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Register a new userA Compartment Model of Human Mobility and Early Covid-19 Dynamics in NYC
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Ian Frankenburg
Publication date
2021
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Mathematical Statistics
and research's language is
English
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In this paper, we build a mechanistic system to understand the relation between a reduction in human mobility and Covid-19 spread dynamics within New York City. To this end, we propose a multivariate compartmental model that jointly models smartphone mobility data and case counts during the first 90 days of the epidemic. Parameter calibration is achieved through the formulation of a general Bayesian hierarchical model to provide uncertainty quantification of resulting estimates. The open-source probabilistic programming language Stan is used for the requisite computation. Through sensitivity analysis and out-of-sample forecasting, we find our simple and interpretable model provides evidence that reductions in human mobility altered case dynamics.
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The outbreak of COVID-19 highlights the need for a more harmonized, less privacy-concerning, easily accessible approach to monitoring the human mobility that has been proved to be associated with the viral transmission. In this study, we analyzed 587 million tweets worldwide to see how global collaborative efforts in reducing human mobility are reflected from the user-generated information at the global, country, and the U.S. state scale. Considering the multifaceted nature of mobility, we propose two types of distance: the single-day distance and the cross-day distance. To quantify the responsiveness in certain geographical regions, we further propose a mobility-based responsive index (MRI) that captures the overall degree of mobility changes within a time window. The results suggest that mobility patterns obtained from Twitter data are amendable to quantitatively reflect the mobility dynamics. Globally, the proposed two distances had greatly deviated from their baselines after March 11, 2020, when WHO declared COVID-19 as a pandemic. The considerably less periodicity after the declaration suggests that the protection measures have obviously affected peoples travel routines. The country scale comparisons reveal the discrepancies in responsiveness, evidenced by the contrasting mobility patterns in different epidemic phases. We find that the triggers of mobility changes correspond well with the national announcements of mitigation measures. In the U.S., the influence of the COVID-19 pandemic on mobility is distinct. However, the impacts varied substantially among states. The strong mobility recovering momentum is further fueled by the Black Lives Matter protests, potentially fostering the second wave of infections in the U.S.
Social distancing is widely acknowledged as an effective public health policy combating the novel coronavirus. But extreme social distancing has costs and it is not clear how much social distancing is needed to achieve public health effects. In this article, we develop a design-based framework to make inference about the dose-response relationship between social distancing and COVID-19 related death toll and case numbers. We first discuss how to embed observational data with a time-independent, continuous treatment dose into an approximate randomized experiment, and develop a randomization-based procedure that tests if a structured dose-response relationship fits the data. We then generalize the design and testing procedure to accommodate a time-dependent, treatment dose trajectory, and generalize a dose-response relationship to a longitudinal setting. Finally, we apply the proposed design and testing procedures to investigate the effect of social distancing during the phased reopening in the United States on public health outcomes using data compiled from sources including Unacast, the United States Census Bureau, and the County Health Rankings and Roadmaps Program. We rejected a primary analysis null hypothesis that stated the social distancing from April 27, 2020, to June 28, 2020, had no effect on the COVID-19-related death toll from June 29, 2020, to August 2, 2020 (p-value < 0.001), and found that it took more reduction in mobility to prevent exponential growth in case numbers for non-rural counties compared to rural counties.
A finite mixture model is used to learn trends from the currently available data on coronavirus (COVID-19). Data on the number of confirmed COVID-19 related cases and deaths for European countries and the United States (US) are explored. A semi-supervised clustering approach with positive equivalence constraints is used to incorporate country and state information into the model. The analysis of trends in the rates of cases and deaths is carried out jointly using a mixture of multivariate Gaussian non-linear regression models with a mean trend specified using a generalized logistic function. The optimal number of clusters is chosen using the Bayesian information criterion. The resulting clusters provide insight into different mitigation strategies adopted by US states and European countries. The obtained results help identify the current relative standing of individual states and show a possible future if they continue with the chosen mitigation technique
Currently, novel coronavirus disease 2019 (COVID-19) is a big threat to global health. The rapid spread of the virus has created pandemic, and countries all over the world are struggling with a surge in COVID-19 infected cases. There are no drugs or other therapeutics approved by the US Food and Drug Administration to prevent or treat COVID-19: information on the disease is very limited and scattered even if it exists. This motivates the use of data integration, combining data from diverse sources and eliciting useful information with a unified view of them. In this paper, we propose a Bayesian hierarchical model that integrates global data for real-time prediction of infection trajectory for multiple countries. Because the proposed model takes advantage of borrowing information across multiple countries, it outperforms an existing individual country-based model. As fully Bayesian way has been adopted, the model provides a powerful predictive tool endowed with uncertainty quantification. Additionally, a joint variable selection technique has been integrated into the proposed modeling scheme, which aimed to identify possible country-level risk factors for severe disease due to COVID-19.
We propose a general Bayesian approach to modeling epidemics such as COVID-19. The approach grew out of specific analyses conducted during the pandemic, in particular an analysis concerning the effects of non-pharmaceutical interventions (NPIs) in reducing COVID-19 transmission in 11 European countries. The model parameterizes the time varying reproduction number $R_t$ through a regression framework in which covariates can e.g be governmental interventions or changes in mobility patterns. This allows a joint fit across regions and partial pooling to share strength. This innovation was critical to our timely estimates of the impact of lockdown and other NPIs in the European epidemics, whose validity was borne out by the subsequent course of the epidemic. Our framework provides a fully generative model for latent infections and observations deriving from them, including deaths, cases, hospitalizations, ICU admissions and seroprevalence surveys. One issue surrounding our models use during the COVID-19 pandemic is the confounded nature of NPIs and mobility. We use our framework to explore this issue. We have open sourced an R package epidemia implementing our approach in Stan. Versions of the model are used by New York State, Tennessee and Scotland to estimate the current situation and make policy decisions.
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