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An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City.

ABSTRACT: Epidemiological models can provide the dynamic evolution of a pandemic but they are based on many assumptions and parameters that have to be adjusted over the time the pandemic lasts. However, often the available data are not sufficient to identify the model parameters and hence infer the unobserved dynamics. Here, we develop a general framework for building a trustworthy data-driven epidemiological model, consisting of a workflow that integrates data acquisition and event timeline, model development, identifiability analysis, sensitivity analysis, model calibration, model robustness analysis, and projection with uncertainties in different scenarios. In particular, we apply this framework to propose a modified susceptible-exposed-infectious-recovered (SEIR) model, including new compartments and model vaccination in order to project the transmission dynamics of COVID-19 in New York City (NYC). We find that we can uniquely estimate the model parameters and accurately project the daily new infection cases, hospitalizations, and deaths, in agreement with the available data from NYC's government's website. In addition, we employ the calibrated data-driven model to study the effects of vaccination and timing of reopening indoor dining in NYC.

SUBMITTER: Zhang S

PROVIDER: S-EPMC8452065 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Importance:Internationally imported cases of measles into the United States can lead to outbreaks requiring extensive and rapid control measures. Importation of measles from an unvaccinated adolescent in 2013 led to what has been the largest outbreak of measles in New York City, New York, since 1992. Objective:To describe the epidemiology and public health burden in terms of resources and cost of the 2013 measles outbreak in New York City. Design, Setting, and Participants:This epidemiologic assessment and cost analysis conducted between August 15, 2013, and August 5, 2014, examined all outbreak-associated cases of measles among persons residing in New York City in 2013. Exposures:Measles virus. Main Outcomes and Measures:Numbers of measles cases and contacts. Total personnel time and total direct cost to the New York City Department of Health and Mental Hygiene (DOHMH), calculated as the sum of inputs (supplies and materials, equipment, and logistics) and personnel time (salary and fringe benefits). Results:Between March 13, 2013, and June 9, 2013, 58 persons in New York City with a median age of 3 years (range, 0-32 years) were identified as having measles. Among these individuals, 45 (78%) were at least 12 months old and were unvaccinated owing to parental refusal or intentional delay. Only 28 individuals (48%) visited a medical health care professional who suspected measles and reported the case to the DOHMH at the initial clinical suspicion. Many case patients were not immediately placed into airborne isolation, resulting in exposures in 11 health care facilities. In total, 3351 exposed contacts were identified. Total direct costs to the New York City DOHMH were $394?448, and a total of 10?054 hours were consumed responding to and controlling the outbreak. Conclusions and Relevance:Vaccine refusals and delays appeared to have propagated a large outbreak following importation of measles into the United States. Prompt recognition of measles along with rapid implementation of airborne isolation of individuals suspected of measles infection in health care facilities and timely reporting to public health agencies may avoid large numbers of exposures. The response and containment of measles outbreaks are resource intensive.

Project description:BackgroundThis study was conducted to identify epidemiological characteristics of the first documented CHIK fever outbreak in China and evaluate the effect of the preventive measures taken.Methodology/principal findingsFrom September 1 to October 29, 2010, China's first documented outbreak of CHIK fever occurred in the Xincun community of Wanjiang District of Dongguan city, Guangdong province; 253 case-patients were recorded, of which 129 were laboratory confirmed, with an attack rate of 1%. Before September 18(th) the number of CHIK fever cases remained relatively low in the Xincun community; from September 19(th) onwards, the number of cases increased drastically, with an outbreak peak on October 4(th). Cases were distributed across nine small village groups in the Xincun community, with an attack rate of 0-12% at the village level. The household attack rates ranged between 20% and 100%. No significant difference was found in the attack rate between males and females. There was a significant difference in the attack rate in different age groups (chi-square=18.35, p=0.005); highest in patients aged 60 years or older and the lowest in patients aged under 10. The major clinical characteristics of patients are fever (100%), joint pain (79%) and rash (54%). Phylogenetic analysis of the E1 gene on the five earliest confirmed cases showed that the strains of CHIKV isolated from their sera were highly homologous (up to 99%) with isogeneic strains isolated in Thailand in 2009. After control measures were taken, including killing adult mosquitoes and cleaning breeding habitats of Aedes mosquitoes, the Breteau index and Mosq-ovitrap index decreased rapidly, and the outbreak ended on October 29.Conclusion/significanceThe infection source of the outbreak was imported. Cases showed obvious temporal, spatial, and population aggregation during the outbreak. Comprehensive control measures based on reducing the density of Aedes mosquitoes were effective in controlling the epidemic.

Project description:Introduction: Many studies have reported the association between air pollution and human health based on regulatory air pollution monitoring data. However, because regulatory monitoring networks were not designed for epidemiological studies, the collected data may not provide sufficient spatial contrasts for assessing such associations. Our goal was to develop a monitoring design supplementary to the regulatory monitoring network in Seoul, Korea. This design focused on the selection of 20 new monitoring sites to represent the variability in PM2.5 across people's residences for cohort studies. Methods: We obtained hourly measurements of PM2.5 at 37 regulatory monitoring sites in 2010 in Seoul, and computed the annual average at each site. We also computed 313 geographic variables representing various pollution sources at the regulatory monitoring sites, 31,097 children's homes from the Atopy Free School survey, and 412 community service centers in Seoul. These three types of locations represented current, subject, and candidate locations. Using the regulatory monitoring data, we performed forward variable selection and chose five variables most related to PM2.5. Then, k-means clustering was applied to categorize all locations into several groups representing a diversity in the spatial variability of the five selected variables. Finally, we computed the proportion of current to subject location in each cluster, and randomly selected new monitoring sites from candidate sites in the cluster with the minimum proportion until 20 sites were selected. Results: The five selected geographic variables were related to traffic or urbanicity with a cross-validated R² value of 0.69. Clustering analysis categorized all locations into nine clusters. Finally, one to eight new monitoring sites were selected from five clusters. Discussion: The proposed monitoring design will help future studies determine the locations of new monitoring sites representing spatial variability across residences for epidemiological analyses.

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An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City.

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