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- Farooq, Zia, 1986-
(författare)
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Navigating epidemics : by leveraging data science and data-driven modelling
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Ours is an era of global change—including climate change, land-use change, urbanization, increased mobility of humans, species and goods, and environmental shifts. Concurrently, we are witnessing a tangible increase in the rate of (re)emerging infectious diseases, mostly driven by global change factors. This complex landscape of infectious diseases necessitates strategies underpinned by computational tools such as data-driven models to enhance our understanding, response, and predictions of potential epidemics.In this thesis, I leveraged data science algorithms and developed data-driven models that extend beyond specific pathogens, providing insights to prepare for future epidemics, with a focus on Europe. I delved into three temporal contexts: 1) retrospective analyses to understand the contribution of global change factors—specifically climate change and human mobility—fuelling the disease outbreaks and expansion (papers I & IV), 2) develop model to improve disease severity estimation during an outbreak for immediate response (paper III), and 3) future disease transmission risk trajectories under various projected scenarios of global change (paper II)—each playing a crucial role in proactive public health planning and response.In paper I, we assessed the predictive ability and the influence of eco-climatic factors on West Nile virus (WNV)—a pathogen with multiple hosts and mosqutio-vectors, and of public health concern in Europe. Utilizing an advanced machine learning classifier XGBoost, trained on a diverse dataset encompassing eco-climatic, sociodemographic predictors to the WNV presence/absence data, the model accurately predicted the WNV risk a season ahead. Furthermore, by employing an explainable AI algorithm, we uncovered both local and European-level drivers of WNV transmission. Higher temperatures in summer and spring, along with drier winters, were pivotal in the escalated frequency of WNV outbreaks in Europe from 2010 to 2019.In paper II, we projected the WNV risk under climate change and socioeconomics scenarios by integrating augmenting the outputs of climate ensemble into machine learning algorithms. We projected transmission risk trends and maps at local, national, regional and European scale. We predicted a three to five fold increase in WNV transmission risk during the next few decades (2040-60) compared 2000-2020 under extreme climate change scenarios. The proportion of diseasereported European land areas could increase from 15% to 23-30%, putting 161 to 244 million people at risk. Western Europe remains at largest relative risk of WNV increase under all scenarios, and Northern Europe under extreme scenarios. With the current rate of spread and in the absence of intervention or vaccines the virus will have sustained suitability even under low carbon emission scenarios in currently endemic European regions.In paper III, we developed a method to quantify an important epidemiological parameter-case fatality ratio (CFR)— commonly used measure to assess the disease severity during novel outbreaks. In our model, we accounted for the time lags between the reporting of a cases and that of the case fatalities and the probability distribution of time lags and derived the CFR and distribution parameters using an optimization algorithm. The method provided more accurate CFR estimations earlier than the widely used estimators under various simulation scenarios. The method also performed well on empirical COVID-19 data from 34 countries. In paper IV, we modelled annual dengue importations in Europe and the United States driven by human mobility and climate. Travel rates were modelled using a radiation model based on population density, geographic distance, and travel volumes. Dengue viraemic travellers were computed considering local mosquito bite risk, travel-associated bite probability, and visit duration. A dynamic vector life-stage model quantified the climatic suitability of transmissionpermissive local areas. Dengue importations linearly increased in Europe and the U.S. from 2015-2019, rising by 588% and 390%, respectively, compared to 1996-2000 estimates, driven by increased travel volumes (373%) and dengue incidence rates (30%) from endemic countries. Transmission seasons lengthened by 53% and 15% in Europe and the U.S., respectively, indicating increasingly permissive climates for local outbreaks. These findings apply to other diseases such as chikungunya, Zika, and yellow fever, sharing common intermediate host vectors, namely Aedes mosquitoes.This thesis highlights Europe's increasing vulnerability to infectious diseases due to global change factors, putting millions at risk. It emphasizes the significance of advanced modelling and innovative data streams in anticipating epidemic risks. Developing digital early warning systems to track disease drivers and taking urgent climate change mitigation and adaptation measures are crucial to anticipate and reduce future epidemic risks. The outcomes of this research can be used to develop technology-driven decision support tools to aid public health authorities and policymakers in making evidence-based decisions during and inter-epidemic periods.
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| 2. |
- Armando, Chaibo Jose, et al.
(författare)
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Spatial-temporal analysis of climate and socioeconomic conditions on cholera incidence in Mozambique from 2000 to 2018 : an ecological longitudinal retrospective study
- 2024
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Ingår i: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 14:8
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: This study aims to assess both socioeconomic and climatic factors of cholera morbidity in Mozambique considering both spatial and temporal dimensions.DESIGN: An ecological longitudinal retrospective study using monthly provincial cholera cases from Mozambican Ministry of Health between 2000 and 2018. The cholera cases were linked to socioeconomic data from Mozambique Demographic and Health Surveys conducted in the period 2000-2018 and climatic data; relative humidity (RH), mean temperature, precipitation and Normalised Difference Vegetation Index (NDVI). A negative binomial regression model in a Bayesian framework was used to model cholera incidence while adjusting for the spatiotemporal covariance, lagged effect of environmental factors and the socioeconomic indicators.SETTING: Eleven provinces in Mozambique.RESULTS: Over the 19-year period, a total of 153 941 cholera cases were notified to the surveillance system in Mozambique. Risk of cholera increased with higher monthly mean temperatures above 24°C in comparison to the reference mean temperature of 23°C. At mean temperature of 19°C, cholera risk was higher at a lag of 5-6 months. At a shorter lag of 1 month, precipitation of 223.3 mm resulted in an 57% increase in cholera risk (relative risk, RR 1.57 (95% CI 1.06 to 2.31)). Cholera risk was greatest at 3 lag months with monthly NDVI of 0.137 (RR 1.220 (95% CI 1.042 to 1.430)), compared with the reference value of 0.2. At an RH of 54%, cholera RR was increased by 62% (RR 1.620 (95% CI 1.124 to 2.342)) at a lag of 4 months. We found that ownership of radio RR 0.29, (95% CI 0.109 to 0.776) and mobile phones RR 0.262 (95% CI 0.097 to 0.711) were significantly associated with low cholera risk.CONCLUSION: The derived lagged patterns can provide appropriate lead times in a climate-driven cholera early warning system that could contribute to the prevention and management of outbreaks.
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