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.

BackgroundTracking 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.AimWe 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.MethodsGenomic 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.ResultsCluster 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.ConclusionIGS 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.

Initial Proportion and Dynamic of B.1.1.7 SARS-CoV-2 in a Large City in the West of Germany.

Rationale: Several mutational variants of SARS-CoV-2 have been identified in the past months with increasing prevalence worldwide. Some variants, such as B.1.1.7, are of high relevance due to increased transmissibility, facilitating virus spread and calling for stricter containment measures. Objectives: The aim of this study was to examine proportion and dynamic of B.1.1.7 in SARS-CoV-2-positive samples in a large city in the west of Germany. Methods: Consecutive SARS-CoV-2-positive samples from a local outpatient clinic, obtained over a period of 4 weeks (mid-January to mid-February 2021), were examined for the presence of the variant B.1.1.7. The size of B.1.1.7 infection clusters was compared with non-B.1.1.7 clusters. The transmissibility of SARS-CoV-2 variant B.1.1.7 was described based on corresponding cases of an infection cluster in a local child daycare centre. Results: Among 226 SARS-CoV-2-positive cases, B.1.1.7 was detected in 74 subjects (33%). The 7-day moving mean of the B.1.1.7 proportion started at 20% and reached 50% only 3 weeks later. B.1.1.7 clusters comprised 10.7 ± 12.1 persons per cluster, while non-B.1.1.7 clusters were considerably smaller (5.1 ± 5.8). One specific B.1.1.7 infection cluster in a 40-children daycare centre started with one teacher leading to 11 infected children and 8 infections among teachers. The infection spread to 6 families and one other daycare centre, with a total 43 SARS-CoV-2-positive subjects. Conclusions: We found a rapid increase in the SARS-CoV-2 variant B.1.1.7 with larger infection clusters than non-B.1.1.7. These results suggested a rapid increase in the B.1.1.7 proportion and a renewed increase in the total number of SARS-CoV-2 infections for the time following the analysed period. Considering the rapid emergence and spread of viral variants, close monitoring of mutation events is essential. Therefore, routine whole-genome sequencing appears to be useful in addition to searching for known mutations.