Date/Time
Date(s) - 25/09/2025
2:30 pm - 3:30 pm

Speaker: Dr. Rowan Durrant (McMaster University)

Location: Hybrid HH-312 (& on zoom)

Title: A simple method of estimating rabies outbreak sizes from genomic data

Abstract: The ability to estimate the size of a disease outbreak is beneficial both for coordinating an outbreak response and for retrospectively evaluating the effectiveness of response measures and surveillance. Methods such as randomised testing can be used for this purpose but are not always suitable for every outbreak. We develop a simple formula to estimate the proportion of cases in an outbreak that have been sequenced using only an estimate of the per-generation substitution rate and the mean branch length of a phylogenetic tree, which can then be used to calculate the outbreak size. We validate this method using subsampled data from simulated outbreaks, and then apply it to an ongoing rabies outbreak in the Romblon province of the Philippines. We find that this method produces reasonably accurate estimates of outbreak size, and that it can be applied to outbreaks with substitution rates and values of R0 within the estimated range for rabies. We estimated that approximately 17.2% of cases from the outbreak in Romblon province had been sequenced, suggesting better than average case detection. This method could make rabies outbreak size estimation more accessible, but further work is required to improve its applicability to other diseases.

Dr. Rowan Durrant is a postdoctoral researcher working at the intersection of outbreak modelling and viral evolution, with Prof. Jonathan Dushoff at MacTheoBio Group.