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 under-stand 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 appli-cation of the integrated genomic surveillance (IGS) system of the German city of Dusseldorf 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 sur-veillance, phylogenetic analysis, and structured case interviews were integrated to elucidate two geneti-cally defined clusters of SARS-CoV-2 isolates detected by IGS in Dusseldorf in July 2021. Results: Cluster 1 (n = 67 Dusseldorf cases) and Cluster 2 (n = 36) were detected in a surveillance dataset of 518 high-quality SARS-CoV-2 genomes from Dusseldorf (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 multi-ple independent introduction events of a viral strain circulating in Catalonia and other European coun-tries, followed by diffuse community transmission in Dusseldorf.