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Simulation-free estimation of an individual-based SEIR model for evaluating nonpharmaceutical interventions with an application to COVID-19 in the District of Columbia.

ABSTRACT: The ongoing COVID-19 pandemic has overwhelmingly demonstrated the need to accurately evaluate the effects of implementing new or altering existing nonpharmaceutical interventions. Since these interventions applied at the societal level cannot be evaluated through traditional experimental means, public health officials and other decision makers must rely on statistical and mathematical epidemiological models. Nonpharmaceutical interventions are typically focused on contacts between members of a population, and yet most epidemiological models rely on homogeneous mixing which has repeatedly been shown to be an unrealistic representation of contact patterns. An alternative approach is individual based models (IBMs), but these are often time intensive and computationally expensive to implement, requiring a high degree of expertise and computational resources. More often, decision makers need to know the effects of potential public policy decisions in a very short time window using limited resources. This paper presents a computation algorithm for an IBM designed to evaluate nonpharmaceutical interventions. By utilizing recursive relationships, our method can quickly compute the expected epidemiological outcomes even for large populations based on any arbitrary contact network. We utilize our methods to evaluate the effects of various mitigation measures in the District of Columbia, USA, at various times and to various degrees. Rcode for our method is provided in the supplementry material, thereby allowing others to utilize our approach for other regions.

SUBMITTER: Sewell DK

PROVIDER: S-EPMC7654811 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Simulation-free estimation of an individual-based SEIR model for evaluating nonpharmaceutical interventions with an application to COVID-19 in the District of Columbia.

Sewell Daniel K DK Miller Aaron A

PloS one 20201110 11

The ongoing COVID-19 pandemic has overwhelmingly demonstrated the need to accurately evaluate the effects of implementing new or altering existing nonpharmaceutical interventions. Since these interventions applied at the societal level cannot be evaluated through traditional experimental means, public health officials and other decision makers must rely on statistical and mathematical epidemiological models. Nonpharmaceutical interventions are typically focused on contacts between members of a p ...[more]

PMID: 33170871

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Project description:ImportanceResurgent COVID-19 cases have resulted in the reinstitution of nonpharmaceutical interventions, including school closures, which can have adverse effects on families. Understanding the associations of school closures with the number of incident and cumulative COVID-19 cases is critical for decision-making.ObjectiveTo estimate the association of schools being open or closed with the number of COVID-19 cases compared with community-based nonpharmaceutical interventions.Design, setting, and participantsThis decision analytical modelling study developed an agent-based transmission model using a synthetic population of 1 000 000 individuals based on the characteristics of the population of Ontario, Canada. Members of the synthetic population were clustered into households, neighborhoods, or rural districts, cities or rural regions, day care facilities, classrooms (ie, primary, elementary, or high school), colleges or universities, and workplaces. Data were analyzed between May 5, 2020, and October 20, 2020.ExposuresSchool reopening on September 15, 2020, vs schools remaining closed under different scenarios for nonpharmaceutical interventions.Main outcomes and measuresIncident and cumulative COVID-19 cases between September 1, 2020, and October 31, 2020.ResultsAmong 1 000 000 simulated individuals, the percentage of infections among students and teachers acquired within schools was less than 5% across modeled scenarios. Incident COVID-19 case numbers on October 31, 2020, were 4414 (95% credible interval [CrI], 3491-5382) cases in the scenario with schools remaining closed and 4740 (95% CrI, 3863-5691) cases in the scenario for schools reopening, with no other community-based nonpharmaceutical intervention. In scenarios with community-based nonpharmaceutical interventions implemented, the incident case numbers on October 31 were 714 (95% CrI, 568-908) cases for schools remaining closed and 780 (95% CrI, 580-993) cases for schools reopening. When scenarios applied the case numbers observed in early October in Ontario, the cumulative case numbers were 777 (95% CrI, 621-993) cases for schools remaining closed and 803 (95% CrI, 617-990) cases for schools reopening. In scenarios with implementation of community-based interventions vs no community-based interventions, there was a mean difference of 39 355 cumulative COVID-19 cases by October 31, 2020, while keeping schools closed vs reopening them yielded a mean difference of 2040 cases.Conclusions and relevanceThis decision analytical modeling study of a synthetic population of individuals in Ontario, Canada, found that most COVID-19 cases in schools were due to acquisition in the community rather than transmission within schools and that the changes in COVID-19 case numbers associated with school reopenings were relatively small compared with the changes associated with community-based nonpharmaceutical interventions.

Project description:Accurate HIV surveillance data are essential to monitor trends to help end the HIV epidemic. Owing to strict policies around data security and confidentiality, HIV surveillance data have not been routinely shared across jurisdictions except a biannual case-by-case review process to identify and remove duplicate cases (Routine Interstate Duplicate Review, RIDR). HIV surveillance estimates for the District of Columbia (DC) are complicated by migration and care seeking throughout the metropolitan area, which includes Maryland and Virginia. To address gaps in HIV surveillance data, health departments of DC, Maryland, and Virginia have established HIV surveillance data sharing agreements. Although the Black Box (a privacy data integration tool external to the health departments) facilitates the secure exchange of data between DC, Maryland, and Virginia, its previous iterations were limited by the frequency and scope of information exchanged. The health departments of DC, Maryland, and Virginia engaged in data sharing to further improve HIV surveillance estimates.This study assessed the impact of cross-jurisdictional data sharing on the estimation of people living with HIV in DC and reduction of cases in the RIDR process.Data sharing agreements established in 2014 allowed for the exchange of HIV case information (eg, current residential address) and laboratory information (eg, test types, result dates, and results) from the enhanced HIV/AIDS Reporting System (eHARS). Regular data exchanges began in 2017. The participating jurisdictions transferred data (via secure file transfer protocol) for individuals having a residential address in a partnering jurisdiction at the time of HIV diagnosis or evidence of receiving HIV-related services at a facility located in a partnering jurisdiction. The DC Department of Health compared the data received to DC eHARS and imported updated data that matched existing cases. Evaluation of changes in current residential address and HIV prevalence was conducted by comparing data before and after HIV surveillance data exchanges.After the HIV surveillance data exchange, an average of 396 fewer cases were estimated to be living in DC each year from 2012 to 2016. Among cases with a residential status change, 66.4% (1316/1982) had relocated to Maryland and 19.8% (392/1982) to Virginia; majority of these had relocated to counties bordering DC. Relocation in and out of DC differed by mode of transmission, race and ethnicity, age group, and gender. After data exchange, the volume of HIV cases needing RIDR decreased by 74% for DC-Maryland and 81% for DC-Virginia.HIV surveillance data exchange between the public health departments of DC, Maryland, and Virginia reduced the number of cases misclassified as DC residents and reduced the number of cases needing RIDR. Continued data exchanges will enhance the ability of DC Department of Health to monitor the local HIV epidemic.

Project description:An epidemic disease caused by a new coronavirus has spread in Northern Italy with a strong contagion rate. We implement an SEIR model to compute the infected population and the number of casualties of this epidemic. The example may ideally regard the situation in the Italian Region of Lombardy, where the epidemic started on February 24, but by no means attempts to perform a rigorous case study in view of the lack of suitable data and the uncertainty of the different parameters, namely, the variation of the degree of home isolation and social distancing as a function of time, the initial number of exposed individuals and infected people, the incubation and infectious periods, and the fatality rate. First, we perform an analysis of the results of the model by varying the parameters and initial conditions (in order for the epidemic to start, there should be at least one exposed or one infectious human). Then, we consider the Lombardy case and calibrate the model with the number of dead individuals to date (May 5, 2020) and constrain the parameters on the basis of values reported in the literature. The peak occurs at day 37 (March 31) approximately, with a reproduction ratio R 0 of 3 initially, 1.36 at day 22, and 0.8 after day 35, indicating different degrees of lockdown. The predicted death toll is approximately 15,600 casualties, with 2.7 million infected individuals at the end of the epidemic. The incubation period providing a better fit to the dead individuals is 4.25 days, and the infectious period is 4 days, with a fatality rate of 0.00144/day [values based on the reported (official) number of casualties]. The infection fatality rate (IFR) is 0.57%, and it is 2.37% if twice the reported number of casualties is assumed. However, these rates depend on the initial number of exposed individuals. If approximately nine times more individuals are exposed, there are three times more infected people at the end of the epidemic and IFR = 0.47%. If we relax these constraints and use a wider range of lower and upper bounds for the incubation and infectious periods, we observe that a higher incubation period (13 vs. 4.25 days) gives the same IFR (0.6 vs. 0.57%), but nine times more exposed individuals in the first case. Other choices of the set of parameters also provide a good fit to the data, but some of the results may not be realistic. Therefore, an accurate determination of the fatality rate and characteristics of the epidemic is subject to knowledge of the precise bounds of the parameters. Besides the specific example, the analysis proposed in this work shows how isolation measures, social distancing, and knowledge of the diffusion conditions help us to understand the dynamics of the epidemic. Hence, it is important to quantify the process to verify the effectiveness of the lockdown.

Dataset Information

Simulation-free estimation of an individual-based SEIR model for evaluating nonpharmaceutical interventions with an application to COVID-19 in the District of Columbia.

Publications

Simulation-free estimation of an individual-based SEIR model for evaluating nonpharmaceutical interventions with an application to COVID-19 in the District of Columbia.

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