Title: Intracounty modeling of COVID-19 infection with human mobility: Assessing spatial heterogeneity with business traffic, age, and race
The COVID-19 pandemic is a global threat presenting health, economic, and social challenges that continue to escalate. Metapopulation epidemic modeling studies in the susceptible–exposed–infectious–removed (SEIR) style have played important roles in informing public health policy making to mitigate the spread of COVID-19. These models typically rely on a key assumption on the homogeneity of the population. This assumption certainly cannot be expected to hold true in real situations; various geographic, socioeconomic, and cultural environments affect the behaviors that drive the spread of COVID-19 in different communities. What’s more, variation of intracounty environments creates spatial heterogeneity of transmission in different regions. To address this issue, we develop a human mobility flow-augmented stochastic SEIR-style epidemic modeling framework with the ability to distinguish different regions and their corresponding behaviors. This modeling framework is then combined with data assimilation and machine learning techniques to reconstruct the historical growth trajectories of COVID-19 confirmed cases in two counties in Wisconsin. The associations between the spread of COVID-19 and business foot traffic, race and ethnicity, and age structure are then investigated. The results reveal that, in a college town (Dane County), the most important heterogeneity is age structure, while, in a large city area (Milwaukee County), racial and ethnic heterogeneity becomes more apparent. Scenario studies further indicate a strong response of the spread rate to various reopening policies, which suggests that policy makers may need to take these heterogeneities into account very carefully when designing policies for mitigating the ongoing spread of COVID-19 and reopening.
Abstract The objective of this study is to examine the transmission risk of COVID-19 based on cross-county population co-location data from Facebook. The rapid spread of COVID-19 in the United States has imposed a major threat to public health, the real economy, and human well-being. With the absence of effective vaccines, the preventive actions of social distancing, travel reduction and stay-at-home orders are recognized as essential non-pharmacologic approaches to control the infection and spatial spread of COVID-19. Prior studies demonstrated that human movement and mobility drove the spatiotemporal distribution of COVID-19 in China. Little is known, however, about the patterns and effects of co-location reduction on cross-county transmission risk of COVID-19. This study utilizes Facebook co-location data for all counties in the United States from March to early May 2020 for conducting spatial network analysis where nodes represent counties and edge weights are associated with the co-location probability of populations of the counties. The analysis examines the synchronicity and time lag between travel reduction and pandemic growth trajectory to evaluate the efficacy of social distancing in ceasing the population co-location probabilities, and subsequently the growth in weekly new cases across counties. The results show that the mitigation effects of co-location reduction appear in the growth of weekly new confirmed cases with one week of delay. The analysis categorizes counties based on the number of confirmed COVID-19 cases and examines co-location patterns within and across groups. Significant segregation is found among different county groups. The results suggest that within-group co-location probabilities (e.g., co-location probabilities among counties with high numbers of cases) remain stable, and social distancing policies primarily resulted in reduced cross-group co-location probabilities (due to travel reduction from counties with large number of cases to counties with low numbers of cases). These findings could have important practical implications for local governments to inform their intervention measures for monitoring and reducing the spread of COVID-19, as well as for adoption in future pandemics. Public policy, economic forecasting, and epidemic modeling need to account for population co-location patterns in evaluating transmission risk of COVID-19 across counties.
Sood, Mansi; Sridhar, Anirudh; Eletreby, Rashad; Wu, Chai Wah; Levin, Simon A.; Yağan, Osman; Poor, H. Vincent(
, Proceedings of the National Academy of Sciences)
A key scientific challenge during the outbreak of novel infectious diseases is to predict how the course of the epidemic changes under countermeasures that limit interaction in the population. Most epidemiological models do not consider the role of mutations and heterogeneity in the type of contact events. However, pathogens have the capacity to mutate in response to changing environments, especially caused by the increase in population immunity to existing strains, and the emergence of new pathogen strains poses a continued threat to public health. Further, in the light of differing transmission risks in different congregate settings (e.g., schools and offices), different mitigation strategies may need to be adopted to control the spread of infection. We analyze a multilayer multistrain model by simultaneously accounting for i) pathways for mutations in the pathogen leading to the emergence of new pathogen strains, and ii) differing transmission risks in different settings, modeled as network layers. Assuming complete cross-immunity among strains, namely, recovery from any infection prevents infection with any other (an assumption that will need to be relaxed to deal with COVID-19 or influenza), we derive the key epidemiological parameters for the multilayer multistrain framework. We demonstrate that reductions to existing models that discount heterogeneity in either the strain or the network layers may lead to incorrect predictions. Our results highlight that the impact of imposing/lifting mitigation measures concerning different contact network layers (e.g., school closures or work-from-home policies) should be evaluated in connection with their effect on the likelihood of the emergence of new strains.
Risk perception and risk averting behaviors of public agencies in the emergence and spread of COVID-19 can be retrieved through online social media (Twitter), and such interactions can be echoed in other information outlets. This study collected time-sensitive online social media data and analyzed patterns of health risk communication of public health and emergency agencies in the emergence and spread of novel coronavirus using data-driven methods. The major focus is toward understanding how policy-making agencies communicate risk and response information through social media during a pandemic and influence community response—ie, timing of lockdown, timing of reopening, etc.—and disease outbreak indicators—ie, number of confirmed cases and number of deaths. Twitter data of six major public organizations (1,000-4,500 tweets per organization) are collected from February 21, 2020 to June 6, 2020. Several machine learning algorithms, including dynamic topic model and sentiment analysis, are applied over time to identify the topic dynamics over the specific timeline of the pandemic. Organizations emphasized on various topics—eg, importance of wearing face mask, home quarantine, understanding the symptoms, social distancing and contact tracing, emerging community transmission, lack of personal protective equipment, COVID-19 testing and medical supplies, effect of tobacco, pandemic stress management, increasing hospitalization rate, upcoming hurricane season, use of convalescent plasma for COVID-19 treatment, maintaining hygiene, and the role of healthcare podcast in different timeline. The findings can benefit emergency management, policymakers, and public health agencies to identify targeted information dissemination policies for public with diverse needs based on how local, federal, and international agencies reacted to COVID-19.
Villanustre, Flavio; Chala, Arjuna; Dev, Roger; Xu, Lili; LexisNexis, Jesse Shaw; Furht, Borko; Khoshgoftaar, Taghi(
, Journal of Big Data)
Abstract This project is funded by the US National Science Foundation (NSF) through their NSF RAPID program under the title “Modeling Corona Spread Using Big Data Analytics.” The project is a joint effort between the Department of Computer & Electrical Engineering and Computer Science at FAU and a research group from LexisNexis Risk Solutions. The novel coronavirus Covid-19 originated in China in early December 2019 and has rapidly spread to many countries around the globe, with the number of confirmed cases increasing every day. Covid-19 is officially a pandemic. It is a novel infection with serious clinical manifestations, including death, and it has reached at least 124 countries and territories. Although the ultimate course and impact of Covid-19 are uncertain, it is not merely possible but likely that the disease will produce enough severe illness to overwhelm the worldwide health care infrastructure. Emerging viral pandemics can place extraordinary and sustained demands on public health and health systems and on providers of essential community services. Modeling the Covid-19 pandemic spread is challenging. But there are data that can be used to project resource demands. Estimates of the reproductive number (R) of SARS-CoV-2 show that at the beginning of the epidemic, each infected person spreads the virus to at least two others, on average (Emanuel et al. in N Engl J Med. 2020, Livingston and Bucher in JAMA 323(14):1335, 2020). A conservatively low estimate is that 5 % of the population could become infected within 3 months. Preliminary data from China and Italy regarding the distribution of case severity and fatality vary widely (Wu and McGoogan in JAMA 323(13):1239–42, 2020). A recent large-scale analysis from China suggests that 80 % of those infected either are asymptomatic or have mild symptoms; a finding that implies that demand for advanced medical services might apply to only 20 % of the total infected. Of patients infected with Covid-19, about 15 % have severe illness and 5 % have critical illness (Emanuel et al. in N Engl J Med. 2020). Overall, mortality ranges from 0.25 % to as high as 3.0 % (Emanuel et al. in N Engl J Med. 2020, Wilson et al. in Emerg Infect Dis 26(6):1339, 2020). Case fatality rates are much higher for vulnerable populations, such as persons over the age of 80 years (> 14 %) and those with coexisting conditions (10 % for those with cardiovascular disease and 7 % for those with diabetes) (Emanuel et al. in N Engl J Med. 2020). Overall, Covid-19 is substantially deadlier than seasonal influenza, which has a mortality of roughly 0.1 %. Public health efforts depend heavily on predicting how diseases such as those caused by Covid-19 spread across the globe. During the early days of a new outbreak, when reliable data are still scarce, researchers turn to mathematical models that can predict where people who could be infected are going and how likely they are to bring the disease with them. These computational methods use known statistical equations that calculate the probability of individuals transmitting the illness. Modern computational power allows these models to quickly incorporate multiple inputs, such as a given disease’s ability to pass from person to person and the movement patterns of potentially infected people traveling by air and land. This process sometimes involves making assumptions about unknown factors, such as an individual’s exact travel pattern. By plugging in different possible versions of each input, however, researchers can update the models as new information becomes available and compare their results to observed patterns for the illness. In this paper we describe the development a model of Corona spread by using innovative big data analytics techniques and tools. We leveraged our experience from research in modeling Ebola spread (Shaw et al. Modeling Ebola Spread and Using HPCC/KEL System. In: Big Data Technologies and Applications 2016 (pp. 347-385). Springer, Cham) to successfully model Corona spread, we will obtain new results, and help in reducing the number of Corona patients. We closely collaborated with LexisNexis, which is a leading US data analytics company and a member of our NSF I/UCRC for Advanced Knowledge Enablement. The lack of a comprehensive view and informative analysis of the status of the pandemic can also cause panic and instability within society. Our work proposes the HPCC Systems Covid-19 tracker, which provides a multi-level view of the pandemic with the informative virus spreading indicators in a timely manner. The system embeds a classical epidemiological model known as SIR and spreading indicators based on causal model. The data solution of the tracker is built on top of the Big Data processing platform HPCC Systems, from ingesting and tracking of various data sources to fast delivery of the data to the public. The HPCC Systems Covid-19 tracker presents the Covid-19 data on a daily, weekly, and cumulative basis up to global-level and down to the county-level. It also provides statistical analysis for each level such as new cases per 100,000 population. The primary analysis such as Contagion Risk and Infection State is based on causal model with a seven-day sliding window. Our work has been released as a publicly available website to the world and attracted a great volume of traffic. The project is open-sourced and available on GitHub. The system was developed on the LexisNexis HPCC Systems, which is briefly described in the paper.
Ever since the outbreak of the COVID-19 epidemic, various public health control strategies have been proposed and tested against the coronavirus SARS-CoV-2. We study three specific COVID-19 epidemic control models: the susceptible, exposed, infectious, recovered (SEIR) model with vaccination control; the SEIR model with shield immunity control; and the susceptible, un-quarantined infected, quarantined infected, confirmed infected (SUQC) model with quarantine control. We express the control requirement in metric temporal logic (MTL) formulas (a type of formal specification languages) which can specify the expected control outcomes such as “ the deaths from the infection should never exceed one thousand per day within the next three months ” or “ the population immune from the disease should eventually exceed 200 thousand within the next 100 to 120 days ”. We then develop methods for synthesizing control strategies with MTL specifications. To the best of our knowledge, this is the first paper to systematically synthesize control strategies based on the COVID-19 epidemic models with formal specifications. We provide simulation results in three different case studies: vaccination control for the COVID-19 epidemic with model parameters estimated from data in Lombardy, Italy; shield immunity control for the COVID-19 epidemic with model parameters estimated from data in Lombardy, Italy; and quarantine control for the COVID-19 epidemic with model parameters estimated from data in Wuhan, China. The results show that the proposed synthesis approach can generate control inputs such that the time-varying numbers of individuals in each category (e.g., infectious, immune) satisfy the MTL specifications. The results also show that early intervention is essential in mitigating the spread of COVID-19, and more control effort is needed for more stringent MTL specifications. For example, based on the model in Lombardy, Italy, achieving less than 100 deaths per day and 10000 total deaths within 100 days requires 441.7% more vaccination control effort than achieving less than 1000 deaths per day and 50000 total deaths within 100 days.
Hou, Xiao, Gao, Song, Li, Qin, Kang, Yuhao, Chen, Nan, Chen, Kaiping, Rao, Jinmeng, Ellenberg, Jordan S., and Patz, Jonathan A. Intracounty modeling of COVID-19 infection with human mobility: Assessing spatial heterogeneity with business traffic, age, and race. Proceedings of the National Academy of Sciences 118.24 Web. doi:10.1073/pnas.2020524118.
Hou, Xiao, Gao, Song, Li, Qin, Kang, Yuhao, Chen, Nan, Chen, Kaiping, Rao, Jinmeng, Ellenberg, Jordan S., & Patz, Jonathan A. Intracounty modeling of COVID-19 infection with human mobility: Assessing spatial heterogeneity with business traffic, age, and race. Proceedings of the National Academy of Sciences, 118 (24). https://doi.org/10.1073/pnas.2020524118
Hou, Xiao, Gao, Song, Li, Qin, Kang, Yuhao, Chen, Nan, Chen, Kaiping, Rao, Jinmeng, Ellenberg, Jordan S., and Patz, Jonathan A.
"Intracounty modeling of COVID-19 infection with human mobility: Assessing spatial heterogeneity with business traffic, age, and race". Proceedings of the National Academy of Sciences 118 (24). Country unknown/Code not available: Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2020524118.https://par.nsf.gov/biblio/10232243.
@article{osti_10232243,
place = {Country unknown/Code not available},
title = {Intracounty modeling of COVID-19 infection with human mobility: Assessing spatial heterogeneity with business traffic, age, and race},
url = {https://par.nsf.gov/biblio/10232243},
DOI = {10.1073/pnas.2020524118},
abstractNote = {The COVID-19 pandemic is a global threat presenting health, economic, and social challenges that continue to escalate. Metapopulation epidemic modeling studies in the susceptible–exposed–infectious–removed (SEIR) style have played important roles in informing public health policy making to mitigate the spread of COVID-19. These models typically rely on a key assumption on the homogeneity of the population. This assumption certainly cannot be expected to hold true in real situations; various geographic, socioeconomic, and cultural environments affect the behaviors that drive the spread of COVID-19 in different communities. What’s more, variation of intracounty environments creates spatial heterogeneity of transmission in different regions. To address this issue, we develop a human mobility flow-augmented stochastic SEIR-style epidemic modeling framework with the ability to distinguish different regions and their corresponding behaviors. This modeling framework is then combined with data assimilation and machine learning techniques to reconstruct the historical growth trajectories of COVID-19 confirmed cases in two counties in Wisconsin. The associations between the spread of COVID-19 and business foot traffic, race and ethnicity, and age structure are then investigated. The results reveal that, in a college town (Dane County), the most important heterogeneity is age structure, while, in a large city area (Milwaukee County), racial and ethnic heterogeneity becomes more apparent. Scenario studies further indicate a strong response of the spread rate to various reopening policies, which suggests that policy makers may need to take these heterogeneities into account very carefully when designing policies for mitigating the ongoing spread of COVID-19 and reopening.},
journal = {Proceedings of the National Academy of Sciences},
volume = {118},
number = {24},
publisher = {Proceedings of the National Academy of Sciences},
author = {Hou, Xiao and Gao, Song and Li, Qin and Kang, Yuhao and Chen, Nan and Chen, Kaiping and Rao, Jinmeng and Ellenberg, Jordan S. and Patz, Jonathan A.},
}
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