Spatio-temporal clustering analysis of COVID-19 cases in Johor

At the end of the year 2019, a virus named SARS-CoV-2 induced the coronavirus disease, which is very contagious and quickly spread around the world. This new infectious disease is called COVID-19. Numerous areas, such as the economy, social services, education, and healthcare system, have suffered grave consequences from the invasion of this deadly virus. Thus, a thorough understanding of the spread of COVID-19 is required in order to deal with this outbreak before it becomes an infectious disaster. In this research, the daily reported COVID-19 cases in 92 sub-districts in Johor state, Malaysia, as well as the population size associated to each sub-district, are used to study the propagation of COVID-19 disease across space and time in Johor. The time frame of this research is about 190 days, which started from August 5, 2021, until February 10, 2022. The clustering technique known as spatio-temporal clustering, which considers the spatio-temporal metric was adapted to determine the hot-spot areas of the COVID-19 disease in Johor at the sub-district level. The results indicated that COVID-19 disease does spike in the dynamic populated sub-districts such as the state's economic centre (Bandar Johor Bahru), and during the festive season. These findings empirically prove that the transmission rate of COVID-19 is directly proportional to human mobility and the presence of holidays. On the other hand, the result of this study will help the authority in charge in stopping and preventing COVID-19 from spreading and become worsen at the national level.

Examining associations between social vulnerability indices and COVID-19 incidence and mortality with spatial-temporal Bayesian modeling

This study compares two social vulnerability indices, the U.S. CDC SVI and SoVI (the Social Vulnerability Index developed at the Hazards Vulnerability & Resilience Institute at the University of South Carolina), on their ability to predict the risk of COVID-19 cases and deaths. We utilize COVID-19 cases and deaths data for the state of Indiana from the Regenstrief Institute in Indianapolis, Indiana, from March 1, 2020, to March 31, 2021. We then aggregate the COVID-19 data to the census tract level, obtain the input variables, domains (components), and composite measures of both CDC SVI and SoVI data to create a Bayesian spatial-temporal ecological regression model. We compare the resulting spatial-temporal patterns and relative risk (RR) of SARS-CoV-2 infection (COVID-19 cases) and associated death. Results show there are discernable spatial-temporal patterns for SARS-CoV-2 infections and deaths with the largest contiguous hotspot for SARS-CoV-2 infections found in the southwest of the Indianapolis metropolitan area. We also observed one large contiguous hotspot for deaths that stretches across Indiana from the Cincinnati area in the southeast to just east and north of Terre Haute (southeast to west central). The spatial-temporal Bayesian model shows that a 1-percentile increase in CDC SVI was significantly (p ≤ 0.05) associated with an increased risk of SARS-CoV-2 infection by 6 % (RR = 1.06, 95 %CI = 1.04 -1.08). Whereas a 1-percentile increase in SoVI was significantly predicted to increase the risk of COVID-19 death by 45 % (RR = 1.45, 95 %CI =1.38 - 1.53). Domain-specific variables related to socioeconomic status, age, and race/ethnicity were shown to increase the risk of SARS-CoV-2 infections and deaths. There were notable differences in the relative risk estimates for SARS-CoV-2 infections and deaths when each of the two indices were incorporated in the model. Observed differences between the two social vulnerability indices and infection and death are likely due to alternative methodologies of formation and differences in input variables. The findings add to the growing literature on the relationship between social vulnerability and COVID-19 and further the development of COVID-19-specific vulnerability indices by illustrating the utility of local spatial-temporal analysis.

Psychosis prevalence in London neighbourhoods; A case study in spatial confounding

Analysis of impacts of neighbourhood risk factors on mental health outcomes frequently adopts a disease mapping approach, with unknown neighbourhood influences summarised by random effects. However, such effects may show confounding with observed predictors, especially when such predictors have a clear spatial pattern. Here, the standard disease mapping model is compared to methods which account and adjust for spatial confounding in an analysis of psychosis prevalence in London neighbourhoods. Established area risk factors such as area deprivation, non-white ethnicity, greenspace access and social fragmentation are considered as influences on psychosis. The results show evidence of spatial confounding in the standard disease mapping model. Impacts expected on substantive grounds and available evidence are either nullified or reversed in direction. It is argued that the potential for spatial confounding to affect inferences about geographic disease patterns and risk factors should be routinely considered in ecological studies of health based on disease mapping.

Relative risk of childhood and adolescence cancer in Iran: spatiotemporal analysis from 1999 to 2016

OBJECTIVE

Cancer is the third leading cause of death in the world with increasing trends in Iran. The study of epidemiology, trend, and geospatial distribution of pediatric cancers provides important information for screening as well as early detection of cancer and policy making. We aimed to assess the spatio-temporal disparity of childhood and adolescence cancer risk among provinces of Iran.

METHODS

In this retrospective study, we estimated geospatial relative risk (RR) of childhood cancer in provinces of Iran using data from 29198 cases. We used BYM and its extended spatiotemporal model in Bayesian setting. This hierarchical model takes spatial and temporal effects into account in the incidence rate estimation simultaneously.

RESULTS

The relative risk of cancer was > 1 for 45% of the provinces, where 27% of provinces had significantly ascending trend. North Khorasan, Yazd and Qazvin provinces had the highest risk rates while Sistan-Baluchistan province showed the lowest risk of cancer. However, the differential trends was highest in Sistan-Baluchistan, Bushehr, Hormozgan, and Kohgilouyeh-Boyerahmad. Both the point estimate and the trend of risk was high in Tehran.

CONCLUSION

The geographic pattern and trend of cancer in children seems to be different from that in adults that urges further studies. This could lead to increased health system capacity and facilitate the access to effective detection, research, care and treatment of childhood cancer.

Mapping the prevalence of cancer risk factors at the small area level in Australia

BACKGROUND

Cancer is a significant health issue globally and it is well known that cancer risk varies geographically. However in many countries there are no small area-level data on cancer risk factors with high resolution and complete reach, which hinders the development of targeted prevention strategies.

METHODS

Using Australia as a case study, the 2017-2018 National Health Survey was used to generate prevalence estimates for 2221 small areas across Australia for eight cancer risk factor measures covering smoking, alcohol, physical activity, diet and weight. Utilising a recently developed Bayesian two-stage small area estimation methodology, the model incorporated survey-only covariates, spatial smoothing and hierarchical modelling techniques, along with a vast array of small area-level auxiliary data, including census, remoteness, and socioeconomic data. The models borrowed strength from previously published cancer risk estimates provided by the Social Health Atlases of Australia. Estimates were internally and externally validated.

RESULTS

We illustrated that in 2017-2018 health behaviours across Australia exhibited more spatial disparities than previously realised by improving the reach and resolution of formerly published cancer risk factors. The derived estimates revealed higher prevalence of unhealthy behaviours in more remote areas, and areas of lower socioeconomic status; a trend that aligned well with previous work.

CONCLUSIONS

Our study addresses the gaps in small area level cancer risk factor estimates in Australia. The new estimates provide improved spatial resolution and reach and will enable more targeted cancer prevention strategies at the small area level. Furthermore, by including the results in the next release of the Australian Cancer Atlas, which currently provides small area level estimates of cancer incidence and relative survival, this work will help to provide a more comprehensive picture of cancer in Australia by supporting policy makers, researchers, and the general public in understanding the spatial distribution of cancer risk factors. The methodology applied in this work is generalisable to other small area estimation applications and has been shown to perform well when the survey data are sparse.

Understanding the spread of infectious diseases in edge areas of hotspots: dengue epidemics in tropical metropolitan regions

Identifying clusters or hotspots from disease maps is critical in research and practice. Hotspots have been shown to have a higher potential for transmission risk and may be the source of infections, making them a priority for controlling epidemics. However, the role of edge areas of hotspots in disease transmission remains unclear. This study aims to investigate the role of edge areas in disease transmission by examining whether disease incidence rate growth is higher in the edges of disease hotspots during outbreaks. Our data is based on the three most severe dengue epidemic years in Kaohsiung city, Taiwan, from 1998 to 2020. We employed conditional autoregressive (CAR) models and Bayesian areal Wombling methods to identify significant edge areas of hotspots based on the extent of risk difference between adjacent areas. The difference-in-difference (DID) estimator in spatial panel models measures the growth rate of risk by comparing the incidence rate between two groups (hotspots and edge areas) over two time periods. Our results show that in years characterized by exceptionally large-scale outbreaks, the edge areas of hotspots have a more significant increase in disease risk than hotspots, leading to a higher risk of disease transmission and potential disease foci. This finding explains the geographic diffusion mechanism of epidemics, a pattern mixed with expansion and relocation, indicating that the edge areas play an essential role. The study highlights the importance of considering edge areas of hotspots in disease transmission. Furthermore, it provides valuable insights for policymakers and health authorities in designing effective interventions to control large-scale disease outbreaks.

Joint spatial modeling of the risks of co-circulating mosquito-borne diseases in Ceará, Brazil

Mosquito-borne diseases such as dengue and chikungunya have been co-circulating in the Americas, causing great damage to the population. In 2021, for instance, almost 1.5 million cases were reported on the continent, being Brazil the responsible for most of them. Even though they are transmitted by the same mosquito, it remains unclear whether there exists a relationship between both diseases. In this paper, we model the geographic distributions of dengue and chikungunya over the years 2016 to 2021 in the Brazilian state of Ceará. We use a Bayesian hierarchical spatial model for the joint analysis of two arboviruses that includes spatial covariates as well as specific and shared spatial effects that take into account the potential autocorrelation between the two diseases. Our findings allow us to identify areas with high risk of one or both diseases. Only 7% of the areas present high relative risk for both diseases, which suggests a competition between viruses. This study advances the understanding of the geographic patterns and the identification of risk factors of dengue and chikungunya being able to help health decision-making.

Spatial Difference Boundary Detection for Multiple Outcomes Using Bayesian Disease Mapping

Regional aggregates of health outcomes over delineated administrative units (e.g., states, counties, and zip codes), or areal units, are widely used by epidemiologists to map mortality or incidence rates and capture geographic variation. To capture health disparities over regions, we seek "difference boundaries" that separate neighboring regions with significantly different spatial effects. Matters are more challenging with multiple outcomes over each unit, where we capture dependence among diseases as well as across the areal units. Here, we address multivariate difference boundary detection for correlated diseases. We formulate the problem in terms of Bayesian pairwise multiple comparisons and seek the posterior probabilities of neighboring spatial effects being different. To achieve this, we endow the spatial random effects with a discrete probability law using a class of multivariate areally referenced Dirichlet process models that accommodate spatial and interdisease dependence. We evaluate our method through simulation studies and detect difference boundaries for multiple cancers using data from the Surveillance, Epidemiology, and End Results Program of the National Cancer Institute.

Space-time modelling of monthly malaria incidence for seasonal associated drivers and early epidemic detection in Southern Ethiopia

BACKGROUND

Although Ethiopia has made great strides in recent years to reduce the threat of malaria, the disease remains a significant issue in most districts of the country. It constantly disappears in parts of the areas before reappearing in others with erratic transmission rates. Thus, developing a malaria epidemic early warning system is important to support the prevention and control of the incidence.

METHODS

Space-time malaria risk mapping is essential to monitor and evaluate priority zones, refocus intervention, and enable planning for future health targets. From August 2013 to May 2019, the researcher considered an aggregated count of genus Plasmodium falciparum from 149 districts in Southern Ethiopia. Afterwards, a malaria epidemic early warning system was developed using model-based geostatistics, which helped to chart the disease's spread and future management.

RESULTS

Risk factors like precipitation, temperature, humidity, and nighttime light are significantly associated with malaria with different rates across the districts. Districts in the southwest, including Selamago, Bero, and Hamer, had higher rates of malaria risk, whereas in the south and centre like Arbaminch and Hawassa had moderate rates. The distribution is inconsistent and varies across time and space with the seasons.

CONCLUSION

Despite the importance of spatial correlation in disease risk mapping, it may occasionally be a good idea to generate epidemic early warning independently in each district to get a quick picture of disease risk. A system like this is essential for spotting numerous inconsistencies in lower administrative levels early enough to take corrective action before outbreaks arise.

Bayesian spatiotemporal modelling for disease mapping: an application to preeclampsia and gestational diabetes in Florida, United States

Morbidities generally show patterns of concentration that vary by space and time. Disease mapping models are useful in estimating the spatiotemporal patterns of disease risks and are therefore pivotal for effective disease surveillance, resource allocation, and the development of prevention strategies. This study considers six spatiotemporal Bayesian hierarchical models based on two spatial conditional autoregressive priors. It could serve as a guideline on the development and application of Bayesian hierarchical models to assess the emerging risk trends, risk clustering, and spatial inequality trends, with estimation of covariables' effects on the interested disease risk. The method is applied to the Florida Birth Record data between 2006 and 2015 to study two cardiovascular risk factors: preeclampsia and gestational diabetes. High-risk clusters were detected in North Central Florida for preeclampsia and in Central Florida for gestational diabetes. While the adjusted disease trend was stable, spatial inequality peaked in 2011-2012 for both diseases. Exposure to PM2.5 at first or/and second trimester increased the risk of preeclampsia and gestational diabetes, but the magnitude is less severe compared to previous studies. In conclusion, this study underscores the significance of selecting appropriate disease mapping models in estimating the intricate spatiotemporal patterns of disease risk and suggests the importance of localized interventions to reduce health disparities. The result also identified an opportunity to study potential risk factors of preeclampsia, as the spike of risk in North Central Florida cannot be explained by current covariables.

Spatio-temporal evaluation of respiratory disease based on the information provided by patients admitted to a medical college hospital in Bangladesh using geographic information system

In Bangladesh respiratory illnesses are one of the leading risk factors for death and disability. Limited access to healthcare services, indoor and outdoor air pollution, large-scale use of smoking materials, allergens, and lack of awareness are among the known leading factors contributing to respiratory illness in Bangladesh. Key initiatives taken by the government to handle respiratory illnesses include, changing of respiratory health policy, building awareness, enhancing healthcare facility, and promoting prevention measures. Despite all these efforts, the number of individuals suffering from respiratory diseases has increased steadily during the recent years. This study aims at examining the distribution pattern of respiratory diseases over space and time using Geographic Information System, which is expected to contribute to the better understand of the factors contributing to respiratory illness development. To achieve the aims of the study two interviews were conducted among patients with respiratory sickness in the medicine and respiratory medicine units of Rajshahi Medical College Hospital between January and April of 2019 and 2020 following the guidelines provided by the Ethics Committee, Department of Geography and Environmental Studies, University of Rajshahi, Bangladesh (ethical approval reference number: 2018/08). Principal component extraction and spatial statistical analyses were performed to identify the key respiratory illnesses and their geographical distribution pattern respectively. The results indicate, during January-February the number of patients was a lot higher compared to March-April. The patients were hospitalized mainly due to four respiratory diseases (chronic obstructive pulmonary disease, asthma, pneumonia, and pulmonary hypertension). Geographical distribution pattern of respiratory disease cases also varied considerably between the years as well as months of the years. This information seems reasonable to elucidate the spatio-temporal distribution of respiratory disease and thus improve the existing prevention, control, and cure practices of respiratory illness of the study area. Approach used in this study to elicit spatio-temporal distribution of repertory disease can easily be implemented in other areas with similar geographical settings and patients' illness information from hospital.

A practical illustration of spatial smoothing methods for disconnected regions with INLA: spatial survey on overweight and obesity in Malaysia

BACKGROUND

National prevalence could mask subnational heterogeneity in disease occurrence, and disease mapping is an important tool to illustrate the spatial pattern of disease. However, there is limited information on techniques for the specification of conditional autoregressive models in disease mapping involving disconnected regions. This study explores available techniques for producing district-level prevalence estimates for disconnected regions, using as an example childhood overweight in Malaysia, which consists of the Peninsular and Borneo regions separated by the South China Sea. We used data from Malaysia National Health and Morbidity Survey conducted in 2015. We adopted Bayesian hierarchical modelling using the integrated nested Laplace approximation (INLA) program in R-software to model the spatial distribution of overweight among 6301 children aged 5-17 years across 144 districts located in two disconnected regions. We illustrate different types of spatial models for prevalence mapping across disconnected regions, taking into account the survey design and adjusting for district-level demographic and socioeconomic covariates.

RESULTS

The spatial model with split random effects and a common intercept has the lowest Deviance and Watanabe Information Criteria. There was evidence of a spatial pattern in the prevalence of childhood overweight across districts. An increasing trend in smoothed prevalence of overweight was observed when moving from the east to the west of the Peninsular and Borneo regions. The proportion of Bumiputera ethnicity in the district had a significant negative association with childhood overweight: the higher the proportion of Bumiputera ethnicity in the district, the lower the prevalence of childhood overweight.

CONCLUSION

This study illustrates different available techniques for mapping prevalence across districts in disconnected regions using survey data. These techniques can be utilized to produce reliable subnational estimates for any areas that comprise of disconnected regions. Through the example, we learned that the best-fit model was the one that considered the separate variations of the individual regions. We discovered that the occurrence of childhood overweight in Malaysia followed a spatial pattern with an east-west gradient trend, and we identified districts with high prevalence of overweight. This information could help policy makers in making informed decisions for targeted public health interventions in high-risk areas.

Spatial distribution of hospital admissions for asthma in the central area of Asturias, Northern Spain

BACKGROUND

Asturias is one of the communities with the highest rates of hospital admission for asthma in Spain. The environmental pollution or people lifestyle are some of the factors that contribute to the appearance or aggravation of this illness. The aim of this study was to show the spatial distribution of asthma admissions risks in the central municipalities of Asturias and to analyze the observed spatial patterns.

METHODS

Urgent hospital admissions for asthma and status asthmaticus occurred between 2016 to 2018 on the public hospitals of the central area of Asturias were used. Population data were assigned in 5 age groups. Standardised admission ratio (SAR), smoothed relative risk (SRR) and posterior risk probability (PP) were calculated for each census tract (CT). A spatial trend analysis was run, a spatial autocorrelation index (Morans I) was calculated and a cluster and outlier analysis (Anselin Local Morans I) was finally performed in order to analyze spatial clusters.

RESULTS

The total number of hospital urgent asthma admissions during the study period was 2324, 1475 (63.46%) men and 849 (36.56%) women. The municipalities with the highest values of SRR and PP were located on the northwest area: Avilés, Gozón, Carreño, Corvera de Asturias, Castrillón and Illas. A high risk cluster was found for the municipalities of Avilés, Gozón y Corvera de Asturias.

CONCLUSIONS

The spatial analysis showed high risk of hospitalization for asthma on the municipalities of the northwest area of the study, which highlight the existence of spatial inequalities on the distribution of urgent hospital admissions.

Narrative minireview of the spatial epidemiology of substance use disorder in the United States: Who is at risk and where?

Drug overdose is the leading cause of death by injury in the United States. The incidence of substance use disorder (SUD) in the United States has increased steadily over the past two decades, becoming a major public health problem for the country. The drivers of the SUD epidemic in the United States have changed over time, characterized by an initial heroin outbreak between 1970 and 1999, followed by a painkiller outbreak, and finally by an ongoing synthetic opioid outbreak. The nature and sources of these abused substances reveal striking differences in the socioeconomic and behavioral factors that shape the drug epidemic. Moreover, the geospatial distribution of the SUD epidemic is not homogeneous. The United States has specific locations where vulnerable communities at high risk of SUD are concentrated, reaffirming the multifactorial socioeconomic nature of this epidemic. A better understanding of the SUD epidemic under a spatial epidemiology framework is necessary to determine the factors that have shaped its spread and how these patterns can be used to predict new outbreaks and create effective mitigation policies. This narrative minireview summarizes the current records of the spatial distribution of the SUD epidemic in the United States across different periods, revealing some spatiotemporal patterns that have preceded the occurrence of outbreaks. By analyzing the epidemic of SUD-related deaths, we also describe the epidemic behavior in areas with high incidence of cases. Finally, we describe public health interventions that can be effective for demographic groups, and we discuss future challenges in the study and control of the SUD epidemic in the country.

Spatial distribution of unscheduled hospital admissions for chronic obstructive pulmonary disease in the central area of Asturias, Spain

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is one of the major causes of mortality worldwide and also reports high morbidity rates and the global burden COPD has continued to rise over the last several decades. The best-known COPD risk factors are tobacco smoke and air pollution, but genetics, age, sex, and socioeconomic status are additional factors. This study aimed to assess the spatial distribution of unscheduled COPD hospital admissions of men and women in the central area of Asturias during 2016-2018 and identify trends, spatial patterns, or clusters in the area.

METHODS

Unscheduled COPD hospital admissions in the central area of Asturias were registered, geocoded, and grouped by census tracts (CTs), age, and sex. Standardized admission ratio, smoothed relative risk, posterior risk probability, and spatial clusters between relative risks throughout the study area were calculated and mapped.

RESULTS

The spatial distribution of COPD hospital admissions differed between men and women. For men, high-risk values were located primarily in the northwestern area of the study, whereas for women the cluster pattern was not as clear and high-risk CTs also reached central and southern areas. In both men and women, the north-northwest area included the majority of CTs with high-risk values.

CONCLUSIONS

The present study showed the existence of a spatial distribution pattern of unscheduled COPD hospital admissions in the central area of Asturias that was more pronounced for men than for women. This study could provide a starting point for generating knowledge about COPD epidemiology in Asturias.

Computational network analysis of host genetic risk variants of severe COVID-19

BACKGROUND

Genome-wide association studies have identified numerous human host genetic risk variants that play a substantial role in the host immune response to SARS-CoV-2. Although these genetic risk variants significantly increase the severity of COVID-19, their influence on body systems is poorly understood. Therefore, we aim to interpret the biological mechanisms and pathways associated with the genetic risk factors and immune responses in severe COVID-19. We perform a deep analysis of previously identified risk variants and infer the hidden interactions between their molecular networks through disease mapping and the similarity of the molecular functions between constructed networks.

RESULTS

We designed a four-stage computational workflow for systematic genetic analysis of the risk variants. We integrated the molecular profiles of the risk factors with associated diseases, then constructed protein-protein interaction networks. We identified 24 protein-protein interaction networks with 939 interactions derived from 109 filtered risk variants in 60 risk genes and 56 proteins. The majority of molecular functions, interactions and pathways are involved in immune responses; several interactions and pathways are related to the metabolic and cardiovascular systems, which could lead to multi-organ complications and dysfunction.

CONCLUSIONS

This study highlights the importance of analyzing molecular interactions and pathways to understand the heterogeneous susceptibility of the host immune response to SARS-CoV-2. We propose new insights into pathogenicity analysis of infections by including genetic risk information as essential factors to predict future complications during and after infection. This approach may assist more precise clinical decisions and accurate treatment plans to reduce COVID-19 complications.

An integrated abundance model for estimating county-level prevalence of opioid misuse in Ohio

Opioid misuse is a national epidemic and a significant drug related threat to the United States. While the scale of the problem is undeniable, estimates of the local prevalence of opioid misuse are lacking, despite their importance to policy-making and resource allocation. This is due, in part, to the challenge of directly measuring opioid misuse at a local level. In this paper, we develop a Bayesian hierarchical spatio-temporal abundance model that integrates indirect county-level data on opioid-related outcomes with state-level survey estimates on prevalence of opioid misuse to estimate the latent county-level prevalence and counts of people who misuse opioids. A simulation study shows that our integrated model accurately recovers the latent counts and prevalence. We apply our model to county-level surveillance data on opioid overdose deaths and treatment admissions from the state of Ohio. Our proposed framework can be applied to other applications of small area estimation for hard to reach populations, which is a common occurrence with many health conditions such as those related to illicit behaviors.

Combining school-catchment area models with geostatistical models for analysing school survey data from low-resource settings: Inferential benefits and limitations

School-based sampling has been used to inform targeted responses for malaria and neglected tropical diseases. Standard geostatistical methods for mapping disease prevalence use the school location to model spatial correlation, which is questionable since exposure to the disease is more likely to occur in the residential location. In this paper, we propose to overcome the limitations of standard geostatistical methods by introducing a modelling framework that accounts for the uncertainty in the location of the residence of the students. By using cost distance and cost allocation models to define spatial accessibility and in absence of any information on the travel mode of students to school, we consider three school catchment area models that assume walking only, walking and bicycling and, walking and motorized transport. We illustrate the use of this approach using two case studies of malaria in Kenya and compare it with the standard approach that uses the school locations to build geostatistical models. We argue that the proposed modelling framework presents several inferential benefits, such as the ability to combine data from multiple surveys some of which may also record the residence location, and to deal with ecological bias when estimating the effects of malaria risk factors. However, our results show that invalid assumptions on the modes of travel to school can worsen the predictive performance of geostatistical models. Future research in this area should focus on collecting information on the modes of transportation to school which can then be used to better parametrize the catchment area models.

Spatio-temporal small area surveillance of the COVID-19 pandemic

The emergence of COVID-19 requires new effective tools for epidemiological surveillance. Spatio-temporal disease mapping models, which allow dealing with small units of analysis, are a priority in this context. These models provide geographically detailed and temporally updated overviews of the current state of the pandemic, making public health interventions more effective. These models also allow estimating epidemiological indicators highly demanded for COVID-19 surveillance, such as the instantaneous reproduction number R t , even for small areas. In this paper, we propose a new spatio-temporal spline model particularly suited for COVID-19 surveillance, which allows estimating and monitoring R t for small areas. We illustrate our proposal on the study of the disease pandemic in two Spanish regions. As a result, we show how tourism flows have shaped the spatial distribution of the disease in these regions. In these case studies, we also develop new epidemiological tools to be used by regional public health services for small area surveillance.

Space-time interactions in Bayesian disease mapping with recent tools: Making things easier for practitioners

Spatio-temporal disease mapping studies the distribution of mortality or incidence risks in space and its evolution in time, and it usually relies on fitting hierarchical Poisson mixed models. These models are complex for practitioners as they generally require adding constraints to correctly identify and interpret the different model terms. However, including constraints may not be straightforward in some recent software packages. This paper focuses on NIMBLE, a library of algorithms that contains among others a configurable system for Markov chain Monte Carlo (MCMC) algorithms. In particular, we show how to fit different spatio-temporal disease mapping models with NIMBLE making emphasis on how to include sum-to-zero constraints to solve identifiability issues when including spatio-temporal interactions. Breast cancer mortality data in Spain during the period 1990-2010 is used for illustration purposes. A simulation study is also conducted to compare NIMBLE with R-INLA in terms of parameter estimates and relative risk estimation. The results are very similar but differences are observed in terms of computing time.

Regional now- and forecasting for data reported with delay: toward surveillance of COVID-19 infections

Governments around the world continue to act to contain and mitigate the spread of COVID-19. The rapidly evolving situation compels officials and executives to continuously adapt policies and social distancing measures depending on the current state of the spread of the disease. In this context, it is crucial for policymakers to have a firm grasp on what the current state of the pandemic is, and to envision how the number of infections is going to evolve over the next days. However, as in many other situations involving compulsory registration of sensitive data, cases are reported with delay to a central register, with this delay deferring an up-to-date view of the state of things. We provide a stable tool for monitoring current infection levels as well as predicting infection numbers in the immediate future at the regional level. We accomplish this through nowcasting of cases that have not yet been reported as well as through predictions of future infections. We apply our model to German data, for which our focus lies in predicting and explain infectious behavior by district.

Identifying extreme COVID-19 mortality risks in English small areas: a disease cluster approach

The COVID-19 pandemic is having a huge impact worldwide and has highlighted the extent of health inequalities between countries but also in small areas within a country. Identifying areas with high mortality is important both of public health mitigation in COVID-19 outbreaks, and of longer term efforts to tackle social inequalities in health. In this paper we consider different statistical models and an extension of a recent method to analyze COVID-19 related mortality in English small areas during the first wave of the epidemic in the first half of 2020. We seek to identify hotspots, and where they are most geographically concentrated, taking account of observed area factors as well as spatial correlation and clustering in regression residuals, while also allowing for spatial discontinuities. Results show an excess of COVID-19 mortality cases in small areas surrounding London and in other small areas in North-East and and North-West of England. Models alleviating spatial confounding show ethnic isolation, air quality and area morbidity covariates having a significant and broadly similar impact on COVID-19 mortality, whereas nursing home location seems to be slightly less important.

Identifying extreme COVID-19 mortality risks in English small areas: a disease cluster approach

The COVID-19 pandemic is having a huge impact worldwide and has highlighted the extent of health inequalities between countries but also in small areas within a country. Identifying areas with high mortality is important both of public health mitigation in COVID-19 outbreaks, and of longer term efforts to tackle social inequalities in health. In this paper we consider different statistical models and an extension of a recent method to analyze COVID-19 related mortality in English small areas during the first wave of the epidemic in the first half of 2020. We seek to identify hotspots, and where they are most geographically concentrated, taking account of observed area factors as well as spatial correlation and clustering in regression residuals, while also allowing for spatial discontinuities. Results show an excess of COVID-19 mortality cases in small areas surrounding London and in other small areas in North-East and and North-West of England. Models alleviating spatial confounding show ethnic isolation, air quality and area morbidity covariates having a significant and broadly similar impact on COVID-19 mortality, whereas nursing home location seems to be slightly less important.

Assessment of Cystic Fibrosis Distribution Based on Air Pollution by Geographical Information System (GIS)

BACKGROUND

It is widely accepted that concerns have been recently raised regarding the impact of air pollution on the health of children with cystic fibrosis (CF). Air pollution probably affects the exacerbation of CF and its laboratory findings. On the other hand, the World Health Organization (WHO) has asked all countries to update their data and reports on the distribution and prevalence of CF in different areas. The purpose of the present study was to investigate the distribution and prevalence of CF based on the levels of atmospheric pollutants, such as PM₁₀, PM_2.5, SO₂, NO₂, CO, and O₃ in 22 zones of Tehran, and to report the abnormal laboratory findings that might indicate the exacerbation of CF.

MATERIALS AND METHODS

The studied statistical population included children with CF referred to Masih Daneshvari Hospital from 2003 to 2020. Demographic data, location of living area, and laboratory findings were extracted from patient records. The geographic information system (GIS) was applied to indicate the distribution and dispersion of the disease. The information related to air pollutants was collected from all stations in Tehran during the studied period by the Department of Environment of Tehran Province, and the average levels were used for final reporting.

RESULTS

The analysis results on 287 CF patients demonstrated that the risk of disease exacerbation significantly increased by the presence of air pollutants. In areas with multiple air pollutants, more laboratory findings were observed to be abnormal, and the lower survival rate for patients with CF was recorded. Investigating the CF distribution pattern based on climatic layers and above mean sea level (AMSL) indicated that distribution of the disease was higher in dry areas with lower AMSL and the higher volume of the atmospheric pollutants, which were primarily centralized in southern and central Tehran.

CONCLUSION

Environmental factors, such as air pollution, can be considered vital parameters, along with high-risk factors, such as pure and integrated race, migration, and mutation, influencing the prevalence and exacerbation of CF symptoms. Considering the higher prevalence of CF in deprived areas of Tehran, households' cultural and economic level appears to be a factor in the lack of diagnostic screening and prevention of CF in these areas. On the other hand, continuous monitoring of the air pollution caused by traffic and giving warnings to CF patients and their parents is particularly important.

Spatio-temporal modeling for confirmed cases of lyme disease in Virginia

Epidemiological data often include characteristics such as spatial and/or temporal dependencies and excess zero counts, which pose modeling challenges. Excess zeros in such data may arise from imperfect detection and/or relative rareness of the disease in a given location. Here, we studied the spatio-temporal variation in annual Lyme disease cases in Virginia from 2001-2016 and modeled the disease with a spatio-temporal hierarchical Bayesian model. Using observed ecological and environmental covariates, we constructed a predictive model for the disease spread over space and time, including spatial and temporal random effects. We considered several different models and found that the negative binomial hurdle model performs the best for such epidemiological data. Among the various ecological predictors, the North-South (V component) of winds and relative humidity significantly contributed to predicting the Lyme cases. Our model results provide important insights on the spread of the disease in Virginia and the proposed modeling framework offers epidemiologists and health policymakers a useful tool for improving disease preparedness and control plans for the future.

Associated health and social determinants of mobile populations across HIV epidemic gradients in Southern Africa

Background

Growing travel connectivity and economic development have dramatically increased the magnitude of human mobility in Africa. In public health, vulnerable population groups such as mobile individuals are at an elevated risk of sexually transmitted diseases, including HIV.

Methods

The population-based Demographic Health Survey data of five Southern African countries with different HIV epidemic intensities (Angola, Malawi, South Africa, Zambia, and Zimbabwe) were used to investigate the association between HIV serostatus and population mobility adjusting for socio-demographic, sexual behavior and spatial covariates.

Results

Mobility was associated with HIV seropositive status only in Zimbabwe (adjusted odds ratio [AOR] = 1.37 [95% confidence interval [CI]: 1.01–1.67]). These associations were not significant in Angola, Malawi, South Africa, and Zambia. Females had higher odds of mobility than males in Zimbabwe (AOR = 1.37, CI: 1.10–1.69). The odds of mobility decreased with age in all five countries.

Conclusions

Our findings highlight the heterogeneity of the social and health determinants of mobile populations in several countries with different HIV epidemic intensities. Effective interventions using precise geographic focus combined with detailed attribute characterization of mobile populations can enhance their impact especially in areas with high density of mobile individuals and high HIV prevalence.

Spatial epidemiology of diabetes: Methods and insights

Diabetes mellitus (DM) is a growing epidemic with global proportions. It is estimated that in 2019, 463 million adults aged 20-79 years were living with DM. The latest evidence shows that DM continues to be a significant global health challenge and is likely to continue to grow substantially in the next decades, which would have major implications for healthcare expenditures, particularly in developing countries. Hence, new conceptual and methodological approaches to tackle the epidemic are long overdue. Spatial epidemiology has been a successful approach to control infectious disease epidemics like malaria and human immunodeficiency virus. The implementation of this approach has been expanded to include the study of non-communicable diseases like cancer and cardiovascular diseases. In this review, we discussed the implementation and use of spatial epidemiology and Geographic Information Systems to the study of DM. We reviewed several spatial methods used to understand the spatial structure of the disease and identify the potential geographical drivers of the spatial distribution of DM. Finally, we discussed the use of spatial epidemiology on the design and implementation of geographically targeted prevention and treatment interventions against DM.

Epidemiological characteristics and initial spatiotemporal visualisation of COVID-19 in a major city in the Middle East

Background

The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) emerged initially in China in December 2019 causing the COVID-19 disease, which quickly spread worldwide. Iran was one of the first countries outside China to be affected in a major way and is now under the spell of a fourth wave. This study aims to investigate the epidemiological characteristics of COVID-19 cases in north-eastern Iran through mapping the spatiotemporal trend of the disease.

Methods

The study comprises data of 4000 patients diagnosed by laboratory assays or clinical investigation from the beginning of the disease on Feb 14, 2020, until May 11, 2020. Epidemiological features and spatiotemporal trends of the disease in the study area were explored by classical statistical approaches and Geographic Information Systems.

Results

Most common symptoms were dyspnoea (69.4%), cough (59.4%), fever (54.4%) and weakness (19.5%). Approximately 82% of those who did not survive suffered from dyspnoea. The highest Case Fatality Rate (CFR) was related to those with cardiovascular disease (27.9%) and/or diabetes (18.1%). Old age (≥60 years) was associated with an almost five-fold increased CFR. Odds Ratio (OR) showed malignancy (3.8), nervous diseases (2.2), and respiratory diseases (2.2) to be significantly associated with increased CFR with developments, such as hospitalization at the ICU (2.9) and LOS (1.1) also having high correlations. Furthermore, spatial analyses revealed a geographical pattern in terms of both incidence and mortality rates, with COVID-19 first being observed in suburban areas from where the disease swiftly spread into downtown reaching a peak between 25 February to 06 March (4 incidences per km²). Mortality peaked 3 weeks later after which the infection gradually decreased. Out of patients investigated by the spatiotemporal approach (n = 727), 205 (28.2%) did not survive and 66.8% of them were men.

Conclusions

Older adults and people with severe co-morbidities were at higher risk for developing serious complications due to COVID-19. Applying spatiotemporal methods to identify the transmission trends and high-risk areas can rapidly be documented, thereby assisting policymakers in designing and implementing tailored interventions to control and prevent not only COVID-19 but also other rapidly spreading epidemics/pandemics.

Geospatial analysis, web-based mapping and determinants of prostate cancer incidence in Georgia counties: evidence from the 2012-2016 SEER data

Background

Prostate cancer (CaP) cases are high in the United States. According to the American Cancer Society, there are an estimated number of 174,650 CaP new cases in 2019. The estimated number of deaths from CaP in 2019 is 31,620, making CaP the second leading cause of cancer deaths among American men with lung cancer been the first. Our goal is to estimate and map prostate cancer relative risk, with the ultimate goal of identifying counties at higher risk where interventions and further research can be targeted.

Methods

The 2012–2016 Surveillance, Epidemiology, and End Results (SEER) Program data was used in this study. Analyses were conducted on 159 Georgia counties. The outcome variable is incident prostate cancer. We employed a Bayesian geospatial model to investigate both measured and unmeasured spatial risk factors for prostate cancer. We visualised the risk of prostate cancer by mapping the predicted relative risk and exceedance probabilities. We finally developed interactive web-based maps to guide optimal policy formulation and intervention strategies.

Results

Number of persons above age 65 years and below poverty, higher median family income, number of foreign born and unemployed were risk factors independently associated with prostate cancer risk in the non-spatial model. Except for the number of foreign born, all these risk factors were also significant in the spatial model with the same direction of effects. Substantial geographical variations in prostate cancer incidence were found in the study. The predicted mean relative risk was 1.20 with a range of 0.53 to 2.92. Individuals residing in Towns, Clay, Union, Putnam, Quitman, and Greene counties were at increased risk of prostate cancer incidence while those residing in Chattahoochee were at the lowest risk of prostate cancer incidence.

Conclusion

Our results can be used as an effective tool in the identification of counties that require targeted interventions and further research by program managers and policy makers as part of an overall strategy in reducing the prostate cancer burden in Georgia State and the United States as a whole.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08254-0.

Dynamics of the COVID-19 epidemic in urban and rural areas in the United States

Purpose

There is a growing concern about the COVID-19 epidemic intensifying in rural areas in the United States (U.S.). In this study, we described the dynamics of COVID-19 cases and deaths in rural and urban counties in the U.S.

Methods

Using data from April 1 to November 12, 2020, from Johns Hopkins University, we estimated COVID-19 incidence and mortality rates and conducted comparisons between urban and rural areas in three time periods at the national level, and in states with higher and lower COVID-19 incidence rates.

Results

Results at the national level showed greater COVID-19 incidence rates in urban compared to rural counties in the Northeast and Mid-Atlantic regions of the U.S. at the beginning of the epidemic. However, the intensity of the epidemic has shifted to a rapid surge in rural areas. In particular, high incidence states located in the Mid-west of the country had more than 3,400 COVID-19 cases per 100,000 people compared to 1,284 cases per 100,000 people in urban counties nationwide during the third period (August 30 to November 12).

Conclusions

Overall, the current epicenter of the epidemic is located in states with higher infection rates and mortality in rural areas. Infection prevention and control efforts including healthcare capacity should be scaled up in these vulnerable rural areas.

Software application profile: the Rapid Inquiry Facility 4.0: an open access tool for environmental public health tracking

The Rapid Inquiry Facility 4.0 (RIF) is a new user-friendly and open-access tool, developed by the UK Small Area Health Statistics Unit (SAHSU), to facilitate environment public health tracking (EPHT) or surveillance (EPHS). The RIF is designed to help public health professionals and academics to rapidly perform exploratory investigations of health and environmental data at the small-area level (e.g. postcode or detailed census areas) in order to identify unusual signals, such as disease clusters and potential environmental hazards, whether localized (e.g. industrial site) or widespread (e.g. air and noise pollution). The RIF allows the use of advanced disease mapping methods, including Bayesian small-area smoothing and complex risk analysis functionalities, while accounting for confounders. The RIF could be particularly useful to monitor spatio-temporal trends in mortality and morbidity associated with cardiovascular diseases, cancers, diabetes and chronic lung diseases, or to conduct local or national studies on air pollution, flooding, low-magnetic fields or nuclear power plants.

A hierarchical spatio-temporal model to analyze relative risk variations of COVID-19: a focus on Spain, Italy and Germany

The novel coronavirus disease (COVID-19) has spread rapidly across the world in a short period of time and with a heterogeneous pattern. Understanding the underlying temporal and spatial dynamics in the spread of COVID-19 can result in informed and timely public health policies. In this paper, we use a spatio-temporal stochastic model to explain the temporal and spatial variations in the daily number of new confirmed cases in Spain, Italy and Germany from late February 2020 to mid January 2021. Using a hierarchical Bayesian framework, we found that the temporal trends of the epidemic in the three countries rapidly reached their peaks and slowly started to decline at the beginning of April and then increased and reached their second maximum in the middle of November. However decline and increase of the temporal trend seems to show different patterns in Spain, Italy and Germany.

Beyond standardized mortality ratios; some uses of smoothed age-specific mortality rates on small areas studies

Background

Most epidemiological risk indicators strongly depend on the age composition of populations, which makes the direct comparison of raw (unstandardized) indicators misleading because of the different age structures of the spatial units of study. Age-standardized rates (ASR) are a common solution for overcoming this confusing effect. The main drawback of ASRs is that they depend on age-specific rates which, when working with small areas, are often based on very few, or no, observed cases for most age groups. A similar effect occurs with life expectancy at birth and many more epidemiological indicators, which makes standardized mortality ratios (SMR) the omnipresent risk indicator for small areas epidemiologic studies.

Methods

To deal with this issue, a multivariate smoothing model, the M-model, is proposed in order to fit the age-specific probabilities of death (PoDs) for each spatial unit, which assumes dependence between closer age groups and spatial units. This age–space dependence structure enables information to be transferred between neighboring consecutive age groups and neighboring areas, at the same time, providing more reliable age-specific PoDs estimates.

Results

Three case studies are presented to illustrate the wide range of applications that smoothed age specific PoDs have in practice . The first case study shows the application of the model to a geographical study of lung cancer mortality in women. This study illustrates the convenience of considering age–space interactions in geographical studies and to explore the different spatial risk patterns shown by the different age groups. Second, the model is also applied to the study of ischaemic heart disease mortality in women in two cities at the census tract level. Smoothed age-standardized rates are derived and compared for the census tracts of both cities, illustrating some advantages of this mortality indicator over traditional SMRs. In the latest case study, the model is applied to estimate smoothed life expectancy (LE), which is the most widely used synthetic indicator for characterizing overall mortality differences when (not so small) spatial units are considered.

Conclusion

Our age–space model is an appropriate and flexible proposal that provides more reliable estimates of the probabilities of death, which allow the calculation of enhanced epidemiological indicators (smoothed ASR, smoothed LE), thus providing alternatives to traditional SMR-based studies of small areas.

Can COVID-19 symptoms as reported in a large-scale online survey be used to optimise spatial predictions of COVID-19 incidence risk in Belgium?

Although COVID-19 has been spreading throughout Belgium since February, 2020, its spatial dynamics in Belgium remain poorly understood, partly due to the limited testing of suspected cases during the epidemic's early phase. We analyse data of COVID-19 symptoms, as self-reported in a weekly online survey, which is open to all Belgian citizens. We predict symptoms' incidence using binomial models for spatially discrete data, and we introduce these as a covariate in the spatial analysis of COVID-19 incidence, as reported by the Belgian government during the days following a survey round. The symptoms' incidence is moderately predictive of the variation in the relative risks based on the confirmed cases; exceedance probability maps of the symptoms' incidence and confirmed cases' relative risks overlap partly. We conclude that this framework can be used to detect COVID-19 clusters of substantial sizes, but it necessitates spatial information on finer scales to locate small clusters.

Overcoming inefficiencies arising due to the impact of the modifiable areal unit problem on single-aggregation disease maps

BACKGROUND

In disease mapping, fine-resolution spatial health data are routinely aggregated for various reasons, for example to protect privacy. Usually, such aggregation occurs only once, resulting in 'single-aggregation disease maps' whose representation of the underlying data depends on the chosen set of aggregation units. This dependence is described by the modifiable areal unit problem (MAUP). Despite an extensive literature, in practice, the MAUP is rarely acknowledged, including in disease mapping. Further, despite single-aggregation disease maps being widely relied upon to guide distribution of healthcare resources, potential inefficiencies arising due to the impact of the MAUP on such maps have not previously been investigated.

RESULTS

We introduce the overlay aggregation method (OAM) for disease mapping. This method avoids dependence on any single set of aggregate-level mapping units through incorporating information from many different sets. We characterise OAM as a novel smoothing technique and show how its use results in potentially dramatic improvements in resource allocation efficiency over single-aggregation maps. We demonstrate these findings in a simulation context and through applying OAM to a real-world dataset: ischaemic stroke hospital admissions in Perth, Western Australia, in 2016.

CONCLUSIONS

The ongoing, widespread lack of acknowledgement of the MAUP in disease mapping suggests that unawareness of its impact is extensive or that impact is underestimated. Routine implementation of OAM can help avoid resource allocation inefficiencies associated with this phenomenon. Our findings have immediate worldwide implications wherever single-aggregation disease maps are used to guide health policy planning and service delivery.

Space-time analysis of ovarian cancer mortality rates by age groups in spanish provinces (1989-2015)

BACKGROUND

Ovarian cancer is a silent and largely asymptomatic cancer, leading to late diagnosis and worse prognosis. The late-stage detection and low survival rates, makes the study of the space-time evolution of ovarian cancer particularly relevant. In addition, research of this cancer in small areas (like provinces or counties) is still scarce.

METHODS

The study presented here covers all ovarian cancer deaths for women over 50 years of age in the provinces of Spain during the period 1989-2015. Spatio-temporal models have been fitted to smooth ovarian cancer mortality rates in age groups [50,60), [60,70), [70,80), and [80,+), borrowing information from spatial and temporal neighbours. Model fitting and inference has been carried out using the Integrated Nested Laplace Approximation (INLA) technique.

RESULTS

Large differences in ovarian cancer mortality among the age groups have been found, with higher mortality rates in the older age groups. Striking differences are observed between northern and southern Spain. The global temporal trends (by age group) reveal that the evolution of ovarian cancer over the whole of Spain has remained nearly constant since the early 2000s.

CONCLUSION

Differences in ovarian cancer mortality exist among the Spanish provinces, years, and age groups. As the exact causes of ovarian cancer remain unknown, spatio-temporal analyses by age groups are essential to discover inequalities in ovarian cancer mortality. Women over 60 years of age should be the focus of follow-up studies as the mortality rates remain constant since 2002. High-mortality provinces should also be monitored to look for specific risk factors.

Geostatistical COVID-19 infection risk maps for Portugal

The rapid spread of the SARS-CoV-2 epidemic has simultaneous time and space dynamics. This behaviour results from a complex combination of factors, including social ones, which lead to significant differences in the evolution of the spatiotemporal pattern between and within countries. Usually, spatial smoothing techniques are used to map health outcomes, and rarely uncertainty of the spatial predictions are assessed. As an alternative, we propose to apply direct block sequential simulation to model the spatial distribution of the COVID-19 infection risk in mainland Portugal. Given the daily number of infection data provided by the Portuguese Directorate-General for Health, the daily updates of infection rates are calculated by municipality and used as experimental data in the geostatistical simulation. The model considers the uncertainty/error associated with the size of each municipality's population. The calculation of daily updates of the infection risk maps results from the median model of one ensemble of 100 geostatistical realizations of daily updates of the infection risk. The ensemble of geostatistical realizations is also used to calculate the associated spatial uncertainty of the spatial prediction using the interquartile distance. The risk maps are updated daily and show the regions with greater risks of infection and the critical dynamics related to its development over time.

Childhood type 1 diabetes: an environment-wide association study across England

AIMS/HYPOTHESIS

Type 1 diabetes is an autoimmune disease affecting ~400,000 people across the UK. It is likely that environmental factors trigger the disease process in genetically susceptible individuals. We assessed the associations between a wide range of environmental factors and childhood type 1 diabetes incidence in England, using an agnostic, ecological environment-wide association study (EnWAS) approach, to generate hypotheses about environmental triggers.

METHODS

We undertook analyses at the local authority district (LAD) level using a national hospital episode statistics-based incident type 1 diabetes dataset comprising 13,948 individuals with diabetes aged 0-9 years over the period April 2000 to March 2011. We compiled LAD level estimates for a range of potential demographic and environmental risk factors including meteorological, land use and environmental pollution variables. The associations between type 1 diabetes incidence and risk factors were assessed via Poisson regression, disease mapping and ecological regression.

RESULTS

Case counts by LAD varied from 1 to 236 (median 33, interquartile range 24-46). Overall type 1 diabetes incidence was 21.2 (95% CI 20.9, 21.6) per 100,000 individuals. The EnWAS and disease mapping indicated that 15 out of 53 demographic and environmental risk factors were significantly associated with diabetes incidence, after adjusting for multiple testing. These included air pollutants (particulate matter, nitrogen dioxide, nitrogen oxides, carbon monoxide; all inversely associated), as well as lead in soil, radon, outdoor light at night, overcrowding, population density and ethnicity. Disease mapping revealed spatial heterogeneity in type 1 diabetes risk. The ecological regression found an association between type 1 diabetes and the living environment domain of the Index of Multiple Deprivation (RR 0.995; 95% credible interval [CrI] 0.991, 0.998) and radon potential class (RR 1.044; 95% CrI 1.015, 1.074).

CONCLUSIONS/INTERPRETATION

Our analysis identifies a range of demographic and environmental factors associated with type 1 diabetes in children in England.

Spatiotemporal analysis of insecticide-treated net use for children under 5 in relation to socioeconomic gradients in Central and East Africa

BACKGROUND

Insecticide-treated net (ITN) use is the core intervention among the strategies against malaria in sub-Saharan Africa (SSA) and the percentage of ITN ownership has increased from 47% in 2010 to 72% in 2017 across countries in SSA. Regardless of this massive expansion of ITN distribution, considerable gap between ownership and use of ITNs has been reported. Using data from more than 100,000 households in Central and East Africa (CEA) countries, the main aim of this study was to identify barriers associated with low ITN use and conduct geospatial analyses to estimate numbers and locations of vulnerable children living in areas with high malaria and low ITN use.

METHODS

Main sources of data for this study were the Demographic and Health Surveys and Malaria Indicator Surveys conducted in 11 countries in CEA. Logistic regression models for each country were built to assess the association between ITN ownership or ITN use and several socioeconomic and demographic variables. A density map of children under 5 living in areas at high-risk of malaria and low ITN use was generated to estimate the number of children who are living in these high malaria burden areas.

RESULTS

Results obtained suggest that factors such as the number of members in the household, total number of children in the household, education and place of residence can be key factors linked to the use of ITN for protecting children against malaria in CEA. Results from the spatiotemporal analyses found that although total rates of ownership and use of ITNs across CEA have increased up to 70% and 48%, respectively, a large proportion of children under 5 (19,780,678; 23% of total number of children) still lives in high-risk malaria areas with low use of ITNs.

CONCLUSION

The results indicate that despite substantial progress in the distribution of ITNs in CEA, with about 70% of the households having an ITN, several socioeconomic factors have compromised the effectiveness of this control intervention against malaria, and only about 48% of the households protect their children under 5 with ITNs. Increasing the effective ITN use by targeting these factors and the areas where vulnerable children reside can be a core strategy meant to reducing malaria transmission.

Increased prevalence of multiple sclerosis and clusters of different disease risk in Northern Italy

BACKGROUND

The increasing multiple sclerosis (MS) prevalence is varying across the macroscopic regional areas. Only few studies have explored the microscopic geographic variation of MS prevalence, which could highlight MS spatial clusters.

OBJECTIVE

In this ecological study, we aimed to estimate 2016 MS prevalence in the province of Pavia (Northern Italy) and to describe MS risk geographical variation across small area units, compared to the year 2000.

METHODS

Bayesian models were fit to estimate area-specific MS relative risks. The mean of the posterior marginal distribution of relative risks differences for each area were used to describe the risk variation.

RESULTS

The 2016 overall prevalence was 169.4 per 100,000 inhabitants (95% CI 158.8-180.6). The Bayesian mapping of MS showed some clusters of higher and lower disease prevalence. Furthermore, several municipalities located in the north part of the province were more at risk with respect to the year 2000.

CONCLUSIONS

The current MS prevalence sets the province of Pavia among high-risk areas and, compared with the previous prevalence estimate (86 per 100,000 in year 2000), indicates an increased MS risk. The Bayesian mapping highlighted area with a significantly higher/lower MS risk where to investigate etiologic hypotheses based on environmental and genetic exposures.

Spatial disease mapping using directed acyclic graph auto-regressive (DAGAR) models

Hierarchical models for regionally aggregated disease incidence data commonly involve region specific latent random effects that are modeled jointly as having a multivariate Gaussian distribution. The covariance or precision matrix incorporates the spatial dependence between the regions. Common choices for the precision matrix include the widely used ICAR model, which is singular, and its nonsingular extension which lacks interpretability. We propose a new parametric model for the precision matrix based on a directed acyclic graph (DAG) representation of the spatial dependence. Our model guarantees positive definiteness and, hence, in addition to being a valid prior for regional spatially correlated random effects, can also directly model the outcome from dependent data like images and networks. Theoretical results establish a link between the parameters in our model and the variance and covariances of the random effects. Substantive simulation studies demonstrate that the improved interpretability of our model reaps benefits in terms of accurately recovering the latent spatial random effects as well as for inference on the spatial covariance parameters. Under modest spatial correlation, our model far outperforms the CAR models, while the performances are similar when the spatial correlation is strong. We also assess sensitivity to the choice of the ordering in the DAG construction using theoretical and empirical results which testify to the robustness of our model. We also present a large-scale public health application demonstrating the competitive performance of the model.

Comparison of different software implementations for spatial disease mapping

Disease mapping is a scientific field that aims to understand and predict disease risk based on counts of observed cases within small regions of a study area of interest. Hierarchical model-based approaches that borrow information from neighbouring areas via conditional autoregressive (CAR) random effects on the local disease rates have gained a lot of popularity, thanks to the readily implemented Markov chain Monte Carlo methods. Nowadays, many software implementations to model risk distributions exist. Many of these applications differ, to varying degrees, in the underlying methodology. This paper provides an in-depth comparison between analysis results, coming from R-packages CARBayes, R2OpenBUGS, NIMBLE, R2BayesX, R-INLA, and RStan. We investigate CAR models typically used in disease mapping for spatially discrete count data. Data about diabetics in children and young adults in Belgium are used in a case study, while simulation studies are undertaken to assess software performance in different settings.

Estimating the changing nature of Scotland's health inequalities by using a multivariate spatiotemporal model

Health inequalities are the unfair and avoidable differences in people's health between different social groups. These inequalities have a huge influence on people's lives, particularly those who live at the poorer end of the socio-economic spectrum, as they result in prolonged ill health and shorter lives. Most studies estimate health inequalities for a single disease, but this will give an incomplete picture of the overall inequality in population health. Here we propose a novel multivariate spatiotemporal model for quantifying health inequalities in Scotland across multiple diseases, which will enable us to understand better how these inequalities vary across disease and have changed over time. In developing this model we are interested in estimating health inequalities between Scotland's 14 regional health boards, who are responsible for the protection and improvement of their population's health. The methodology is applied to hospital admissions data for cerebrovascular disease, coronary heart disease and respiratory disease, which are three of the leading causes of death, from 2003 to 2012 across Scotland.

Molecular serotyping of clinical strains of Haemophilus (Glaesserella) parasuis brings new insights regarding Glässer's disease outbreaks in Brazil

Glässer’s disease (GD) is an important infectious disease of swine caused by Haemophilus (Glaesserella) parasuis. Vaccination with inactivated whole cell vaccines is the major approach for prevention of H. parasuis infection worldwide, but the immunity induced is predominantly against the specific polysaccharide capsule. As a consequence, the available vaccines may not induce adequate protection against the field strains, when the capsules present in the vaccine strains are different from those in strains isolated from the farms. Therefore, it is crucial to map H. parasuis serovars associated with regional outbreaks so that appropriate bacterin vaccines can be developed and distributed for prevention of infection. In this study, 459 H. parasuis field strains isolated from different Glässer’s disease outbreaks that occurred in 10 different Brazilian States were analyzed for serotype using PCR-based approaches. Surprisingly, non-typeable (NT) strains were the second most prevalent group of field strains and along with serovars 4, 5 and 1 comprised more than 70% of the isolates. A PCR-based approach designed to amplify the entire polysaccharide capsule locus revealed 9 different band patterns in the NT strains, and 75% of the NT strains belonged to three clusters, suggesting that a number of new serovars are responsible for a substantial proportion of disease. These results indicate that commercially available vaccines in Brazil do not cover the most prevalent H. parasuis serovars associated with GD.

A joint spatial model of opioid-associated deaths and treatment admissions in Ohio

PURPOSE

Opioid misuse is a national epidemic, and Ohio is one of the states most impacted by this crisis. Ohio collects county-level counts of opioid-associated deaths and treatment admissions. We jointly model these two outcomes and assess the association of each rate with social and structural factors.

METHODS

We use a joint spatial rates model of death and treatment counts using a generalized common spatial factor model. In addition to covariate effects, we estimate a spatial factor for each county that characterizes structural factors not accounted for by other covariates in the model that are associated with both outcomes.

RESULTS

We observed an association of health professional shortage area with death rates and the rate of people 18-64 on disability with treatment rates. The proportion of single female households was associated with both outcomes. We estimated the presence of unmeasured risk factors in the southwestern part of the state and unmeasured protective factors in the eastern region.

CONCLUSIONS

We described associations of social and structural covariates with the death and treatment rates. We also characterized counties with latent risk that can provide a launching point for future investigations to determine potential sources of that risk.

Exploring socio-demographic-and geographical-variations in prevalence of diabetes and hypertension in Bangladesh: Bayesian spatial analysis of national health survey data. Spat Spatiotemporal Epidemiol. 2019;29:71-83. [PMID: 31128633 DOI: 10.1016/j.sste.2019.03.003]

Bangladesh has been experiencing an epidemiological transition from communicable diseases to non-communicable disease (NCDs), with a rapid increase in the NCD related morbidity and mortality in the last decade. Hypertension and diabetes are two important risk factors of NCDs that significantly increase the burden of cardiovascular diseases and risk of death. While the prevalence of people with both hypertension and diabetes has been increasing dramatically over time, it is essential to identify relatively more prevalent socio-demographic groups and geographical regions (local administrative districts) to reduce the NCDs related deaths in an urgent basis. This study focused on examining the association of socio-demographic factors with both hypertension and diabetes and exploring the regional variations in their prevalence using nationally representative survey data on adult population of age over 35 years. Bayesian spatial analysis was performed for both hypertension and diabetes data separately by fitting a model, that accounts for spatial variations, using integrated nested laplace approximation. The area-specific prevalence was then estimated as weighted average of the corresponding individual level predicted probabilities of being diseased derived from the fitted model, with weight from the individual level sampling weight. Finally, the estimated area-specific prevalence estimates were sketched in country-map to explore regional variations and identify regions with relatively higher prevalence. The results revealed that people of older age, higher education, better socio-economic condition, higher BMI are at greater risk of having hypertension and diabetes. Significant regional variations were observed with prevalence for hypertension ranges between 10% and 35% and for diabetes between 6% and 19% while their national prevalence were reported as 24% and 11%, respectively. The western regions of the country including middle capital city were found to be relatively more prevalent for hypertension while the middle-east and south-east regions were observed to be more prevalent for diabetes. The capital Dhaka region was observed as the most prevalent for both diabetes and hypertension. Details explanations of the findings and evidence based policy implications were discussed.

Online relative risks/rates estimation in spatial and spatio-temporal disease mapping

BACKGROUND AND OBJECTIVE

Spatial and spatio-temporal analyses of count data are crucial in epidemiology and other fields to unveil spatial and spatio-temporal patterns of incidence and/or mortality risks. However, fitting spatial and spatio-temporal models is not easy for non-expert users. The objective of this paper is to present an interactive and user-friendly web application (named SSTCDapp) for the analysis of spatial and spatio-temporal mortality or incidence data. Although SSTCDapp is simple to use, the underlying statistical theory is well founded and all key issues such as model identifiability, model selection, and several spatial priors and hyperpriors for sensitivity analyses are properly addressed.

METHODS

The web application is designed to fit an extensive range of fairly complex spatio-temporal models to smooth the very often extremely variable standardized incidence/mortality risks or crude rates. The application is built with the R package shiny and relies on the well founded integrated nested Laplace approximation technique for model fitting and inference.

RESULTS

The use of the web application is shown through the analysis of Spanish spatio-temporal breast cancer data. Different possibilities for the analysis regarding the type of model, model selection criteria, and a range of graphical as well as numerical outputs are provided.

CONCLUSIONS

Unlike other software used in disease mapping, SSTCDapp facilitates the fit of complex statistical models to non-experts users without the need of installing any software in their own computers, since all the analyses and computations are made in a powerful remote server. In addition, a desktop version is also available to run the application locally in those cases in which data confidentiality is a serious issue.

Mapping rates of inpatient hospitalizations related to mental disorders in the state of Missouri: A conditional autoregressive model with zip code-level data

Nearly one in five American adults suffers from mental illness in a given year. Mental health conditions are known to be spatially clustered, but no prior work has examined the clustering of mental health related hospitalizations. This analysis uses Bayesian hierarchical models to predict rates of inpatient hospitalizations attributed to mental disorders within zip codes in Missouri, USA. Eight separate models were run, and all models yielded similar estimates for the average rate of mental health related hospitalizations (around 13 per 1000 population). The percent of families receiving food stamps and percent of vacant housing were found to be significantly associated with hospitalization rates, after controlling for age, gender, and race. These rates were also significantly spatially clustered (Moran's I > 0.3 and p < 0.05 for all models). Health professionals can use these results to prioritize regions throughout the state that have the greatest need for mental health service providers and interventions.

Revisiting area risk classification of visceral leishmaniasis in Brazil

BACKGROUND

Visceral leishmaniasis (VL) is a neglected tropical disease of public health relevance in Brazil. To prioritize disease control measures, the Secretaria de Vigilância em Saúde of Brazil's Ministry of Health (SVS/MH) uses retrospective human case counts from VL surveillance data to inform a municipality-based risk classification. In this study, we compared the underlying VL risk, using a spatiotemporal explicit Bayesian hierarchical model (BHM), with the risk classification currently in use by the Brazil's Ministry of Health. We aim to assess how well the current risk classes capture the underlying VL risk as modelled by the BHM.

METHODS

Annual counts of human VL cases and the population at risk for all Brazil's 5564 municipalities between 2004 and 2014 were used to fit a relative risk BHM. We then computed the predicted counts and exceedence risk for each municipality and classified them into four categories to allow comparison with the four risk categories by the SVS/MH.

RESULTS

Municipalities identified as high-risk by the model partially agreed with the current risk classification by the SVS/MH. Our results suggest that counts of VL cases may suffice as general indicators of the underlying risk, but can underestimate risks, especially in areas with intense transmission.

CONCLUSION

According to our BHM the SVS/MH risk classification underestimated the risk in several municipalities with moderate to intense VL transmission. Newly identified high-risk areas should be further evaluated to identify potential risk factors and assess the needs for additional surveillance and mitigation efforts.

Innovation to impact in spatial epidemiology

Spatial epidemiology is a rapidly advancing field, pushing our abilities to measure, monitor and map pathogens at increasingly finer spatiotemporal scales. However, these scales often do not align with the abilities of control programmes to act at them, building a disconnect between academia and implementation. Efforts are being made to feed innovations into government, build spatial data skills, and strengthen links between disease control programmes and universities, yet work remains to be done if goals for disease control, elimination and 'leaving no one behind' are to be met.