Hofmann K; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Spaeth PM; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Bender S; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany., Kääb S; Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Zwissler B; Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany., Mayerle J; Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Behr J; Department of Medicine V, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany., von Bergwelt-Baildon M; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.; German Cancer Consortium (DKTK), Munich, Germany., Reincke M; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.; Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany., Grabein B; Department of Clinical Microbiology and Hospital Hygiene, University Hospital, LMU Munich, Munich, Germany., Hinske CL; Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.; Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany., Blum H; Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany., Keppler OT; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.; German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
Jazyk:	angličtina
Zdroj:	Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin [Euro Surveill] 2021 Oct; Vol. 26 (43).
DOI:	10.2807/1560-7917.ES.2021.26.43.2002066
Abstrakt:	BackgroundIn 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.AimWe 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.MethodsWe 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.ResultsWe 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.ConclusionsEarly 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.
Databáze:	MEDLINE
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