A statistical framework for tracking the time-varying superspreading potential of COVID-19 epidemic

modelSSE: An R Package for Characterizing Infectious Disease Superspreading from Contact Tracing Data

Infectious disease superspreading is a phenomenon where few primary cases generate unexpectedly large numbers of secondary cases. Superspreading, is frequently documented in epidemiology literature, and is considered a consequence of heterogeneity in transmission. Since understanding the risks of superspreading became a rising concern from both statistical modelling and public health aspects, the R package modelSSE provides comprehensive analytical tools to characterize transmission heterogeneity. The package modelSSE integrates recent advances in statistical methods, such as decomposition of reproduction number, for modelling infectious disease superspreading using various types and sources of contact tracing data that allow models to be grounded in real-world observations. This study provided an overview of the theoretical background and implementation of modelSSE, designed to facilitate learning infectious disease transmission, and explore novel research questions for transmission risks and superspreading potentials. Detailed examples of classic, historical infectious disease datasets are given for demonstration and model extensions.

Improved estimation of the effective reproduction number with heterogeneous transmission rates and reporting delays

In the face of an infectious disease, a key epidemiological measure is the basic reproduction number, which quantifies the average secondary infections caused by a single case in a susceptible population. In practice, the effective reproduction number, denoted as R t , is widely used to assess the transmissibility of the disease at a given time t. Real-time estimating this metric is vital for understanding and managing disease outbreaks. Traditional statistical inference often relies on two assumptions. One is that samples are assumed to be drawn from a homogeneous population distribution, neglecting significant variations in individual transmission rates. The other is the ideal case reporting assumption, disregarding time delays between infection and reporting. In this paper, we thoroughly investigate these critical factors and assess their impact on estimating R t . We first introduce negative binomial and Weibull distributions to characterize transmission rates and reporting delays, respectively, based on which observation and state equations are formulated. Then, we employ a Bayesian filtering for estimating R t . Finally, validation using synthetic and empirical data demonstrates a significant improvement in estimation accuracy compared to conventional methods that ignore these factors.

Consistent Healthcare Safety Recommendation System for Preventing Contagious Disease Infections in Human Crowds

The recent impact of COVID-19, as a contagious disease, led researchers to focus on designing and fabricating personal healthcare devices and systems. With the help of wearable sensors, sensing and communication technologies, and recommendation modules, personal healthcare systems were designed for ease of use. More specifically, personal healthcare systems were designed to provide recommendations for maintaining a safe distance and avoiding contagious disease spread after the COVID-19 pandemic. The personal recommendations are analyzed based on the wearable sensor signals and their consistency in sensing. This consistency varies with human movements or other activities that hike/cease the sensor values abruptly for a short period. Therefore, a consistency-focused recommendation system (CRS) for personal healthcare (PH) was designed in this research. The hardware sensing intervals for the system are calibrated per the conventional specifications from which abrupt changes can be observed. The changes are analyzed for their saturation and fluctuations observed from neighbors within the threshold distance. The saturation and fluctuation classifications are performed using random forest learning to differentiate the above data from the previously sensed healthy data. In this process, the saturated data and consistency data provide safety recommendations for the moving user. The consistency is verified for a series of intervals for the fluctuating sensed data. This alerts the user if the threshold distance for a contagious disease is violated. The proposed system was validated using a prototype model and experimental analysis through false rates, data analysis rates, and fluctuations.

Time-varying overdispersion of SARS-CoV-2 transmission during the periods when different variants of concern were circulating in Japan

Japan has implemented a cluster-based approach for coronavirus disease 2019 (COVID-19) from the pandemic's beginning based on the transmission heterogeneity (overdispersion) of severe acute respiratory coronavirus 2 (SARS-CoV-2). However, studies analyzing overdispersion of transmission among new variants of concerns (VOCs), especially for Omicron, were limited. Thus, we aimed to clarify how the transmission heterogeneity has changed with the emergence of VOCs (Alpha, Delta, and Omicron) using detailed contact tracing data in Yamagata Prefecture, Japan. We estimated the time-varying dispersion parameter ([Formula: see text]) by fitting a negative binomial distribution for each transmission generation. Our results showed that even after the emergence of VOCs, there was transmission heterogeneity of SARS-CoV-2, with changes in [Formula: see text] during each wave. Continuous monitoring of transmission dynamics is vital for implementing appropriate measures. However, a feasible and sustainable epidemiological analysis system should be established to make this possible.

Are the epidemic prevention facilities effective? How cities should choose epidemic prevention facilities: Taking Wuhan as an example

The COVID-19 pandemic highlighted the limitations of urban public health emergency response capabilities. Taking Wuhan as an example, this study used breakpoint regression, kernel density analysis, overlay analysis, and accessibility analysis from Stata and ArcGIS, and divided epidemic prevention facilities into the basic epidemic prevention facilities (hospitals), and the emergency epidemic prevention facilities (mobile cabin hospitals) for further analysis. The results showed that over 70% of the basic epidemic prevention facilities in Wuhan were located in high density population areas. On the contrary, most of the emergency epidemic prevention facilities were located in low density population areas. The local treatment effect of the implementation of the emergency epidemic prevention facility policy is about 1, indicating that there was a significant impact of emergency epidemic prevention facilities on outbreak control, which passed the bandwidth test. What’s more, the analysis of the accessibility of residential points revealed that more than 67.3% of people from the residential points could arrive at the epidemic prevention facilities within 15 min, and only 0.1% of them took more than 20 min to arrive. Therefore, the epidemic prevention facilities can effectively curb the spread of the epidemic, and people from residential areas can quickly get there. This study summarized the spatial characteristics of epidemic prevention facilities in Wuhan and analyzed the importance of them, thus providing a new perspective for future research on upgrading the city’s comprehensive disaster prevention system.