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 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.

Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory

“…In the present COVID-19 pandemic, rapid SARS-CoV-2 WGS, combined with epidemiologic methods, identified or excluded nosocomial transmission events to directly affect outbreak management in real time 23 . Hospital-based WGS set up in collaboration with public health departments has also facilitated real-time outbreak investigations and identification of transmission chains 24 . At a national level, the Coronavirus Disease 2019 (COVID-19) Genomics UK Consortium (COG-UK) has developed high-throughput sequencing and analysis workflows to generate hundreds of thousands of SARS-CoV-2 genomic sequences, enabling large-scale genomic epidemiology to inform public health response ( https://www.cogconsortium.uk/ ).…”

Development and Validation of a High-Throughput Next-Generation Sequencing Workflow for SARS-CoV-2 Whole Genome Sequencing: Results from Over 65,000 Clinical Cases

“…In the present COVID-19 pandemic, rapid SARS-CoV-2 whole genome sequencing, combined with epidemiologic methods, identi ed or excluded nosocomial transmission events to directly affect outbreak management in real time 23 . Hospital-based whole genome sequencing set up in collaboration with public health departments has also facilitated real-time outbreak investigations and identi cation of transmission chains 24 Large scale and high-throughput whole genome sequencing of SARS-CoV-2 is essential to enable realtime epidemiologic surveillance and to better understand the evolution and spread of the pandemic, improve epidemiologic tracking, and enhance treatment and prevention strategies for COVID-19. To date, several groups have developed different protocols and work ows for SARS-CoV-2 whole genome sequencing by NGS.…”

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021

“…The IGSD has been described elsewhere [ 10 ]. Briefly, when fully operational, the system operates as follows.…”

“…Integrated genomic surveillance (IGS) is an emerging approach that refers to the integrated analysis of genetic and complementary epidemiological data. As we and others have shown [ 10 - 13 ], IGS can contribute to identification of otherwise unrecognised SARS-CoV-2 transmission chains in the general population even under conditions of high-incidence community transmission and thus provide important complementary information for the design and implementation of NPIs.…”