Quantifying the impact of vaccination on pertussis dynamics in Sweden

The last few decades have witnessed a resurgence in pertussis notifications in a number of countries with high vaccine coverage, including Sweden. The underlying causes of the resurgence have been the subject of much scientific debate. To arbitrate among the putative drivers of the resurgence in Sweden, we formulated a mechanistic transmission model which we fit to age-structured time-series notifications data via likelihood maximisation. Given our model, we find the data are best explained by the combined effects of a low basic reproductive number, incomplete (leaky) DTaP-derived immunity, a much lower reporting probability of infections in older individuals and waning of vaccine-derived immunity. In addition, our modelling explains the post-2014 resurgence as a combination of two factors. First, a dynamical transient known as the honeymoon effect, in which a rebound in transmission follows after a rapid decrease in the average population susceptibility. Second, an increase in the infection reporting probability from 2014 onwards, likely due to the use of new laboratory testing methods. Additionally, we used our fitted transmission model to reconstruct indirect protective effects of vaccination. Our results suggest immunization prevents about 50% of potential infections in individuals too young to receive vaccination. However, our statistical inference demonstrates that pertussis elimination is not possible with routine immunization using acellular vaccines due to the combined effects of vaccine leakiness and waning immunity.