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Mathematical models in ecology and epidemiology must be consistent with observed data in order to generate reliable knowledge and evidence-based policy. Metapopulation systems, which consist of a network of connected sub-populations, pose technical challenges in statistical inference owing to nonlinear, stochastic interactions. Numerical difficulties encountered in conducting inference can obstruct the core scientific questions concerning the link between the mathematical models and the data. Recently, an algorithm has been proposed that enables computationally tractable likelihood-based inference for high-dimensional partially observed stochastic dynamic models of metapopulation systems. We use this algorithm to build a statistically principled data analysis workflow for metapopulation systems. Via a case study of COVID-19, we show how this workflow addresses the limitations of previous approaches. The COVID-19 pandemic provides a situation where mathematical models and their policy implications are widely visible, and we revisit an influential metapopulation model used to inform basic epidemiological understanding early in the pandemic. Our methods support self-critical data analysis, enabling us to identify and address model weaknesses, leading to a new model with substantially improved statistical fit and parameter identifiability. Our results suggest that the lockdown initiated on 23 January 2020 in China was more effective than previously thought. 

The role of climate factors on transmission of mosquito-borne infections within urban landscapes must be considered in the context of the pronounced spatial heterogeneity of such environments. Socio-demographic and environmental variation challenge control efforts for emergent arboviruses transmitted via the urban mosquitoAedes aegypti. We address at high resolution, the spatial heterogeneity of dengue transmission risk in the megacity of Delhi, India, as a function of both temperature and the carrying-capacity of the human environment for the mosquito. Based on previous results predicting maximum mosquitoes per human for different socio-economic typologies, and on remote sensing temperature data, we produce a map of the reproductive number of dengue at a resolution of 250m by 250m. We focus on dengue risk hotspots during inter-epidemic periods, places where chains of transmission can persist for longer. We assess the resulting high-resolution risk map of dengue with reported cases for three consecutive boreal winters. We find that both temperature and vector carrying-capacity per human co-vary in space because of their respective dependence on population density. The synergistic action of these two factors results in larger variation of dengue’s reproductive number than when considered separately, with poor and dense locations experiencing the warmest conditions and becoming the most likely reservoirs off-season. The location of observed winter cases is accurately predicted for different risk threshold criteria. Results underscore the inequity of risk across a complex urban landscape, whereby individuals in dense poor neighborhoods face the compounded effect of higher temperatures and mosquito carrying capacity. Targeting chains of transmission in inter-epidemic periods at these locations should be a priority of control efforts. A better mapping is needed of the interplay between climate factors that are dominant determinants of the seasonality of vector-borne infections and the socio-economic conditions behind unequal exposure. 

Identifying climate drivers is essential to understand and predict epidemics of mosquito-borne infections whose population dynamics typically exhibit seasonality and multiannual cycles. Which climate covariates to consider varies across studies, from local factors such as temperature to remote drivers such as the El Niño–Southern Oscillation. With partial wavelet coherence, we present a systematic investigation of nonstationary associations between mosquito-borne disease incidence and a given climate factor while controlling for another. Analysis of almost 200 time series of dengue and malaria around the globe at different geographical scales shows a systematic effect of global climate drivers on interannual variability and of local ones on seasonality. This clear separation of time scales of action enhances detection of climate drivers and indicates those best suited for building early-warning systems.