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