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

Abstract

Background Tracking person-to-person SARS-CoV-2 transmission in the population is important to understand the epidemiology of community transmission and may contribute to the containment of SARS-CoV-2. Neither contact tracing nor genomic surveillance alone, however, are typically sufficient to achieve this objective. Aim We demonstrate the successful application of the integrated genomic surveillance (IGS) system of the German city of Düsseldorf for tracing SARS-CoV-2 transmission chains in the population as well as detecting and investigating travel-associated SARS-CoV-2 infection clusters. Methods Genomic surveillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two genetically defined clusters of SARS-CoV-2 isolates detected by IGS in Düsseldorf in July 2021. Results Cluster 1 (n = 67 Düsseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Düsseldorf (53% of total cases, sampled mid-June to July 2021). Cluster 1 could be traced back to a complex pattern of transmission in nightlife venues following a putative importation by a SARS-CoV-2-infected return traveller (IP) in late June; 28 SARS-CoV-2 cases could be epidemiologically directly linked to IP. Supported by viral genome data from Spain, Cluster 2 was shown to represent multiple independent introduction events of a viral strain circulating in Catalonia and other European countries, followed by diffuse community transmission in Düsseldorf. Conclusion IGS enabled high-resolution tracing of SARS-CoV-2 transmission in an internationally connected city during community transmission and provided infection chain-level evidence of the downstream propagation of travel-imported SARS-CoV-2 cases.

HantaNet: A New MicrobeTrace Application for Hantavirus Classification, Genomic Surveillance, Epidemiology and Outbreak Investigations

“…MicrobeTrace was originally developed as a browser-based web application for secure, local HIV surveillance data analysis for cluster detection and outbreak response [40]. Its use has expanded for the study of other pathogen outbreaks [38,[46][47][48][49]. During the 2022-2023 global mpox outbreak, the MicrobeTrace team at the CDC built a local Nextstrain [65] and MicrobeTrace pipeline for continued US mpox genomic surveillance and to support secure cluster analysis of HIV-mpox coinfections [66].…”

“…MicrobeTrace is a secure web browser tool developed at the CDC [38] that remains operational without an internet connection and facilitates data integration and analysis with a suite of customizable views, including networks, phylogenetic trees, world maps, tables and charts that could be tailored as a dashboard view for real-time data analytics and reporting. MicrobeTrace has been widely used to integrate, visualize and analyze data from several pathogens, including HIV [39][40][41][42][43], hepatitis [44,45], tuberculosis [46] and SARS-CoV-2 [47][48][49]. We describe the expansion of MicrobeTrace as a pathogen-specific tool for genomic surveillance and variant classification.…”

Etablierung der Genomischen Erreger-Surveillance zur Stärkung des Pandemie- und Infektionsschutzes in Deutschland

“…Bezogen auf die SARS-CoV-2-Pandemie stellt die kombinierte Nutzung von genomischen Erregerinformationen mit Angaben zu Person, Ort und Zeit zur verbesserten Charakterisierung von SARS-CoV-2-Übertragungsketten in der Bevölkerung ein großes, bisher wenig genutztes Potenzial zur Verbesserung des Pandemiemanagements dar. Die Integration dieser Informationen in das Kontaktmanagement der lokalen Gesundheitsbehörden könnte somit einen erheblichen gesellschaftlichen Nutzen schaffen, sofern organisatorische und technologische Herausforderungen bewältigt werden [ 10 , 11 ].…”