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.

COVID-19 / epidemiology Contact Tracing Disease Outbreaks / prevention & control Genomics Humans SARS-CoV-2 / genetics

Nanopore sequencing community transmission genomic epidemiology infection chain rapid sequencing

Journal

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

ISSN: 1537-6591

Titre abrégé: Clin Infect Dis

Pays: United States

ID NLM: 9203213

Informations de publication

Date de publication:
23 03 2022

Historique:

received: 19 04 2021

pubmed: 29 6 2021

medline: 30 3 2022

entrez: 28 6 2021

Statut: ppublish

Résumé

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

Sections du résumé

BACKGROUND

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.

Identifiants

DOI: 10.1093/cid/ciab588 PMID: 34181711 PMC: PMC8406867

pubmed: 34181711

pii: 6310838

doi: 10.1093/cid/ciab588

pmc: PMC8406867

doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

1039-1046

Subventions

Organisme : Jürgen Manchot Foundation German Research Foundation

ID : 428994620

Organisme : German Federal Ministry of Education and Research

ID : 031L0184B

Investigateurs

Janine Altmüller (J)

Angel Angelov (A)

Anna C Aschenbrenner (AC)

Robert Bals (R)

Alexander Bartholomäus (A)

Anke Becker (A)

Daniela Bezdan (D)

Michael Bitzer (M)

Helmut Blum (H)

Ezio Bonifacio (E)

Peer Bork (P)

Nicolas Casadei (N)

Thomas Clavel (T)

Maria Colome-Tatche (M)

Inti Alberto De La Rosa Velázquez (IA)

Andreas Diefenbach (A)

Alexander Dilthey (A)

Nicole Fischer (N)

Konrad Förstner (K)

Sören Franzenburg (S)

Julia-Stefanie Frick (JS)

Gisela Gabernet (G)

Julien Gagneur (J)

Tina Ganzenmüller (T)

Marie Gauder (M)

Alexander Goesmann (A)

Siri Göpel (S)

Adam Grundhoff (A)

Hajo Grundmann (H)

Torsten Hain (T)

André Heimbach (A)

Michael Hummel (M)

Thomas Iftner (T)

Angelika Iftner (A)

Stefan Janssen (S)

Jörn Kalinowski (J)

René Kallies (R)

Birte Kehr (B)

Andreas Keller (A)

Oliver Keppler (O)

Sarah Kim-Hellmuth (S)

Christoph Klein (C)

Michael Knop (M)

Oliver Kohlbacher (O)

Karl Köhrer (K)

Jan Korbel (J)

Peter G Kremsner (PG)

Denise Kühnert (D)

Ingo Kurth (I)

Markus Landthaler (M)

Yang Li (Y)

Kerstin Ludwig (K)

Oliwia Makarewicz (O)

Manja Marz (M)

Alice McHardy (A)

Christian Mertes (C)

Maximilian Münchhoff (M)

Sven Nahnsen (S)

Markus Nöthen (M)

Francine Ntoumi (F)

Peter Nürnberg (P)

Uwe Ohler (U)

Stephan Ossowski (S)

Jörg Overmann (J)

Silke Peter (S)

Klaus Pfeffer (K)

Anna R Poetsch (AR)

Ulrike Protzer (U)

Alfred Pühler (A)

Nikolaus Rajewsky (N)

Markus Ralser (M)

Olaf Rieß (O)

Stephan Ripke (S)

Ulisses Rocha (U)

Philip Rosenstiel (P)

Emmanuel Saliba (E)

Leif Erik Sander (LE)

Birgit Sawitzki (B)

Simone Scheithauer (S)

Philipp Schiffer (P)

Jonathan Schmid-Burgk (J)

Wulf Schneider (W)

Eva-Christina Schulte (EC)

Joachim Schultze (J)

Alexander Sczyrba (A)

Mariam L Sharaf (ML)

Yogesh Singh (Y)

Michael Sonnabend (M)

Oliver Stegle (O)

Jens Stoye (J)

Fabian Theis (F)

Janne Vehreschild (J)

Thirumalaisamy P Velavan (TP)

Jörg Vogel (J)

Max von Kleist (M)

Andreas Walker (A)

Jörn Walter (J)

Dagmar Wieczorek (D)

Sylke Winkler (S)

John Ziebuhr (J)