DENcode: A model for haplotype-informed transmission probability of dengue virus

Dengue virus transmission networks are often only partially resolved, due to gaps in sampling, unobserved mosquito-mediated transmission, and using methods (phylogenetics) that describe evolutionary relatedness but not explicit, probabilistic transmission links between individual infections. We developed DENcode, a framework to estimate the relative likelihood of vector-mediated transmission between pairs of dengue cases by combining a temperature- and time-modulated epidemiological kernel, which captures the extrinsic incubation period and human infectiousness, with a phylogenetically informed genetic similarity kernel derived from patristic distances between viral haplotypes or consensus sequences. Validation with a real-life dataset of 90 dengue infections sampled from Colombo, Sri Lanka between 2017 - 2020 and sequenced to resolve within-host haplotypes, DENcode estimates were stable across 100 Monte Carlo iterations, yielding narrow credible intervals (median width <0.001) and consistent top-ranked transmission pairs. Sensitivity analyses using ablation experiments showed that removing either the genetic or epidemiological component substantially altered the distribution of linkage probabilities, indicating that both contribute meaningfully to the inferred transmission structure. Serotype-specific transmission networks constructed from pairwise linkage probabilities from DENcode were analysed using degree- and path-based centrality measures at probability thresholds of 0.1 and 0.5, revealing relative importance of cases to disease transmission within the community. Haplotype-derived networks were more informative than consensus-based networks (x 3.6 and x 1.6 times more edges for DENV2 and 3 respectively). DENcode is a robust framework to explore dengue transmission within a community that provides an output of network of transmission probabilities informed by pathogen genetic similarity and clinical epidemiological parameters. Author summaryTracing epidemics of dengue in setting where dengue transmission happens continuously poses many challenges especially with limited availability of genomic surveillance. Here we introduce a model that uses genomic data together with time and location data to calculate a probability of two cases of dengue being related to each other. Using data from the Colombo dengue study, from 2017 to 2020, Sri Lanka, we evaluated the model. We used haplotype level sequences that correspond to the viral variation within the human host and consensus level sequences that average the data from a single human host into a single sequence. We constructed transmission probability networks for each dengue serotype and were able to identify patients who played key roles in the corresponding networks. We were able to show that this model is robust and will be a valuable tool in the context of dengue control.