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Genomic epidemiology reveals multiple introductions of SARS-CoV-2 followed by community and nosocomial spread, Germany, February to May 2020.
Muenchhoff, Maximilian; Graf, Alexander; Krebs, Stefan; Quartucci, Caroline; Hasmann, Sandra; Hellmuth, Johannes C; Scherer, Clemens; Osterman, Andreas; Boehm, Stephan; Mandel, Christopher; Becker-Pennrich, Andrea Sabine; Zoller, Michael; Stubbe, Hans Christian; Munker, Stefan; Munker, Dieter; Milger, Katrin; Gapp, Madeleine; Schneider, Stephanie; Ruhle, Adrian; Jocham, Linda; Nicolai, Leo; Pekayvaz, Kami; Weinberger, Tobias; Mairhofer, Helga; Khatamzas, Elham; Hofmann, Katharina; Spaeth, Patricia M; Bender, Sabine; Kääb, Stefan; Zwissler, Bernhard; Mayerle, Julia; Behr, Juergen; von Bergwelt-Baildon, Michael; Reincke, Martin; Grabein, Beatrice; Hinske, Christian Ludwig; Blum, Helmut; Keppler, Oliver T.
  • Muenchhoff M; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
  • Graf A; German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
  • Krebs S; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Quartucci C; Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany.
  • Hasmann S; Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany.
  • Hellmuth JC; Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Munich, Germany.
  • Scherer C; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.
  • Osterman A; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Boehm S; Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany.
  • Mandel C; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Becker-Pennrich AS; Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.
  • Zoller M; German Cancer Consortium (DKTK), Munich, Germany.
  • Stubbe HC; Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.
  • Munker S; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.
  • Munker D; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Milger K; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
  • Gapp M; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
  • Schneider S; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Ruhle A; Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany.
  • Jocham L; Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.
  • Nicolai L; Department of Medical Information Processing, Biometry and Epidemiology (IBE), LMU Munich, Munich, Germany.
  • Pekayvaz K; Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.
  • Weinberger T; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Mairhofer H; Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.
  • Khatamzas E; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Hofmann K; Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.
  • Spaeth PM; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Bender S; 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.
  • Kääb S; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU Munich, Munich, Germany.
  • Zwissler B; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.
  • Mayerle 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.
  • Behr J; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany.
  • von Bergwelt-Baildon M; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
  • Reincke M; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
  • Grabein B; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
  • Hinske CL; Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany.
  • Blum H; Department of Medicine I, University Hospital, LMU Munich, Munich, Germany.
  • Keppler OT; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.
Euro Surveill ; 26(43)2021 10.
Article in English | MEDLINE | ID: covidwho-1547185
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Cross Infection / COVID-19 Type of study: Prognostic study / Randomized controlled trials / Screening study Limits: Humans Country/Region as subject: Europa Language: English Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: 1560-7917.ES.2021.26.43.2002066

Full text: Available Collection: International databases Database: MEDLINE Main subject: Cross Infection / COVID-19 Type of study: Prognostic study / Randomized controlled trials / Screening study Limits: Humans Country/Region as subject: Europa Language: English Journal subject: Communicable Diseases Year: 2021 Document Type: Article Affiliation country: 1560-7917.ES.2021.26.43.2002066