Walker, Andreas ORCID: 0000-0002-8736-0863, Houwaart, Torsten, Finzer, Patrick, Ehlkes, Lutz ORCID: 0000-0002-0143-7154, Tyshaieva, Alona, Damagnez, Maximilian, Strelow, Daniel ORCID: 0000-0003-1530-2717, Duplessis, Ashley, Nicolai, Jessica, Wienemann, Tobias, Tamayo, Teresa, Vasconcelos, Malte Kohns, Huelse, Lisanna, Hoffmann, Katrin, Luebke, Nadine, Hauka, Sandra, Andree, Marcel, Daeumer, Martin P., Thielen, Alexander, Kolbe-Busch, Susanne, Goebels, Klaus, Zotz, Rainer, Pfeffer, Klaus, Timm, Joerg and Dilthey, Alexander T. . 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. Clin. Infect. Dis.. CARY: OXFORD UNIV PRESS INC. ISSN 1537-6591

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Abstract

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. Tracing of SARS-CoV-2 population transmission chains is still a major challenge. We present an integrated system of genomic surveillance and show it to be capable of detecting infection chains in a large city during ongoing community transmission.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Walker, AndreasUNSPECIFIEDorcid.org/0000-0002-8736-0863UNSPECIFIED
Houwaart, TorstenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Finzer, PatrickUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ehlkes, LutzUNSPECIFIEDorcid.org/0000-0002-0143-7154UNSPECIFIED
Tyshaieva, AlonaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Damagnez, MaximilianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Strelow, DanielUNSPECIFIEDorcid.org/0000-0003-1530-2717UNSPECIFIED
Duplessis, AshleyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Nicolai, JessicaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wienemann, TobiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tamayo, TeresaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vasconcelos, Malte KohnsUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Huelse, LisannaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hoffmann, KatrinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Luebke, NadineUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hauka, SandraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Andree, MarcelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Daeumer, Martin P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thielen, AlexanderUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kolbe-Busch, SusanneUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Goebels, KlausUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zotz, RainerUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pfeffer, KlausUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Timm, JoergUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dilthey, Alexander T.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-586803
DOI: 10.1093/cid/ciab588
Journal or Publication Title: Clin. Infect. Dis.
Publisher: OXFORD UNIV PRESS INC
Place of Publication: CARY
ISSN: 1537-6591
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
REAL-TIME; VIRUS; ZIKAMultiple languages
Immunology; Infectious Diseases; MicrobiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/58680

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