Transmission Networks and Intervention Effects From SARS-CoV-2 Genomic and Social Network Data in Denmark

Decision-making by governments during disease outbreaks is increasingly reliant on large-scale pathogen genomics and detailed individual-level data. We use 293,841 SARS-CoV-2 genomes collected in Denmark, between September 1st 2020 and December 31st 2021, and combine these with comprehensive individual-level data on settings, including households, schools, workplaces and family relationships, to infer plausible transmission pathways. Next, we use the plausible transmission pathways to assess the effectiveness of specific non-pharmaceutical interventions (NPIs) and quantify transmission heterogeneities, providing a more detailed understanding than is possible from aggregate national estimates. School restrictions were associated with reduced community transmission; face coverings and gathering restrictions were associated with reduced transmission across all settings. We find that those vaccinated with two doses, compared to the unvaccinated, had onward transmission reduced by 23.5% (95% highest posterior density interval: 21.5-25.2%). Our proposed approach is pathogen agnostic, and can be used in future outbreaks where genomic data and data on social relationships are available.