Fig 1.
Diagram of models and data sources where R0 denotes the basic reproduction number and λ, the force of infection.
Circles denote a product of calculation or inference; square boxes denote data sources.
Fig 2.
Location of serological surveys used in the models.
The colour intensity indicates number of studies covering each province where grey = 0, pale blue = 1 and darker blue = 2 or more. Further details on serological surveys are available in Table A in S1 Text [1, 9, 18–23]. Maps were produced from GADM version 2.0.
Fig 3.
Diagram of model inference at one iteration.
Aspects relating the λ model are contained in the blue box. There are two main data sets that the models are estimated from, occurrence data, shown in white, and serological data, shown in black. Elements contained within circles denote families of model parameters with the vaccine efficacy (Ve) parameter common to both transmission model formulations. When a model is not activated (R0 in this figure) the model-specific parameters are informed by pseudopriors, shown in purple. Solid arrows imply that the parameter is being informed by that data source or pseudoprior in this iteration; dashed arrows imply that the parameter family is currently not informed by that data source or pseudoprior in this iteration.
Fig 4.
Geographical distribution of yellow fever occurrence.
Presence/ absence of yellow fever over 30 year period by province where white indicates absence and brown, presence (a). Median model predictions of the probability of at least one report of yellow fever (b). Countries not considered endemic for yellow fever are shown in black. The AUC of the shown fit is 0.9157. Maps were produced from GADM version 2.0.
Fig 5.
Posterior predictive distributions of seroprevalence for each of the included serological studies.
Predictions from the λ model are shown in blue and from the R0 model, red; paler red and blue regions indicate the 95% credible interval of the predictions. The data is shown with black dots with binomial 95% confidence ranges shown with black whiskers.
Fig 6.
Estimated transmission intensity across the African endemic region for yellow fever.
Median posterior estimates of the GLM and transmission model parameters are used to calculate either (a) force of infection or (b) R0 across the African endemic region. Countries not considered endemic for yellow fever are shown in grey. Maps were produced from GADM version 2.0.
Fig 7.
Disease burden estimates for 2018 with equal model priors.
1,000 predictions of the burden in 2018 across the African endemic zone on log10 scale. The probability an infection is severe is drawn from a beta distribution with shape parameters 6.4 and 44.6 [39]. Predictions are drawn from each transmission model proportional to the model evidence under the assumption of equal model priors where pink points come from the λ model and blue points, from the R0 model.