Using a general practice research database to assess the spatio-temporal COVID-19 risk.

BACKGROUND: In Flanders, general practitioners (GPs) were among the first ones to collect data regarding COVID-19 cases. Intego is a GPs' morbidity registry in primary care with data collected from the electronic medical records from a sample of general practices. The Intego database contain elaborate information regarding patient characteristics, such as comorbidities. At the national level, the Belgian Public Health Institute (Sciensano) recorded all test-confirmed COVID-19 cases, but without other patient characteristics. METHODS: Spatio and spatio-temporal analyses were used to analyse the spread of COVID-19 incidence at two levels of spatial aggregation: the municipality and the health sector levels. Our study goal was to compare spatio-temporal modelling results based on the Intego and Sciensano data, in order to see whether the Intego database is capable of detecting epidemiological trends similar to those in the Sciensano data. Comparable results would allow researchers to use these Intego data, and their wealth of patient information, to model COVID-19-related processes. RESULTS: The two data sources provided comparable results. Being a male decreased the odds of having COVID-19 disease. The odds for the age categories (17,35], (35,65] and (65,110] of being a confirmed COVID-19 case were significantly higher than the odds for the age category [0,17]. In the Intego data, having one of the following comorbidities, i.e., chronic kidney disease, heart and vascular disease, and diabetes, was significantly associated with being a COVID-19 case, increasing the odds of being diagnosed with COVID-19. CONCLUSION: We were able to show how an alternative data source, the Intego data, can be used in a pandemic situation. We consider our findings useful for public health officials who plan intervention strategies aimed at monitor and control disease outbreaks such as that of COVID-19.

A spatial model to jointly analyze self-reported survey data of COVID-19 symptoms and official COVID-19 incidence data.

This work presents a joint spatial modeling framework to improve estimation of the spatial distribution of the latent COVID-19 incidence in Belgium, based on test-confirmed COVID-19 cases and crowd-sourced symptoms data as reported in a large-scale online survey. Correction is envisioned for stochastic dependence between the survey's response rate and spatial COVID-19 incidence, commonly known as preferential sampling, but not found significant. Results show that an online survey can provide valuable auxiliary data to optimize spatial COVID-19 incidence estimation based on confirmed cases in situations with limited testing capacity. Furthermore, it is shown that an online survey on COVID-19 symptoms with a sufficiently large sample size per spatial entity is capable of pinpointing the same locations that appear as test-confirmed clusters, approximately 1 week earlier. We conclude that a large-scale online study provides an inexpensive and flexible method to collect timely information of an epidemic during its early phase, which can be used by policy makers in an early phase of an epidemic and in conjunction with other monitoring systems.

The doubling effect of COVID-19 cases on key health indicators.

From the beginning of the COVID-19 pandemic, researchers advised policy makers to make informed decisions towards the adoption of mitigating interventions. Key easy-to-interpret metrics applied over time can measure the public health impact of epidemic outbreaks. We propose a novel method which quantifies the effect of hospitalizations or mortality when the number of COVID-19 cases doubles. Two analyses are used, a country-by-country analysis and a multi-country approach which considers all countries simultaneously. The new measure is applied to several European countries, where the presence of different variants, vaccination rates and intervention measures taken over time leads to a different risk. Based on our results, the vaccination campaign has a clear effect for all countries analyzed, reducing the risk over time. However, the constant emergence of new variants combined with distinct intervention measures impacts differently the risk per country.

Disease mapping method comparing the spatial distribution of a disease with a control disease.

Small-area methods are being used in spatial epidemiology to understand the effect of location on health and detect areas where the risk of a disease is significantly elevated. Disease mapping models relate the observed number of cases to an expected number of cases per area. Expected numbers are often calculated by internal standardization, which requires both accurate population numbers and disease rates per gender and/or age group. However, confidentiality issues or the absence of high-quality information about the characteristics of a population-at-risk can hamper those calculations. Based on methods in point process analysis for situations without accurate population data, we propose the use of a case-control approach in the context of lattice data, in which an unrelated, spatially unstructured disease is used as a control disease. We correct for the uncertainty in the estimation of the expected values, which arises by using the control-disease's observed number of cases as a representation of a fraction of the total population. We apply our methods to a Belgian study of mesothelioma risk, where pancreatic cancer serves as the control disease. The analysis results are in close agreement with those coming from traditional disease mapping models based on internally standardized expected counts. The simulation study results confirm our findings for different spatial structures. We show that the proposed method can adequately address the problem of inaccurate or unavailable population data in disease mapping analysis.

A data-driven metapopulation model for the Belgian COVID-19 epidemic: assessing the impact of lockdown and exit strategies.

BACKGROUND: In response to the ongoing COVID-19 pandemic, several countries adopted measures of social distancing to a different degree. For many countries, after successfully curbing the initial wave, lockdown measures were gradually lifted. In Belgium, such relief started on May 4th with phase 1, followed by several subsequent phases over the next few weeks. METHODS: We analysed the expected impact of relaxing stringent lockdown measures taken according to the phased Belgian exit strategy. We developed a stochastic, data-informed, meta-population model that accounts for mixing and mobility of the age-structured population of Belgium. The model is calibrated to daily hospitalization data and is able to reproduce the outbreak at the national level. We consider different scenarios for relieving the lockdown, quantified in terms of relative reductions in pre-pandemic social mixing and mobility. We validate our assumptions by making comparisons with social contact data collected during and after the lockdown. RESULTS: Our model is able to successfully describe the initial wave of COVID-19 in Belgium and identifies interactions during leisure/other activities as pivotal in the exit strategy. Indeed, we find a smaller impact of school re-openings as compared to restarting leisure activities and re-openings of work places. We also assess the impact of case isolation of new (suspected) infections, and find that it allows re-establishing relatively more social interactions while still ensuring epidemic control. Scenarios predicting a second wave of hospitalizations were not observed, suggesting that the per-contact probability of infection has changed with respect to the pre-lockdown period. CONCLUSIONS: Contacts during leisure activities are found to be most influential, followed by professional contacts and school contacts, respectively, for an impending second wave of COVID-19. Regular re-assessment of social contacts in the population is therefore crucial to adjust to evolving behavioral changes that can affect epidemic diffusion.

Modelling the early phase of the Belgian COVID-19 epidemic using a stochastic compartmental model and studying its implied future trajectories.

Following the onset of the ongoing COVID-19 pandemic throughout the world, a large fraction of the global population is or has been under strict measures of physical distancing and quarantine, with many countries being in partial or full lockdown. These measures are imposed in order to reduce the spread of the disease and to lift the pressure on healthcare systems. Estimating the impact of such interventions as well as monitoring the gradual relaxing of these stringent measures is quintessential to understand how resurgence of the COVID-19 epidemic can be controlled for in the future. In this paper we use a stochastic age-structured discrete time compartmental model to describe the transmission of COVID-19 in Belgium. Our model explicitly accounts for age-structure by integrating data on social contacts to (i) assess the impact of the lockdown as implemented on March 13, 2020 on the number of new hospitalizations in Belgium; (ii) conduct a scenario analysis estimating the impact of possible exit strategies on potential future COVID-19 waves. More specifically, the aforementioned model is fitted to hospital admission data, data on the daily number of COVID-19 deaths and serial serological survey data informing the (sero)prevalence of the disease in the population while relying on a Bayesian MCMC approach. Our age-structured stochastic model describes the observed outbreak data well, both in terms of hospitalizations as well as COVID-19 related deaths in the Belgian population. Despite an extensive exploration of various projections for the future course of the epidemic, based on the impact of adherence to measures of physical distancing and a potential increase in contacts as a result of the relaxation of the stringent lockdown measures, a lot of uncertainty remains about the evolution of the epidemic in the next months.

The impact of contact tracing and household bubbles on deconfinement strategies for COVID-19.

The COVID-19 pandemic caused many governments to impose policies restricting social interactions. A controlled and persistent release of lockdown measures covers many potential strategies and is subject to extensive scenario analyses. Here, we use an individual-based model (STRIDE) to simulate interactions between 11 million inhabitants of Belgium at different levels including extended household settings, i.e., "household bubbles". The burden of COVID-19 is impacted by both the intensity and frequency of physical contacts, and therefore, household bubbles have the potential to reduce hospital admissions by 90%. In addition, we find that it is crucial to complete contact tracing 4 days after symptom onset. Assumptions on the susceptibility of children affect the impact of school reopening, though we find that business and leisure-related social mixing patterns have more impact on COVID-19 associated disease burden. An optimal deployment of the mitigation policies under study require timely compliance to physical distancing, testing and self-isolation.

On the impact of residential history in the spatial analysis of diseases with a long latency period: A study of mesothelioma in Belgium.

Mesothelioma is a rare cancer caused by exposure to asbestos. Belgium has a known long history of asbestos production, resulting in one of the highest mesothelioma mortality rates worldwide. While the production of asbestos has stopped completely, the long latency period of mesothelioma, which can fluctuate between 20 and 40 years after exposure, causes incidences still to be frequent. Mesothelioma's long incubation time affects our assessment of its geographical distribution as well. Since patients' residential locations are likely to change a number of times throughout their lives, the location where the patients develop the disease is often far from the location where they were exposed to asbestos. Using the residential history of patients, we propose the use of a convolution multiple membership model (MMM), which includes both a spatial conditional autoregressive and an unstructured random effect. Pancreatic cancer patients are used as a control population, reflecting the population at risk for mesothelioma. Results show the impact of the residential mobility on the geographical risk estimation, as well as the importance of acknowledging the latency period of a disease. A simulation study was conducted to investigate the properties of the convolution MMM. The robustness of the results for the convolution MMM is assessed via a sensitivity analysis.