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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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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; Houwaart, Torsten; Finzer, Patrick; Ehlkes, Lutz; Tyshaieva, Alona; Damagnez, Maximilian; Strelow, Daniel; Duplessis, Ashley; Nicolai, Jessica; Wienemann, Tobias; Tamayo, Teresa; Kohns Vasconcelos, Malte; Hülse, Lisanna; Hoffmann, Katrin; Lübke, Nadine; Hauka, Sandra; Andree, Marcel; Däumer, Martin P; Thielen, Alexander; Kolbe-Busch, Susanne; Göbels, Klaus; Zotz, Rainer; Pfeffer, Klaus; Timm, Jörg; Dilthey, Alexander T; German COVID-19 OMICS Initiative (DeCOI).

In: CLIN INFECT DIS, Vol. 74, No. 6, 23.03.2022, p. 1039-1046.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Walker, A, Houwaart, T, Finzer, P, Ehlkes, L, Tyshaieva, A, Damagnez, M, Strelow, D, Duplessis, A, Nicolai, J, Wienemann, T, Tamayo, T, Kohns Vasconcelos, M, Hülse, L, Hoffmann, K, Lübke, N, Hauka, S, Andree, M, Däumer, MP, Thielen, A, Kolbe-Busch, S, Göbels, K, Zotz, R, Pfeffer, K, Timm, J, Dilthey, AT & German COVID-19 OMICS Initiative (DeCOI) 2022, '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, vol. 74, no. 6, pp. 1039-1046. https://doi.org/10.1093/cid/ciab588

APA

Walker, A., Houwaart, T., Finzer, P., Ehlkes, L., Tyshaieva, A., Damagnez, M., Strelow, D., Duplessis, A., Nicolai, J., Wienemann, T., Tamayo, T., Kohns Vasconcelos, M., Hülse, L., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Däumer, M. P., Thielen, A., ... German COVID-19 OMICS Initiative (DeCOI) (2022). 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, 74(6), 1039-1046. https://doi.org/10.1093/cid/ciab588

Vancouver

Walker A, Houwaart T, Finzer P, Ehlkes L, Tyshaieva A, Damagnez M et al. 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. 2022 Mar 23;74(6):1039-1046. https://doi.org/10.1093/cid/ciab588

Bibtex

@article{d544124e0101482da8ab990cc1a7dfcf,
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",
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.",
keywords = "COVID-19/epidemiology, Contact Tracing, Disease Outbreaks/prevention & control, Genomics, Humans, SARS-CoV-2/genetics",
author = "Andreas Walker and Torsten Houwaart and Patrick Finzer and Lutz Ehlkes and Alona Tyshaieva and Maximilian Damagnez and Daniel Strelow and Ashley Duplessis and Jessica Nicolai and Tobias Wienemann and Teresa Tamayo and {Kohns Vasconcelos}, Malte and Lisanna H{\"u}lse and Katrin Hoffmann and Nadine L{\"u}bke and Sandra Hauka and Marcel Andree and D{\"a}umer, {Martin P} and Alexander Thielen and Susanne Kolbe-Busch and Klaus G{\"o}bels and Rainer Zotz and Klaus Pfeffer and J{\"o}rg Timm and Dilthey, {Alexander T} and {German COVID-19 OMICS Initiative (DeCOI)}",
note = "{\textcopyright} The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.",
year = "2022",
month = mar,
day = "23",
doi = "10.1093/cid/ciab588",
language = "English",
volume = "74",
pages = "1039--1046",
journal = "CLIN INFECT DIS",
issn = "1058-4838",
publisher = "Oxford University Press",
number = "6",

}

RIS

TY - JOUR

T1 - 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

AU - Walker, Andreas

AU - Houwaart, Torsten

AU - Finzer, Patrick

AU - Ehlkes, Lutz

AU - Tyshaieva, Alona

AU - Damagnez, Maximilian

AU - Strelow, Daniel

AU - Duplessis, Ashley

AU - Nicolai, Jessica

AU - Wienemann, Tobias

AU - Tamayo, Teresa

AU - Kohns Vasconcelos, Malte

AU - Hülse, Lisanna

AU - Hoffmann, Katrin

AU - Lübke, Nadine

AU - Hauka, Sandra

AU - Andree, Marcel

AU - Däumer, Martin P

AU - Thielen, Alexander

AU - Kolbe-Busch, Susanne

AU - Göbels, Klaus

AU - Zotz, Rainer

AU - Pfeffer, Klaus

AU - Timm, Jörg

AU - Dilthey, Alexander T

AU - German COVID-19 OMICS Initiative (DeCOI)

N1 - © The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America.

PY - 2022/3/23

Y1 - 2022/3/23

N2 - 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.

AB - 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.

KW - COVID-19/epidemiology

KW - Contact Tracing

KW - Disease Outbreaks/prevention & control

KW - Genomics

KW - Humans

KW - SARS-CoV-2/genetics

U2 - 10.1093/cid/ciab588

DO - 10.1093/cid/ciab588

M3 - SCORING: Journal article

C2 - 34181711

VL - 74

SP - 1039

EP - 1046

JO - CLIN INFECT DIS

JF - CLIN INFECT DIS

SN - 1058-4838

IS - 6

ER -