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. 2022 Oct;27(43):2101089.
doi: 10.2807/1560-7917.ES.2022.27.43.2101089.

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

Torsten Houwaart  1 , Samir Belhaj  2 , Emran Tawalbeh  2 , Dirk Nagels  2 , Yara Fröhlich  3 , Patrick Finzer  1   4 , Pilar Ciruela  5   6 , Aurora Sabrià  5 , Mercè Herrero  5 , Cristina Andrés  7 , Andrés Antón  7 , Assia Benmoumene  3 , Dounia Asskali  3 , Hussein Haidar  3 , Janina von Dahlen  3 , Jessica Nicolai  1 , Mygg Stiller  8 , Jacqueline Blum  8 , Christian Lange  8 , Carla Adelmann  9 , Britta Schroer  9 , Ute Osmers  10 , Christiane Grice  10 , Phillipp P Kirfel  10 , Hassan Jomaa  10 , Daniel Strelow  1 , Lisanna Hülse  1 , Moritz Pigulla  2 , Pascal Kreuzer  2 , Alona Tyshaieva  1 , Jonas Weber  1 , Tobias Wienemann  1 , Malte Kohns Vasconcelos  1 , Katrin Hoffmann  4 , Nadine Lübke  3 , Sandra Hauka  3 , Marcel Andree  3 , Claus Jürgen Scholz  11 , Nathalie Jazmati  11 , Klaus Göbels  2 , Rainer Zotz  12   4 , Klaus Pfeffer  1 , Jörg Timm  3 , Lutz Ehlkes  2 , Andreas Walker  3 , Alexander T Dilthey  1 ; German COVID-19 OMICS Initiative (DeCOI)  13 ; German COVID-19 OMICs Initiative (DeCOI)
Collaborators, Affiliations

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

Torsten Houwaart et al. Euro Surveill. 2022 Oct.

Abstract

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.

Keywords: Genomic surveillance; Nanopore real-time sequencing; Next generation sequencing; SARS-CoV-2; contact tracing; deep backward contact tracing; travel-associated SARS-CoV-2 infections.

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Conflict of interest statement

Conflict of interest: None declared

Figures

Figure 1
Figure 1
Phylogenetic analysis of the extended dataset of sequences of SARS-CoV-2 registered cases, Düsseldorf and Solingen, Germany, 15 June–01 August 2021 (n = 699 sequences)a
Figure 2
Figure 2
Cluster 1 contact tracing results, Düsseldorf and Solingen, Germany, 15 June–01 August 2021 (n = 68 cases)
Figure 3
Figure 3
Distribution of SARS-CoV-2 cases according to time, their cluster, and epidemiological or genomic basis for inclusion in a cluster, Düsseldorf, Germany, 01 July–31 July 2021 (n = 850 cases)
Figure 4
Figure 4
Cluster 2 genetic structure and contact tracing results, Düsseldorf and Solingen, Germany, 15 June–01 August 2021 (n = 42 cases)
See this image and copyright information in PMC

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