A novel methodology for assessing contact tracing precision: Phylogenetic validation of a contact tracing program for COVID-19 in Belgium

Abstract

During the COVID-19 pandemic, contact tracing was widely used to limit virus propagation and implement targeted disease control measures. It can however be difficult to assess whether infected cases are actually linked to the traced index case. In this study, we developed and applied an analytical pipeline using genomic data to assess the precision of contact tracing, defined as the proportion of transmission events suggested by contact tracing that are not contradicted by genomic analysis. We exemplify our approach by examining the transmission of SARS-CoV-2 among students at Belgium’s largest university, in Leuven, during the Omicron BA.1 and BA.2 epidemic waves. We analysed 459 case-contact pairs identified through contact tracing. We then aimed to determine whether the pairs, where patients were infected with the same variant, clustered together within a time-scaled phylogeny. Our findings indicate that 34.6 % of transmission events suggested by contact tracing were not invalidated by our combined phylogenetic and single nucleotide polymorphism analysis. Only considering non invalidated transmission events, we estimated serial intervals with a smaller standard deviation than with all case-contact pairs. Our genomic-based pipeline allows us to assess the ability of our contact tracing program to correctly identify transmission chains. While contact tracing is crucial for early outbreak detection and control, monitoring its precision is vital for using this data in public health decisions.