Forecasting hospital-level COVID-19 admissions using real-time mobility data

The Crucial Role of Laboratory Medicine in Addressing Future Public Health Infectious Threats: Insights Gained from the COVID-19 Pandemic

Laboratory testing has played a pivotal role throughout the coronavirus disease 2019 (COVID-19) pandemic, exemplifying the importance of in vitro diagnostics in addressing public health threats posed by outbreaks of infectious diseases. This article aims to present key insights from our expertise, derived from evidence gathered during the COVID-19 pandemic, to inform strategies for managing future infectious challenges. Current scientific evidence underscores that patient sample testing not only allows to diagnose an acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but also supports outbreak prediction, improved control measures, anticipation of pressure on the healthcare system, mitigation of adverse clinical outcomes, and early detection of emerging SARS-CoV-2 variants. Additionally, wastewater monitoring has emerged as a powerful tool for forecasting disease burden, including both prevalence and severity. Collectively, these findings underscore the value of diagnostic testing and wastewater surveillance in guiding healthcare planning and optimizing resource allocation during the COVID-19 pandemic, offering a valid framework to be applied to future public health threats, especially to any potential outbreak of "Disease X" that may emerge in the future.

Forecasting the relative abundance of Aedes vector populations to enhance situational awareness for mosquito control operations

Aedes-borne diseases represent a major public health threat and mosquito control operations represent a key line of defense. Improving the real-time awareness of mosquito control authorities by providing reliable forecasts of the relative abundance of mosquito vectors could greatly enhance control efforts. To this aim, we developed an analytical tool that forecasts Aedes aegypti relative abundance 1 to 4 weeks ahead. Forecasts were validated against mosquito surveillance data (2,760 data points) collected over multiple years in four jurisdictions in the US. The symmetric absolute percentage error was in the range 0.43-0.69, and the 90% interquantile range of the forecasts had a coverage of 83-92%. Our forecasts consistently outperformed a reference "naïve" model for all analyzed study sites, forecasting horizon, and for periods with medium/high Ae. aegypti activity. The developed tool can be instrumental to address the need for evidence-based decision making.

Epidemic spreading on spatial higher-order network

Higher-order interactions exist widely in mobile populations and are extremely important in spreading epidemics, such as influenza. However, research on high-order interaction modeling of mobile crowds and the propagation dynamics above is still insufficient. Therefore, this study attempts to model and simulate higher-order interactions among mobile populations and explore their impact on epidemic transmission. This study simulated the spread of the epidemic in a spatial high-order network based on agent-based model modeling. It explored its propagation dynamics and the impact of spatial characteristics on it. Meanwhile, we construct state-specific rate equations based on the uniform mixing assumption for further analysis. We found that hysteresis loops are an inherent feature of high-order networks in this space under specific scenarios. The evolution curve roughly presents three different states with the initial value change, showing different levels of the endemic balance of low, medium, and high, respectively. Similarly, network snapshots and parameter diagrams also indicate these three types of equilibrium states. Populations in space naturally form components of different sizes and isolations, and higher initial seeds generate higher-order interactions in this spatial network, leading to higher infection densities. This phenomenon emphasizes the impact of high-order interactions and high-order infection rates in propagation. In addition, crowd density and movement speed act as protective and inhibitory factors for epidemic transmission, respectively, and depending on the degree of movement weaken or enhance the effect of hysteresis loops.

Nonlinear bias toward complex contagion in uncertain transmission settings

Current epidemics in the biological and social domains are challenging the standard assumptions of mathematical contagion models. Chief among them are the complex patterns of transmission caused by heterogeneous group sizes and infection risk varying by orders of magnitude in different settings, like indoor versus outdoor gatherings in the COVID-19 pandemic or different moderation practices in social media communities. However, quantifying these heterogeneous levels of risk is difficult, and most models typically ignore them. Here, we include these features in an epidemic model on weighted hypergraphs to capture group-specific transmission rates. We study analytically the consequences of ignoring the heterogeneous transmissibility and find an induced superlinear infection rate during the emergence of a new outbreak, even though the underlying mechanism is a simple, linear contagion. The dynamics produced at the individual and group levels are therefore more similar to complex, nonlinear contagions, thus blurring the line between simple and complex contagions in realistic settings. We support this claim by introducing a Bayesian inference framework to quantify the nonlinearity of contagion processes. We show that simple contagions on real weighted hypergraphs are systematically biased toward the superlinear regime if the heterogeneity of the weights is ignored, greatly increasing the risk of erroneous classification as complex contagions. Our results provide an important cautionary tale for the challenging task of inferring transmission mechanisms from incidence data. Yet, it also paves the way for effective models that capture complex features of epidemics through nonlinear infection rates.

Wastewater-based epidemiology predicts COVID-19-induced weekly new hospital admissions in over 150 USA counties

Although the coronavirus disease (COVID-19) emergency status is easing, the COVID-19 pandemic continues to affect healthcare systems globally. It is crucial to have a reliable and population-wide prediction tool for estimating COVID-19-induced hospital admissions. We evaluated the feasibility of using wastewater-based epidemiology (WBE) to predict COVID-19-induced weekly new hospitalizations in 159 counties across 45 states in the United States of America (USA), covering a population of nearly 100 million. Using county-level weekly wastewater surveillance data (over 20 months), WBE-based models were established through the random forest algorithm. WBE-based models accurately predicted the county-level weekly new admissions, allowing a preparation window of 1-4 weeks. In real applications, periodically updated WBE-based models showed good accuracy and transferability, with mean absolute error within 4-6 patients/100k population for upcoming weekly new hospitalization numbers. Our study demonstrated the potential of using WBE as an effective method to provide early warnings for healthcare systems.

Intermunicipal travel networks of Mexico during the COVID-19 pandemic

Human mobility networks are widely used for diverse studies in geography, sociology, and economics. In these networks, nodes usually represent places or regions and links refer to movement between them. They become essential when studying the spread of a virus, the planning of transit, or society's local and global structures. Therefore, the construction and analysis of human mobility networks are crucial for a vast number of real-life applications. This work presents a collection of networks that describe the human travel patterns between municipalities in Mexico in the 2020-2021 period. Using anonymized mobile location data, we constructed directed, weighted networks representing the volume of travels between municipalities. We analysed changes in global, local, and mesoscale network features. We observe that changes in these features are associated with factors such as COVID-19 restrictions and population size. In general, the implementation of restrictions at the start of the COVID-19 pandemic in early 2020, induced more intense changes in network features than later events, which had a less notable impact in network features. These networks will result very useful for researchers and decision-makers in the areas of transportation, infrastructure planning, epidemic control and network science at large.