Characterization of SARS-CoV-2 infection clusters in an urban setting based on integrated real-time genomic surveillance, outbreak analysis, and contact tracing

Alexander Dilthey

Alexander Dilthey, Heinrich Heine University Düsseldorf, Germany


The ability to genetically track SARS-CoV-2 transmission through the population could contribute to significantly improved management of the SARS-CoV-2 pandemic. We present a proof-of-concept implementation of a fully-integrated system of genomic surveillance in a large German city, that integrates real-time nanopore sequencing with routine public health contact tracing data, which feeds analyzed genetic data to public health authorities 48 – 72 hours after initial PCR-based diagnosis. We show that the system enables the high-level characterization of viral population structure, as well as the detection of previously unrecognized community transmission infection chains.  A live version is available at


Alexander Dilthey is Professor of Genomic Microbiology and Immunity at Heinrich Heine University Düsseldorf. His research interests include SARS-CoV-2 genomic epidemiology, microbiome and cell-free DNA analysis, and bioinformatics method development for long reads and complex regions like the HLA/MHC. Previous positions include Oxford University in the McVean group, and NHGRI with the Phillippy group, as well as co-founding two companies in the biomedical space.