Genomics-enhanced contact tracing enabled the characterization of SARS-CoV-2 transmission chains and their associated infection contexts in the general population during community transmission

Understanding pathogen transmission is key to effective infection prevention. From February to December 2021, we implemented genomics-enhanced contact tracing for SARS-CoV-2 in Dusseldorf, Germany, integrating data on 32,380 cases, 49,906 contact tracing records, 162 outbreaks, and 8,028 viral genomes (sequencing coverage 24.5%). Combining epidemiological and genetic data, we found a putative infection source for 19% of sequenced and 44% of all cases. Household-associated transmission accounted for up to 40% of all cases; classical contact tracing had limited sensitivity for non-household contacts, and gastronomy, hospital, school and kindergarten contexts were genetically found to be likely enriched for undetected transmissions. Outbreaks were associated with 8% of cases; school, kindergarten and nightlife outbreaks were strongly connected to the community, with nightlife outbreaks showing a strong post-outbreak increase in genetically associated cases. Sequencing detected previously unrecognized links between school outbreaks and 18% additional outbreak-associated sequenced cases. In conclusion, in addition to classical contact tracing, SARS-CoV-2 sequencing was required to achieve an improved resolution of transmission dynamics; future implementations of genomics-enhanced contact tracing should aim for sequencing rates of at least 15% to enable effective characterization of infection contexts and outbreaks.