Dataset Information

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.

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.

SUBMITTER: Walker A

PROVIDER: S-EPMC8406867 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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Publications

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.

Walker Andreas A Houwaart Torsten T Finzer Patrick P Ehlkes Lutz L Tyshaieva Alona A Damagnez Maximilian M Strelow Daniel D Duplessis Ashley A Nicolai Jessica J Wienemann Tobias T Tamayo Teresa T Kohns Vasconcelos Malte M Hülse Lisanna L Hoffmann Katrin K Lübke Nadine N Hauka Sandra S Andree Marcel M Däumer Martin P MP Thielen Alexander A Kolbe-Busch Susanne S Göbels Klaus K Zotz Rainer R Pfeffer Klaus K Timm Jörg J Dilthey Alexander T AT

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20220301 6

<h4>Background</h4>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.<h4>Methods</h4>In collaboration wit ...[more]

PMID: 34181711

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Dataset Information

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.

Background

Methods

Results

Conclusions

Publications

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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