Introduction to the Special Issue on Understanding the Spread of COVID-19, Part 1

Infectious diseases are transmitted between human hosts when in close contact over space and time. Recently, an unprecedented amount of spatial and spatiotemporal data have been made available that can be used to improve our understanding of the spread of COVID-19 and other infectious diseases. This understanding will be paramount to prepare for future pandemics through spatial algorithms and systems to collect, capture, curate, and analyze complex, multi-scale human movement data to solve problems such as infectious diseases prediction, contact tracing, and risk assessment. In exploring and deepening the conversation around this topic, the eight articles included in the first volume of this special issue employ diverse theoretical perspectives, methodologies, and frameworks, including but not limited to infectious diseases simulation, risk prediction, response policy design, mobility analysis, and case diagnosis. Rather than focusing on a narrow set of problems, these articles provide a glimpse into the diverse possibilities of leveraging spatial and spatiotemporal data for pandemic preparedness. © 2022 held by the owner/author(s).

Introduction to the Special Issue on Understanding the Spread of COVID-19, Part 1

Infectious diseases are transmitted between human hosts when in close contact over space and time. Recently, an unprecedented amount of spatial and spatiotemporal data have been made available that can be used to improve our understanding of the spread of COVID-19 and other infectious diseases. This understanding will be paramount to prepare for future pandemics through spatial algorithms and systems to collect, capture, curate, and analyze complex, multi-scale human movement data to solve problems such as infectious diseases prediction, contact tracing, and risk assessment. In exploring and deepening the conversation around this topic, the eight articles included in the first volume of this special issue employ diverse theoretical perspectives, methodologies, and frameworks, including but not limited to infectious diseases simulation, risk prediction, response policy design, mobility analysis, and case diagnosis. Rather than focusing on a narrow set of problems, these articles provide a glimpse into the diverse possibilities of leveraging spatial and spatiotemporal data for pandemic preparedness.

Spatiotemporal disease case prediction using contrastive predictive coding

Time series prediction models have played a vital role in guiding effective policymaking and response during the COVID-19 pandemic by predicting future cases and deaths at the country, state, and county levels. However, for emerging diseases, there is not sufficient historic data to fit traditional supervised prediction models. In addition, such models do not consider human mobility between regions. To mitigate the need for supervised models and to include human mobility data in the prediction, we propose Spatial Probabilistic Contrastive Predictive Coding (SP-CPC) which leverages Contrastive Predictive Coding (CPC), an unsupervised time-series representation learning approach. We augment CPC to incorporate a covariate mobility matrix into the loss function, representing the relative number of individuals traveling between each county on a given day. The proposal distribution learned by the algorithm is then sampled by the Metropolis-Hastings algorithm to give a final prediction of the number of COVID-19 cases. We find that the model applied to COVID-19 data can make accurate short-term predictions, more accurate than ARIMA and simple time-series extrapolation methods, one day into the future. However, for longer-term prediction windows of seven or more days into the future, we find that our predictions are not as competitive and require future research. © 2022 ACM.

PhyloView: A System to Visualize the Ecology of Infectious Diseases Using Phylogenetic Data

Since the onset of the COVID-19 pandemic, mil-lions of coronavirus sequences have been rapidly deposited in publicly available repositories. The sequences have been used primarily to monitor the evolution and transmission of the virus. In addition, the data can be combined with spatiotemporal information and mapped over space and time to understand transmission dynamics further. For example, the first COVID-19 cases in Australia were genetically related to the dominant strain in Wuhan, China, and spread via international travel. These data are currently available through the Global Initiative on Sharing Avian Influenza Data (GISAID) yet generally remains an untapped resource for data scientists to analyze such multi-dimensional data. Therefore, in this study, we demonstrate a system named Phyloview, a highly interactive visual environment that can be used to examine the spatiotemporal evolution of COVID-19 (from-to) over time using the case study of Louisiana, USA. PhyloView (powered by ArcGIsInsights) facilitates the visualization and exploration of the different dimensions of the phylogenetic data and can be layered with other types of spatiotemporal data for further investigation. Our system has the potential to be shared as a model to be used by health officials that can access relevant data through GISAID, visualize, and analyze it. Such data is essential for a better understanding, predicting, and responding to infectious diseases. © 2022 IEEE.

Clustering Adverse Events of COVID-19 Vaccines Across the United States

We study the similarity of adverse effects of COVID-19 vaccines across different states in the United States. We use data of 300,000 COVID-19 vaccine adverse event reports obtained from the Vaccine Adverse Event Reporting System (VAERS). We extract latent topics from the reported adverse events using a topic modeling approach based on Latent Dirichlet allocation (LDA). This approach allows us to represent each U.S. state as a low-dimensional distribution over topics. Using Moran’s index of spatial autocorrelation we show that some of the topics of adverse events exhibit significant spatial autocorrelation, indicating that there exist spatial clusters of nearby states that exhibit similar adverse events. Using Anselin’s local indicator of spatial association we discover and report these clusters. Our results show that adverse events of COVID-19 vaccines vary across states which justifies further research to understand the underlying causality to better understand adverse effects and to reduce vaccine hesitancy. © 2021, Springer Nature Switzerland AG.

Data-driven mobility models for COVID-19 simulation

Agent-based models (ABM) play a prominent role in guiding critical decision-making and supporting the development of effective policies for better urban resilience and response to the COVID-19 pandemic. However, many ABMs lack realistic representations of human mobility, a key process that leads to physical interaction and subsequent spread of disease. Therefore, we propose the application of Latent Dirichlet Allocation (LDA), a topic modeling technique, to foot-traffic data to develop a realistic model of human mobility in an ABM that simulates the spread of COVID-19. In our novel approach, LDA treats POIs as "words"and agent home census block groups (CBGs) as "documents"to extract "topics"of POIs that frequently appear together in CBG visits. These topics allow us to simulate agent mobility based on the LDA topic distribution of their home CBG. We compare the LDA based mobility model with competitor approaches including a naive mobility model that assumes visits to POIs are random. We find that the naive mobility model is unable to facilitate the spread of COVID-19 at all. Using the LDA informed mobility model, we simulate the spread of COVID-19 and test the effect of changes to the number of topics, various parameters, and public health interventions. By examining the simulated number of cases over time, we find that the number of topics does indeed impact disease spread dynamics, but only in terms of the outbreak's timing. Further analysis of simulation results is needed to better understand the impact of topics on simulated COVID-19 spread. This study contributes to strengthening human mobility representations in ABMs of disease spread. © 2020 ACM.