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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

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Item Type:Article
Title: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
Creators Name:Walker, A. and Houwaart, T. and Finzer, P. and Ehlkes, L. and Tyshaieva, A. and Damagnez, M. and Strelow, D. and Duplessis, A. and Nicolai, J. and Wienemann, T. and Tamayo, T. and Kohns Vasconcelos, M. and Hülse, L. and Hoffmann, K. and Lübke, N. and Hauka, S. and Andree, M. and Däumer, M.P. and Thielen, A. and Kolbe-Busch, S. and Göbels, K. and Zotz, R. and Pfeffer, K. and Timm, J. and Dilthey, A.T.
Abstract:BACKGROUND: Tracing of 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 four outbreaks at a maximum care hospital, and genetically based identification of five 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.
Keywords:Genomic Epidemiology, Infection Chain, Community Transmission, Rapid Sequencing, Nanopore Sequencing
Source:Clinical Infectious Diseases
ISSN:1058-4838
Publisher:Oxford University Press
Volume:74
Number:6
Page Range:1039-1046
Date:15 March 2021
Additional Information:Markus Landthaler, Uwe Ohler and Nikolaus Rajewsky are members of the Deutsche COVID-19 Omics Initiative (DeCOI).
Official Publication:https://doi.org/10.1093/cid/ciab588
PubMed:View item in PubMed

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