Projecting the end of the Zika virus epidemic in Latin America: a modelling analysis

Kathleen M O’Reilly; Rachel Lowe; W John Edmunds; Philippe Mayaud; Adam Kucharski; Rosalind M Eggo; Sebastian Funk; Deepit Bhatia; Kamran Khan; Moritz U Kraemar; Annelies Wilder-Smith; Laura C Rodrigues; Patricia Brasil; Eduardo Massad; Thomas Jaenisch; Simon Cauchemez; Oliver J Brady; Laith Yakob

Owing to the difficulties in ZIKV disease surveillance, 23 the weekly incidence of reported cases was unlikely to reflect the true incidence in each setting and we did not fit the model to weekly incidence data. We therefore used summary statistics in the model fitting procedure, focussing on the timing of the peak in incidence and whether the annual incidence was above 1 case per 100,000 in each country. The timing of the peak in outbreaks has been previously shown to be a useful summary statistic for epidemic dynamics, 32, 33 and preliminary analysis illustrated that annual incidence had a good discriminatory power for the estimating parameters of the model. Although surveillance quality varies between settings the timing of the reported peak within countries is less sensitive to systematic To validate the parameter estimates and model output a cross-validation approach was used. The data was split into ten randomly allocated groups by country, each group was sequentially excluded from the parameter estimation procedure and the peak timing of the out-of-sample parameter estimates were compared to the data. The 95% CI of the cross-validated estimates were compared to . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/323915 doi: bioRxiv preprint the within-sample peak estimates. For the 2018 projections we reported the median number of cases, accounting for the estimated reporting rate and uncertainty in model output. The 95% prediction interval had a variance equal to the sum of the variance of the model prediction and the variance of the expected value assuming a Poisson distribution. Comparison of 2018 predictions to data were not possible as data from affected countries have not been made publicly available (as of 2 May 2018).