Modeling of the Long-Term Epidemic Dynamics of COVID-19 in the United States.
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ABSTRACT:
SUBMITTER: Huang D
PROVIDER: S-EPMC8305610 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:As of January 19, 2021, the cumulative number of people infected with coronavirus disease-2019 (COVID-19) in the United States has reached 24,433,486, and the number is still rising. The outbreak of the COVID-19 epidemic has not only affected the development of the global economy but also seriously threatened the lives and health of human beings around the world. According to the transmission characteristics of COVID-19 in the population, this study established a theoretical differential equation mathematical model, estimated model parameters through epidemiological data, obtained accurate mathematical models, and adopted global sensitivity analysis methods to screen sensitive parameters that significantly affect the development of the epidemic. Based on the established precise mathematical model, we calculate the basic reproductive number of the epidemic, evaluate the transmission capacity of the COVID-19 epidemic, and predict the development trend of the epidemic. By analyzing the sensitivity of parameters and finding sensitive parameters, we can provide effective control strategies for epidemic prevention and control. After appropriate modifications, the model can also be used for mathematical modeling of epidemics in other countries or other infectious diseases.
| S-EPMC8761816 | biostudies-literature
Project description:PurposeThere is a growing concern about the COVID-19 epidemic intensifying in rural areas in the United States (U.S.). In this study, we described the dynamics of COVID-19 cases and deaths in rural and urban counties in the U.S.MethodsUsing data from April 1 to November 12, 2020, from Johns Hopkins University, we estimated COVID-19 incidence and mortality rates and conducted comparisons between urban and rural areas in three time periods at the national level, and in states with higher and lower COVID-19 incidence rates.ResultsResults at the national level showed greater COVID-19 incidence rates in urban compared to rural counties in the Northeast and Mid-Atlantic regions of the U.S. at the beginning of the epidemic. However, the intensity of the epidemic has shifted to a rapid surge in rural areas. In particular, high incidence states located in the Mid-west of the country had more than 3,400 COVID-19 cases per 100,000 people compared to 1,284 cases per 100,000 people in urban counties nationwide during the third period (August 30 to November 12).ConclusionsOverall, the current epicenter of the epidemic is located in states with higher infection rates and mortality in rural areas. Infection prevention and control efforts including healthcare capacity should be scaled up in these vulnerable rural areas.
| S-EPMC8061094 | biostudies-literature
Project description:We use COVID-19 case and mortality data from 1 February 2020 to 21 September 2020 and a deterministic SEIR (susceptible, exposed, infectious and recovered) compartmental framework to model possible trajectories of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and the effects of non-pharmaceutical interventions in the United States at the state level from 22 September 2020 through 28 February 2021. Using this SEIR model, and projections of critical driving covariates (pneumonia seasonality, mobility, testing rates and mask use per capita), we assessed scenarios of social distancing mandates and levels of mask use. Projections of current non-pharmaceutical intervention strategies by state-with social distancing mandates reinstated when a threshold of 8 deaths per million population is exceeded (reference scenario)-suggest that, cumulatively, 511,373 (469,578-578,347) lives could be lost to COVID-19 across the United States by 28 February 2021. We find that achieving universal mask use (95% mask use in public) could be sufficient to ameliorate the worst effects of epidemic resurgences in many states. Universal mask use could save an additional 129,574 (85,284-170,867) lives from September 22, 2020 through the end of February 2021, or an additional 95,814 (60,731-133,077) lives assuming a lesser adoption of mask wearing (85%), when compared to the reference scenario.
| S-EPMC7806509 | biostudies-literature
Project description:BackgroundA range of near-real-time online/mobile mapping dashboards and applications have been used to track the coronavirus disease 2019 (COVID-19) pandemic worldwide; however, small area-based spatiotemporal patterns of COVID-19 in the United States remain unknown.MethodsWe obtained county-based counts of COVID-19 cases confirmed in the United States from 22 January to 13 May 2020 (N = 1 386 050). We characterized the dynamics of the COVID-19 epidemic through detecting weekly hotspots of newly confirmed cases using Spatial and Space-Time Scan Statistics and quantifying the trends of incidence of COVID-19 by county characteristics using the Joinpoint analysis.ResultsAlong with the national plateau reached in early April, COVID-19 incidence significantly decreased in the Northeast (estimated weekly percentage change [EWPC]: -16.6%) but continued increasing in the Midwest, South, and West (EWPCs: 13.2%, 5.6%, and 5.7%, respectively). Higher risks of clustering and incidence of COVID-19 were consistently observed in metropolitan versus rural counties, counties closest to core airports, the most populous counties, and counties with the highest proportion of racial/ethnic minorities. However, geographic differences in incidence have shrunk since early April, driven by a significant decrease in the incidence in these counties (EWPC range: -2.0%, -4.2%) and a consistent increase in other areas (EWPC range: 1.5-20.3%).ConclusionsTo substantially decrease the nationwide incidence of COVID-19, strict social-distancing measures should be continuously implemented, especially in geographic areas with increasing risks, including rural areas. Spatiotemporal characteristics and trends of COVID-19 should be considered in decision making on the timeline of re-opening for states and localities.
| S-EPMC7454424 | biostudies-literature
Project description:Non-pharmaceutical interventions to combat COVID-19 transmission have worked to slow the spread of the epidemic but can have high socio-economic costs. It is critical we understand the efficacy of non-pharmaceutical interventions to choose a safe exit strategy. Many current models are not suitable for assessing exit strategies because they do not account for epidemic resurgence when social distancing ends prematurely (e.g., statistical curve fits) nor permit scenario exploration in specific locations. We developed an SEIR-type mechanistic epidemiological model of COVID-19 dynamics to explore temporally variable non-pharmaceutical interventions. We provide an interactive tool and code to estimate the transmission parameter, β, and the effective reproduction number, R eff . We fit the model to Santa Clara County, California, where an early epidemic start date and early shelter-in-place orders could provide a model for other regions. As of April 22, 2020, we estimate an R eff of 0.982 (95% CI: 0.849 - 1.107) in Santa Clara County. After June 1 (the end-date for Santa Clara County shelter-in-place as of April 27), we estimate a shift to partial social distancing, combined with rigorous testing and isolation of symptomatic individuals, is a viable alternative to indefinitely maintaining shelter-in-place. We also estimate that if Santa Clara County had waited one week longer before issuing shelter-in-place orders, 95 additional people would have died by April 22 (95% CI: 7 - 283). Given early life-saving shelter-in-place orders in Santa Clara County, longer-term moderate social distancing and testing and isolation of symptomatic individuals have the potential to contain the size and toll of the COVID-19 pandemic in Santa Clara County, and may be effective in other locations.
| S-EPMC7276010 | biostudies-literature
Project description:Post-acute sequelae of SARS-CoV-2 infection are debilitating, clinically heterogeneous, and of unknown molecular etiology. A transcriptome-wide investigation was performed in acutely infected patients followed clinically into the post-acute period. Distinct gene-expression signatures of post-acute sequelae were already present in whole-blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell associated gene-expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in subjects with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development.
2022-12-06 | GSE215865 | GEO
Project description:BackgroundThe coronavirus disease 2019 (COVID-19) is rapidly spreading in China and more than 30 countries over last two months. COVID-19 has multiple characteristics distinct from other infectious diseases, including high infectivity during incubation, time delay between real dynamics and daily observed number of confirmed cases, and the intervention effects of implemented quarantine and control measures.MethodsWe develop a Susceptible, Un-quanrantined infected, Quarantined infected, Confirmed infected (SUQC) model to characterize the dynamics of COVID-19 and explicitly parameterize the intervention effects of control measures, which is more suitable for analysis than other existing epidemic models.ResultsThe SUQC model is applied to the daily released data of the confirmed infections to analyze the outbreak of COVID-19 in Wuhan, Hubei (excluding Wuhan), China (excluding Hubei) and four first-tier cities of China. We found that, before January 30, 2020, all these regions except Beijing had a reproductive number R > 1, and after January 30, all regions had a reproductive number R < 1, indicating that the quarantine and control measures are effective in preventing the spread of COVID-19. The confirmation rate of Wuhan estimated by our model is 0.0643, substantially lower than that of Hubei excluding Wuhan (0.1914), and that of China excluding Hubei (0.2189), but it jumps to 0.3229 after February 12 when clinical evidence was adopted in new diagnosis guidelines. The number of unquarantined infected cases in Wuhan on February 12, 2020 is estimated to be 3,509 and declines to 334 on February 21, 2020. After fitting the model with data as of February 21, 2020, we predict that the end time of COVID-19 in Wuhan and Hubei is around late March, around mid March for China excluding Hubei, and before early March 2020 for the four tier-one cities. A total of 80,511 individuals are estimated to be infected in China, among which 49,510 are from Wuhan, 17,679 from Hubei (excluding Wuhan), and the rest 13,322 from other regions of China (excluding Hubei). Note that the estimates are from a deterministic ODE model and should be interpreted with some uncertainty.ConclusionsWe suggest that rigorous quarantine and control measures should be kept before early March in Beijing, Shanghai, Guangzhou and Shenzhen, and before late March in Hubei. The model can also be useful to predict the trend of epidemic and provide quantitative guide for other countries at high risk of outbreak, such as South Korea, Japan, Italy and Iran.Supplementary materialsThe supplementary materials can be found online with this article at 10.1007/s40484-020-0199-0.
| S-EPMC7095099 | biostudies-literature
Project description:BackgroundCompartmental models dominate epidemic modeling. Transmission parameters between compartments are typically estimated through stochastic parameterization processes that depends on detailed statistics of transmission characteristics, which are economically and resource-wise expensive to collect.ObjectiveWe aim to apply deep learning techniques as a lower data dependency alternative to estimate transmission parameters of a customized compartmental model, for the purpose of simulating the dynamics of the US coronavirus disease (COVID-19) epidemic and projecting its further development.MethodsWe constructed a compartmental model and developed a multistep deep learning methodology to estimate the model's transmission parameters. We then fed the estimated transmission parameters to the model to predict development of the US COVID-19 epidemic for 35 and 42 days. Epidemics are considered suppressed when the basic reproduction number (R0) is less than 1.ResultsThe deep learning-enhanced compartmental model predicts that R0 will fall to <1 around August 17-19, 2020, at which point the epidemic will effectively start to die out, and that the US "infected" population will peak around August 16-18, 2020, at 3,228,574 to 3,308,911 individual cases. The model also predicted that the number of accumulative confirmed cases will cross the 5 million mark around August 7, 2020.ConclusionsCurrent compartmental models require stochastic parameterization to estimate the transmission parameters. These models' effectiveness depends upon detailed statistics on transmission characteristics. As an alternative, deep learning techniques are effective in estimating these stochastic parameters with greatly reduced dependency on data particularity.
| S-EPMC7451112 | biostudies-literature
Project description:The evolution of the COVID-19 pandemic is described through a time-dependent stochastic dynamic model in discrete time. The proposed multi-compartment model is expressed through a system of difference equations. Information on the social distancing measures and diagnostic testing rates are incorporated to characterize the dynamics of the various compartments of the model. In contrast with conventional epidemiological models, the proposed model involves interpretable temporally static and dynamic epidemiological rate parameters. A model fitting strategy built upon nonparametric smoothing is employed for estimating the time-varying parameters, while profiling over the time-independent parameters. Confidence bands of the parameters are obtained through a residual bootstrap procedure. A key feature of the methodology is its ability to estimate latent unobservable compartments such as the number of asymptomatic but infected individuals who are known to be the key vectors of COVID-19 spread. The nature of the disease dynamics is further quantified by relevant epidemiological markers that make use of the estimates of latent compartments. The methodology is applied to understand the true extent and dynamics of the pandemic in various states within the United States (US).
| S-EPMC8831615 | biostudies-literature
Project description:The impact of variable infection risk by race and ethnicity on the dynamics of SARS-CoV-2 spread is largely unknown. Here, we fit structured compartmental models to seroprevalence data from New York State and analyze how herd immunity thresholds (HITs), final sizes, and epidemic risk change across groups. A simple model where interactions occur proportionally to contact rates reduced the HIT, but more realistic models of preferential mixing within groups increased the threshold toward the value observed in homogeneous populations. Across all models, the burden of infection fell disproportionately on minority populations: in a model fit to Long Island serosurvey and census data, 81% of Hispanics or Latinos were infected when the HIT was reached compared to 34% of non-Hispanic whites. Our findings, which are meant to be illustrative and not best estimates, demonstrate how racial and ethnic disparities can impact epidemic trajectories and result in unequal distributions of SARS-CoV-2 infection. K.C.M. was supported by National Science Foundation GRFP grant DGE1745303. Y.H.G. and M.L. were funded by the Morris-Singer Foundation. M.L. was supported by SeroNet cooperative agreement U01 CA261277.
| S-EPMC8221808 | biostudies-literature