Spatiotemporal evolution of COVID-19 in Portugal's Mainland with self-organizing maps.

BACKGROUND: Self-Organizing Maps (SOM) are an unsupervised learning clustering and dimensionality reduction algorithm capable of mapping an initial complex high-dimensional data set into a low-dimensional domain, such as a two-dimensional grid of neurons. In the reduced space, the original complex patterns and their interactions can be better visualized, interpreted and understood. METHODS: We use SOM to simultaneously couple the spatial and temporal domains of the COVID-19 evolution in the 278 municipalities of mainland Portugal during the first year of the pandemic. Temporal 14-days cumulative incidence time series along with socio-economic and demographic indicators per municipality were analyzed with SOM to identify regions of the country with similar behavior and infer the possible common origins of the incidence evolution. RESULTS: The results show how neighbor municipalities tend to share a similar behavior of the disease, revealing the strong spatiotemporal relationship of the COVID-19 spreading beyond the administrative borders of each municipality. Additionally, we demonstrate how local socio-economic and demographic characteristics evolved as determinants of COVID-19 transmission, during the 1st wave school density per municipality was more relevant, where during 2nd wave jobs in the secondary sector and the deprivation score were more relevant. CONCLUSIONS: The results show that SOM can be an effective tool to analysing the spatiotemporal behavior of COVID-19 and synthetize the history of the disease in mainland Portugal during the period in analysis. While SOM have been applied to diverse scientific fields, the application of SOM to study the spatiotemporal evolution of COVID-19 is still limited. This work illustrates how SOM can be used to describe the spatiotemporal behavior of epidemic events. While the example shown herein uses 14-days cumulative incidence curves, the same analysis can be performed using other relevant data such as mortality data, vaccination rates or even infection rates of other disease of infectious nature.

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.

A study protocol to evaluate the relationship between outdoor air pollution and pregnancy outcomes.

BACKGROUND: The present study protocol is designed to assess the relationship between outdoor air pollution and low birth weight and preterm births outcomes performing a semi-ecological analysis. Semi-ecological design studies are widely used to assess effects of air pollution in humans. In this type of analysis, health outcomes and covariates are measured in individuals and exposure assignments are usually based on air quality monitor stations. Therefore, estimating individual exposures are one of the major challenges when investigating these relationships with a semi-ecologic design. METHODS/DESIGN: Semi-ecologic study consisting of a retrospective cohort study with ecologic assignment of exposure is applied. Health outcomes and covariates are collected at Primary Health Care Center. Data from pregnant registry, clinical record and specific questionnaire administered orally to the mothers of children born in period 2007-2010 in Portuguese Alentejo Litoral region, are collected by the research team. Outdoor air pollution data are collected with a lichen diversity biomonitoring program, and individual pregnancy exposures are assessed with spatial geostatistical simulation, which provides the basis for uncertainty analysis of individual exposures. Awareness of outdoor air pollution uncertainty will improve validity of individual exposures assignments for further statistical analysis with multivariate regression models. DISCUSSION: Exposure misclassification is an issue of concern in semi-ecological design. In this study, personal exposures are assigned to each pregnant using geocoded addresses data. A stochastic simulation method is applied to lichen diversity values index measured at biomonitoring survey locations, in order to assess spatial uncertainty of lichen diversity value index at each geocoded address. These methods assume a model for spatial autocorrelation of exposure and provide a distribution of exposures in each study location. We believe that variability of simulated exposure values at geocoded addresses will improve knowledge on variability of exposures, improving therefore validity of individual exposures to input in posterior statistical analysis.

Traffic represents the main source of pollution in small Mediterranean urban areas as seen by lichen functional groups.

The land-use type (residential, green areas, and traffic) within relatively small Mediterranean urban areas determines significant changes on lichen diversity, considering species richness and functional groups related to different ecological factors. Those areas with larger volume of traffic hold lower species diversity, in terms of species richness and lichen diversity value (LDV). Traffic areas also affect the composition of the lichen community, which is evidenced by sensitive species. The abundance of species of lichens tolerant to low levels of eutrophication diminishes in traffic areas; oppositely, those areas show a higher abundance of species of lichens tolerating high levels of eutrophication. On the other hand, residential and green areas have an opposite pattern, mainly with species highly tolerant to eutrophication being less abundant than low or moderate ones. The characteristics of tree bark do not seem to affect excessively on lichen composition; however, tree species shows some effect that should be considered in further studies.

Geostatistical uncertainty of assessing air quality using high-spatial-resolution lichen data: A health study in the urban area of Sines, Portugal.

In most studies correlating health outcomes with air pollution, personal exposure assignments are based on measurements collected at air-quality monitoring stations not coinciding with health data locations. In such cases, interpolators are needed to predict air quality in unsampled locations and to assign personal exposures. Moreover, a measure of the spatial uncertainty of exposures should be incorporated, especially in urban areas where concentrations vary at short distances due to changes in land use and pollution intensity. These studies are limited by the lack of literature comparing exposure uncertainty derived from distinct spatial interpolators. Here, we addressed these issues with two interpolation methods: regression Kriging (RK) and ordinary Kriging (OK). These methods were used to generate air-quality simulations with a geostatistical algorithm. For each method, the geostatistical uncertainty was drawn from generalized linear model (GLM) analysis. We analyzed the association between air quality and birth weight. Personal health data (n=227) and exposure data were collected in Sines (Portugal) during 2007-2010. Because air-quality monitoring stations in the city do not offer high-spatial-resolution measurements (n=1), we used lichen data as an ecological indicator of air quality (n=83). We found no significant difference in the fit of GLMs with any of the geostatistical methods. With RK, however, the models tended to fit better more often and worse less often. Moreover, the geostatistical uncertainty results showed a marginally higher mean and precision with RK. Combined with lichen data and land-use data of high spatial resolution, RK is a more effective geostatistical method for relating health outcomes with air quality in urban areas. This is particularly important in small cities, which generally do not have expensive air-quality monitoring stations with high spatial resolution. Further, alternative ways of linking human activities with their environment are needed to improve human well-being.