Abstract
Background
The ongoing COVID-19 pandemic significantly burdens hospitals and other healthcare facilities. Therefore, understanding the entry and transmission of SARS-CoV-2 is critical for effective prevention and preparedness measures. We performed surveillance and analysis of testing and transmission of SARS-CoV-2 infections in a tertiary-care hospital in Germany during the second and third pandemic waves in fall/winter 2020.
Methods
Between calendar weeks 41/2020 and 1/2021 40% of all positive patient and staff samples (284 total) were subjected to full-length viral genome sequencing. Clusters were defined based on similar genotypes indicating common sources of infection. We integrated phylogenetic, spatial, and temporal metadata to detect nosocomial infections and outbreaks, uncover transmission chains, and evaluate containment measures’ effectiveness.
Results
Epidemiologic data and contact tracing readily recognize most healthcare-associated patient infections. However, sequencing data reveal that temporally preceding index cases and transmission routes can be missed using epidemiologic methods, resulting in delayed interventions and serially linked outbreaks being counted as independent events. While hospital-associated transmissions were significantly elevated at a moderate rate of community transmission during the second wave, systematic testing and high vaccination rates among staff have led to a substantial decrease in healthcare-associated infections at the end of the second/beginning of the third wave despite high community transmissions.
Conclusions
While epidemiologic analysis is critical for immediate containment of healthcare-associated SARS-CoV-2 outbreaks, integration of genomic surveillance revealed weaknesses in identifying staff contacts. Our study underscores the importance of high testing frequency and genomic surveillance to detect, contain and prevent SARS-CoV-2-associated infections in healthcare settings.
Keywords: SARS-CoV-2 whole genome sequencing, integration of spatial and temporal information, hospital surveillance, molecular epidemiology, containment measurements
Contributor Information
Manja Czech-Sioli, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Thomas Günther, Virus Genomics Unit, Leibniz Institute for Experimental Virology, Hamburg, Germany.
Alexis Robitaille, Virus Genomics Unit, Leibniz Institute for Experimental Virology, Hamburg, Germany.
Hannes Roggenkamp, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Henning Büttner, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Daniela Indenbirken, Virus Genomics Unit, Leibniz Institute for Experimental Virology, Hamburg, Germany.
Martin Christner, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Mark Lütgehetmann, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Johannes Knobloch, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Martin Aepfelbacher, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Adam Grundhoff, Virus Genomics Unit, Leibniz Institute for Experimental Virology, Hamburg, Germany.
Nicole Fischer, Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg Eppendorf, Hamburg, Germany.
Supplementary Material
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