As COVID-19 spread through the United States in 2020, states began to set up alert systems to inform policy decisions and serve as risk communication tools for the general public. Many of these systems, like in Ohio, included indicators based on an assessment of trends in reported cases. However, when cases are indexed by date of disease onset, reporting delays complicate the interpretation of trends. Despite a foundation of statistical literature to address this problem, these methods have not been widely applied in practice. In this paper, we develop a Bayesian spatio-temporal nowcasting model for assessing trends in county-level COVID-19 cases in Ohio. We compare the performance of our model to the current approach used in Ohio and the approach that was recommended by the Centers for Disease Control and Prevention. We demonstrate gains in performance while still retaining interpretability using our model. In addition, we are able to fully account for uncertainty in both the time series of cases and in the reporting process. While we cannot eliminate all of the uncertainty in public health surveillance and subsequent decision-making, we must use approaches that embrace these challenges and deliver more accurate and honest assessments to policymakers.
Epidemic modeling is an essential tool to understand the spread of the novel coronavirus and ultimately assist in disease prevention, policymaking, and resource allocation. In this article, we establish a state of the art interface between classic mathematical and statistical models and propose a novel space-time epidemic modeling framework to study the spatial-temporal pattern in the spread of infectious disease. We propose a quasi-likelihood approach via the penalized spline approximation and alternatively reweighted least-squares technique to estimate the model. Furthermore, we provide a sh…
The COVID-19 pandemic has highlighted delayed reporting as a significant impediment to effective disease surveillance and decision-making. In the absence of timely data, statistical models which account for delays can be adopted to nowcast and forecast cases or deaths. We discuss the four key sources of systematic and random variability in available data for COVID-19 and other diseases, and critically evaluate current state-of-the-art methods with respect to appropriately separating and capturing this variability. We present a general spatio-temporal hierarchical framework for correcting delay…
The emergence of Covid-19 requires new effective tools for epidemiological surveillance. Spatio-temporal disease mapping models, which allow dealing with highly disaggregated spatial and temporal units of analysis, are a priority in this sense. Spatio-temporal models provide a geographically detailed and temporally updated overview of the current state of the pandemics, making public health interventions to be more effective. Moreover, the use of spatio-temporal disease mapping models in the new Covid-19 epidemic context, facilitates estimating newly demanded epidemiological indicators, such a…
The real-time analysis of infectious disease surveillance data, e.g., in the form of a time-series of reported cases or fatalities, is essential in obtaining situational awareness about the current dynamics of an adverse health event such as the COVID-19 pandemic. This real-time analysis is complicated by reporting delays that lead to underreporting of the number of events for the most recent time points (e.g., days or weeks). This can lead to misconceptions by the interpreter, e.g., the media or the public, as was the case with the time-series of reported fatalities during the COVID-19 pandem…
In this chapter, we consider space-time analysis of surveillance count data. Such data are ubiquitous and a number of approaches have been proposed for their analysis. We first describe the aims of a surveillance endeavor, before reviewing and critiquing a number of common models. We focus on models in which time is discretized to the time scale of the latent and infectious periods of the disease under study. In particular, we focus on the time series SIR (TSIR) models originally described by Finkenstadt and Grenfell in their 2000 paper and the epidemic/endemic models first proposed by Held, H…
The scan statistic sets the benchmark for spatio-temporal surveillance methods with its popularity. In its simplest form it scans the target area and time to find regions with disease count higher than expected. If the shape and size of the disease outbreaks are known, then to detect it sufficiently early the scan statistic can design its search area to be efficient for this shape and size. A plan that is efficient at detecting a range of disease outbreak shapes and sizes is important because these vary from one outbreak to the next and are generally never known in advance. This paper offers a…
A spatio-temporal block aggregation model for latent log Gaussian outcomes: application on modelling wastewater virus concentration in Wales
Imperial College London（帝国理工学院）；Lancaster University（兰卡斯特大学）；Northumbria University（诺森比亚大学）；UK Health Security Agency（英国卫生安全局）；Public Health Wales（威尔士公共卫生局）；Bangor University（班戈大学）
Spatiotemporal dynamics and ecological risk factors of highly pathogenic avian influenza A(H5N1) in Canadian wildlife: A One Health surveillance analysis
Auckland University of Technology（奥克兰理工大学）
本研究通过分析加拿大2022-2026年野生动物H5N1疫情监测数据，揭示了该病毒的时空动态及与检测数量相关的风险因素，采用描述流行病学、空间聚类方法和负二项混合模型进行分析，发现 Eurasian-North American 病毒谱系主导检测，并识别出年份、季节和谱系是关键预测因子。
We present an efficient score statistic, called the $\textsf{S}^3 \textsf{T}$ statistic, to detect the emergence of a spatially and temporally correlated signal from either fixed-sample or sequential data. The signal may cause a men shift and/or a change in the covariance structure. The score statistic can capture both spatial and temporal structures of the change and hence is particularly powerful in detecting weak signals. The score statistic is computationally efficient and statistically powerful. Our main theoretical contribution are accurate analytical approximations on the false alarm ra…
Integrating Temporal Disaggregation and Distributed Lag Nonlinear Models for Bayesian Spatio-Temporal Disease Mapping with High-Resolution Environmental Exposures
KU Leuven（荷语鲁汶大学）；Hasselt University（哈瑟尔特大学）；Clinton Health Access Initiative（克林顿健康准入倡议）；National Malaria Control Program, Ministry of Health（卫生部国家疟疾控制项目）；University of Birmingham（伯明翰大学）
Reliable estimation of spatio-temporal trends in population-level HIV incidence is becoming an increasingly critical component of HIV prevention policy-making. However, direct measurement is nearly impossible. Current, widely used models infer incidence from survey and surveillance seroprevalence data, but they require unrealistic assumptions about spatial independence across spatial units. In this study, we present an epidemic model of HIV that explicitly simulates the spatial dynamics of HIV over many small, interacting areal units. By integrating all available population-level data, we are …
Weather radar echoes, correlated in both space and time, are the most important input data for short-term precipitation forecast. Motivated by real datasets, this paper is concerned with the spatio-temporal modeling of two-dimensional radar reflectivity fields from a sequence of radar images. Under a Lagrangian integration scheme, we model the radar reflectivity data by a spatio-temporal conditional autoregressive process which is driven by two hidden sub-processes. The first sub-process is the dynamic velocity field which determines the motion of the weather system, while the second sub-proce…
Viral zoonoses have emerged as the key drivers of recent pandemics. Human infection by zoonotic viruses are either spillover events -- isolated infections that fail to cause a widespread contagion -- or species jumps, where successful adaptation to the new host leads to a pandemic. Despite expensive bio-surveillance efforts, historically emergence response has been reactive, and post-hoc. Here we use machine inference to demonstrate a high accuracy predictive bio-surveillance capability, designed to pro-actively localize an impending species jump via automated interrogation of massive sequence…
James Cook University（詹姆斯库克大学）；College of Science and Engineering（科学与工程学院）
Spatio-temporal sequence forecasting is one of the fundamental tasks in spatio-temporal data mining. It facilitates many real world applications such as precipitation nowcasting, citywide crowd flow prediction and air pollution forecasting. Recently, a few Seq2Seq based approaches have been proposed, but one of the drawbacks of Seq2Seq models is that, small errors can accumulate quickly along the generated sequence at the inference stage due to the different distributions of training and inference phase. That is because Seq2Seq models minimise single step errors only during training, however t…
Routine public health surveillance of notifiable infectious diseases gives rise to weekly counts of reported cases -- possibly stratified by region and/or age group. We investigate how an age-structured social contact matrix can be incorporated into a spatio-temporal endemic-epidemic model for infectious disease counts. To illustrate the approach, we analyze the spread of norovirus gastroenteritis over 6 age groups within the 12 districts of Berlin, 2011-2015, using contact data from the POLYMOD study. The proposed age-structured model outperforms alternative scenarios with homogeneous or no m…
Unsupervised Consensus-Based Anomaly Detection for Spatiotemporal Malaria Incidence in Ghana
Ghana Space Science and Technology Institute, Ghana Atomic Energy Commission（加纳空间科学与技术研究所，加纳原子能委员会）；Department of Medical Microbiology, University of Ghana Medical School（加纳大学医学院医学微生物学系）
Hotspot detection aims at identifying subgroups in the observations that are unexpected, with respect to the some baseline information. For instance, in disease surveillance, the purpose is to detect sub-regions in spatiotemporal space, where the count of reported diseases (e.g. Cancer) is higher than expected, with respect to the population. The state-of-the-art method for this kind of problem is the Space-Time Scan Statistics (STScan), which exhaustively search the whole space through a sliding window looking for significant spatiotemporal clusters. STScan makes some restrictive assumptions …
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 as well as to have an idea of how the infective situation is going to unfold in the next days. However, as in many other situations of compulsorily-notifiable diseases and beyond, cases are reported with de…
The availability of geocoded health data and the inherent temporal structure of communicable diseases have led to an increased interest in statistical models and software for spatio-temporal data with epidemic features. The open source R package surveillance can handle various levels of aggregation at which infective events have been recorded: individual-level time-stamped geo-referenced data (case reports) in either continuous space or discrete space, as well as counts aggregated by period and region. For each of these data types, the surveillance package implements tools for visualization, l…
Malaria transmission in Madagascar is highly heterogeneous, exhibiting spatial, seasonal and long-term trends. Previous efforts to map malaria risk in Madagascar used prevalence data from Malaria Indicator Surveys. These cross-sectional surveys, conducted during the high transmission season most recently in 2013 and 2016, provide nationally representative prevalence data but cover relatively short time frames. Conversely, monthly case data are collected at health facilities but suffer from biases, including incomplete reporting. We combined survey and case data to make monthly maps of prevalen…
Friedrich Schiller University Jena（耶拿弗里德里希·席勒大学）；Carl Zeiss AG（卡尔·蔡司股份公司）
Automatic detection of anomalies in space- and time-varying measurements is an important tool in several fields, e.g., fraud detection, climate analysis, or healthcare monitoring. We present an algorithm for detecting anomalous regions in multivariate spatio-temporal time-series, which allows for spotting the interesting parts in large amounts of data, including video and text data. In opposition to existing techniques for detecting isolated anomalous data points, we propose the "Maximally Divergent Intervals" (MDI) framework for unsupervised detection of coherent spatial regions and time inte…
In this paper we first describe the class of log-Gaussian Cox processes (LGCPs) as models for spatial and spatio-temporal point process data. We discuss inference, with a particular focus on the computational challenges of likelihood-based inference. We then demonstrate the usefulness of the LGCP by describing four applications: estimating the intensity surface of a spatial point process; investigating spatial segregation in a multi-type process; constructing spatially continuous maps of disease risk from spatially discrete data; and real-time health surveillance. We argue that problems of thi…
University of Pittsburgh（匹兹堡大学）；Middle East Technical University（中东技术大学）
Opioid overdose is a growing public health crisis in the United States. This crisis, recognized as "opioid epidemic," has widespread societal consequences including the degradation of health, and the increase in crime rates and family problems. To improve the overdose surveillance and to identify the areas in need of prevention effort, in this work, we focus on forecasting opioid overdose using real-time crime dynamics. Previous work identified various types of links between opioid use and criminal activities, such as financial motives and common causes. Motivated by these observations, we pro…
