Spatiotemporal high-resolution prediction and mapping: methodology and application to dengue disease

Bayesian spatio-temporal analysis of dengue transmission in Lao PDR

Dengue, a zoonotic viral disease transmitted by Aedes mosquitoes, poses a significant public health concern throughout the Lao People's Democratic Republic (Lao PDR). This study aimed to describe spatial-temporal patterns and quantify the effects of environmental and climate variables on dengue transmission at the district level. The dengue data from 2015 to 2020 across 148 districts of Lao PDR were obtained from the Lao PDR National Center for Laboratory and Epidemiology (NCLE). The association between monthly dengue occurrences and environmental and climate variations was investigated using a multivariable Zero-inflated Poisson regression model developed in a Bayesian framework. The study analyzed a total of 72,471 dengue cases with an incidence rate of 174 per 100,000 population. Each year, incidence peaked from June to September and a large spike was observed in 2019. The Bayesian spatio-temporal model revealed a 9.1% decrease (95% credible interval [CrI] 8.9%, 9.2%) in dengue incidence for a 0.1 unit increase in monthly normalized difference vegetation index at a 1-month lag and a 5.7% decrease (95% CrI 5.3%, 6.2%) for a 1 cm increase in monthly precipitation at a 6-month lag. Conversely, dengue incidence increased by 43% (95% CrI 41%, 45%) for a 1 °C increase in monthly mean temperature at a 3-month lag. After accounting for covariates, the most significant high-risk spatial clusters were detected in the southern regions of Lao PDR. Probability analysis highlighted elevated trends in 45 districts, emphasizing the importance of targeted control strategies in high-risk areas. This research underscores the impact of climate and environmental factors on dengue transmission, emphasizing the need for proactive public health interventions tailored to specific contexts in Lao PDR.

A systematic review of the data, methods and environmental covariates used to map Aedes-borne arbovirus transmission risk

BACKGROUND

Aedes (Stegomyia)-borne diseases are an expanding global threat, but gaps in surveillance make comprehensive and comparable risk assessments challenging. Geostatistical models combine data from multiple locations and use links with environmental and socioeconomic factors to make predictive risk maps. Here we systematically review past approaches to map risk for different Aedes-borne arboviruses from local to global scales, identifying differences and similarities in the data types, covariates, and modelling approaches used.

METHODS

We searched on-line databases for predictive risk mapping studies for dengue, Zika, chikungunya, and yellow fever with no geographical or date restrictions. We included studies that needed to parameterise or fit their model to real-world epidemiological data and make predictions to new spatial locations of some measure of population-level risk of viral transmission (e.g. incidence, occurrence, suitability, etc.).

RESULTS

We found a growing number of arbovirus risk mapping studies across all endemic regions and arboviral diseases, with a total of 176 papers published 2002-2022 with the largest increases shortly following major epidemics. Three dominant use cases emerged: (i) global maps to identify limits of transmission, estimate burden and assess impacts of future global change, (ii) regional models used to predict the spread of major epidemics between countries and (iii) national and sub-national models that use local datasets to better understand transmission dynamics to improve outbreak detection and response. Temperature and rainfall were the most popular choice of covariates (included in 50% and 40% of studies respectively) but variables such as human mobility are increasingly being included. Surprisingly, few studies (22%, 31/144) robustly tested combinations of covariates from different domains (e.g. climatic, sociodemographic, ecological, etc.) and only 49% of studies assessed predictive performance via out-of-sample validation procedures.

CONCLUSIONS

Here we show that approaches to map risk for different arboviruses have diversified in response to changing use cases, epidemiology and data availability. We identify key differences in mapping approaches between different arboviral diseases, discuss future research needs and outline specific recommendations for future arbovirus mapping.

Predicting the dengue cluster outbreak dynamics in Yogyakarta, Indonesia: a modelling study

Background

Human mobility and climate conditions are recognised key drivers of dengue transmission, but their combined and individual role in the local spatiotemporal clustering of dengue cases is not well understood. This study investigated the effects of human mobility and weather conditions on dengue risk in an urban area in Yogyakarta, Indonesia.

Methods

We established a Bayesian spatiotemporal model for neighbourhood outbreak prediction and evaluated the performances of two different approaches for constructing an adjacency matrix: one based on geographical proximity and the other based on human mobility patterns. We used population, weather conditions, and past dengue cases as predictors using a flexible distributed lag approach. The human mobility data were estimated based on proxies from social media. Unseen data from February 2017 to January 2020 were used to estimate the one-month ahead prediction accuracy of the model.

Findings

When human mobility proxies were included in the spatial covariance structure, the model fit improved in terms of the log score (from 1.748 to 1.561) and the mean absolute error (from 0.676 to 0.522) based on the validation data. Additionally, showed only few observations outside the credible interval of predictions (1.48%) and weather conditions were not found to contribute additionally to the clustering of cases at this scale.

Interpretation

The study shows that it is possible to make highly accurate predictions of the within-city cluster dynamics of dengue using mobility proxies from social media combined with disease surveillance data. These insights are important for proactive and timely outbreak management of dengue.

Funding

Swedish Research Council Formas, Umeå Centre for Global Health Research, Swedish Council for Working Life and Social Research, Swedish research council VINNOVA and Alexander von Humboldt Foundation (Germany).

A joint Bayesian spatiotemporal risk prediction model of COVID-19 incidence, IC admission, and death with application to Sweden

The three closely related COVID-19 outcomes of incidence, intensive care (IC) admission and death, are commonly modelled separately leading to biased estimation of the parameters and relatively poor forecasts. This paper presents a joint spatiotemporal model of the three outcomes based on weekly data that is used for risk prediction and identification of hotspots. The paper applies a pure spatiotemporal model consisting of structured and unstructured spatial and temporal effects and their interaction capturing the effects of the unobserved covariates. The pure spatiotemporal model limits the data requirements to the three outcomes and the population at risk per spatiotemporal unit. The empirical study for the 21 Swedish regions for the period 1 January 2020-4 May 2021 confirms that the joint model predictions outperform the separate model predictions. The fifteen-week-ahead spatiotemporal forecasts (5 May-11 August 2021) show a significant decline in the relative risk of COVID-19 incidence, IC admission, death and number of hotspots.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00168-022-01191-1.

A Systematic Review on Modeling Methods and Influential Factors for Mapping Dengue-Related Risk in Urban Settings

Dengue fever is an acute mosquito-borne disease that mostly spreads within urban or semi-urban areas in warm climate zones. The dengue-related risk map is one of the most practical tools for executing effective control policies, breaking the transmission chain, and preventing disease outbreaks. Mapping risk at a small scale, such as at an urban level, can demonstrate the spatial heterogeneities in complicated built environments. This review aims to summarize state-of-the-art modeling methods and influential factors in mapping dengue fever risk in urban settings. Data were manually extracted from five major academic search databases following a set of querying and selection criteria, and a total of 28 studies were analyzed. Twenty of the selected papers investigated the spatial pattern of dengue risk by epidemic data, whereas the remaining eight papers developed an entomological risk map as a proxy for potential dengue burden in cities or agglomerated urban regions. The key findings included: (1) Big data sources and emerging data-mining techniques are innovatively employed for detecting hot spots of dengue-related burden in the urban context; (2) Bayesian approaches and machine learning algorithms have become more popular as spatial modeling tools for predicting the distribution of dengue incidence and mosquito presence; (3) Climatic and built environmental variables are the most common factors in making predictions, though the effects of these factors vary with the mosquito species; (4) Socio-economic data may be a better representation of the huge heterogeneity of risk or vulnerability spatial distribution on an urban scale. In conclusion, for spatially assessing dengue-related risk in an urban context, data availability and the purpose for mapping determine the analytical approaches and modeling methods used. To enhance the reliabilities of predictive models, sufficient data about dengue serotyping, socio-economic status, and spatial connectivity may be more important for mapping dengue-related risk in urban settings for future studies.

Post-pandemic COVID-19 estimated and forecasted hotspots in the Association of Southeast Asian Nations (ASEAN) countries in connection to vaccination rate

After a two-year pandemic, coronavirus disease 2019 (COVID-19) is still a serious public health problem and economic stability worldwide, particularly in the Association of Southeast Asian Nations (ASEAN) countries. The objective of this study was to identify the wave periods, provide an accurate space-time forecast of COVID-19 disease and its relationship to vaccination rates. We combined a hierarchical Bayesian pure spatiotemporal model and locally weighted scatterplot smoothing techniques to identify the wave periods and to provide weekly COVID-19 forecasts for the period 15 December 2021 to 5 January 2022 and to identify the relationship between the COVID-19 risk and the vaccination rate. We discovered that each ASIAN country had a unique COVID-19 time wave and duration. Additionally, we discovered that the number of COVID-19 cases was quite low and that no weekly hotspots were identified during the study period. The vaccination rate showed a nonlinear relationship with the COVID-19 risk, with a different temporal pattern for each ASEAN country. We reached the conclusion that vaccination, in comparison to other interventions, has a large influence over a longer time span.