skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Dynamic estimation of epidemiological parameters of COVID-19 outbreak and effects of interventions on its spread
Background: A key challenge in estimating epidemiological parameters for a pandemic such as the initial COVID-19 outbreak in Wuhan is the discrepancy between the officially reported number of infections and the true number of infections. A common approach to tackling the challenge is to use the number of infections exported from the originating city to infer the true number. This approach can only provide a static estimate of the epidemiological parameters before city lockdown because there are almost no exported cases thereafter.Methods: We propose a Bayesian estimation method that dynamically estimates the epidemiological parameters by recovering true numbers of infections from day-to-day official numbers. To illustrate the use of this method, we provide a comprehensive retrospection on how the COVID-19 had progressed in Wuhan from January 19 to March 5, 2020. Particularly, we estimate that the outbreak sizes by January 23 and March 5 were 11,239 [95% CI 4,794–22,372] and 124,506 [95% CI 69,526–265,113], respectively.Results: The effective reproduction number attained its maximum on January 24 (3.42 [95% CI 3.34–3.50]) and became less than 1 from February 7 (0.76 [95% CI 0.65–0.92]). We also estimate the effects of two major government interventions on the spread of COVID-19 in Wuhan.Conclusions: This case study by our proposed method affirms the believed importance and effectiveness of imposing tight non-essential travel restrictions and affirm the importance and effectiveness of government interventions (e.g., transportation suspension and large scale hospitalization) for effective mitigation of COVID-19 community spread.  more » « less
Award ID(s):
1916376
PAR ID:
10250820
Author(s) / Creator(s):
; ; ; ; ; ;
Date Published:
Journal Name:
Journal of Public Health Research
Volume:
10
Issue:
1
ISSN:
2279-9028
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Background The COVID-19 outbreak in Wuhan started in December 2019 and was under control by the end of March 2020 with a total of 50,006 confirmed cases by the implementation of a series of nonpharmaceutical interventions (NPIs) including unprecedented lockdown of the city. This study analyzes the complete outbreak data from Wuhan, assesses the impact of these public health interventions, and estimates the asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan. Methods By taking different stages of the outbreak into account, we developed a time-dependent compartmental model to describe the dynamics of disease transmission and case detection and reporting. Model coefficients were parameterized by using the reported cases and following key events and escalated control strategies. Then the model was used to calibrate the complete outbreak data by using the Monte Carlo Markov Chain (MCMC) method. Finally we used the model to estimate asymptomatic and undetected cases and approximate the overall antibody prevalence level. Results We found that the transmission rate between Jan 24 and Feb 1, 2020, was twice as large as that before the lockdown on Jan 23 and 67.6 % (95% CI [0.584,0.759]) of detectable infections occurred during this period. Based on the reported estimates that around 20% of infections were asymptomatic and their transmission ability was about 70% of symptomatic ones, we estimated that there were about 14,448 asymptomatic and undetected cases (95% CI [12,364,23,254]), which yields an estimate of a total of 64,454 infected cases (95% CI [62,370,73,260]), and the overall antibody prevalence level in the population of Wuhan was 0.745% (95% CI [0.693 % ,0.814 % ]) by March 31, 2020. Conclusions We conclude that the control of the COVID-19 outbreak in Wuhan was achieved via the enforcement of a combination of multiple NPIs: the lockdown on Jan 23, the stay-at-home order on Feb 2, the massive isolation of all symptomatic individuals via newly constructed special shelter hospitals on Feb 6, and the large scale screening process on Feb 18. Our results indicate that the population in Wuhan is far away from establishing herd immunity and provide insights for other affected countries and regions in designing control strategies and planing vaccination programs. 
    more » « less
  2. null (Ed.)
    Background The natural history of disease in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remained obscure during the early pandemic. Aim Our objective was to estimate epidemiological parameters of coronavirus disease (COVID-19) and assess the relative infectivity of the incubation period. Methods We estimated the distributions of four epidemiological parameters of SARS-CoV-2 transmission using a large database of COVID-19 cases and potential transmission pairs of cases, and assessed their heterogeneity by demographics, epidemic phase and geographical region. We further calculated the time of peak infectivity and quantified the proportion of secondary infections during the incubation period. Results The median incubation period was 7.2 (95% confidence interval (CI): 6.9‒7.5) days. The median serial and generation intervals were similar, 4.7 (95% CI: 4.2‒5.3) and 4.6 (95% CI: 4.2‒5.1) days, respectively. Paediatric cases < 18 years had a longer incubation period than adult age groups (p = 0.007). The median incubation period increased from 4.4 days before 25 January to 11.5 days after 31 January (p < 0.001), whereas the median serial (generation) interval contracted from 5.9 (4.8) days before 25 January to 3.4 (3.7) days after. The median time from symptom onset to discharge was also shortened from 18.3 before 22 January to 14.1 days after. Peak infectivity occurred 1 day before symptom onset on average, and the incubation period accounted for 70% of transmission. Conclusion The high infectivity during the incubation period led to short generation and serial intervals, necessitating aggressive control measures such as early case finding and quarantine of close contacts. 
    more » « less
  3. Abstract To support COVID-19 pandemic planning, we develop a model-inference system to estimate epidemiological properties of new SARS-CoV-2 variants of concern using case and mortality data while accounting for under-ascertainment, disease seasonality, non-pharmaceutical interventions, and mass-vaccination. Applying this system to study three variants of concern, we estimate that B.1.1.7 has a 46.6% (95% CI: 32.3–54.6%) transmissibility increase but nominal immune escape from protection induced by prior wild-type infection; B.1.351 has a 32.4% (95% CI: 14.6–48.0%) transmissibility increase and 61.3% (95% CI: 42.6–85.8%) immune escape; and P.1 has a 43.3% (95% CI: 30.3–65.3%) transmissibility increase and 52.5% (95% CI: 0–75.8%) immune escape. Model simulations indicate that B.1.351 and P.1 could outcompete B.1.1.7 and lead to increased infections. Our findings highlight the importance of preventing the spread of variants of concern, via continued preventive measures, prompt mass-vaccination, continued vaccine efficacy monitoring, and possible updating of vaccine formulations to ensure high efficacy. 
    more » « less
  4. null (Ed.)
    The sudden outbreak of the COVID-19 pandemic has brought drastic changes to people’s daily lives, work, and the surrounding environment. Investigations into these changes are very important for decision makers to implement policies on economic loss assessments and stimulation packages, city reopening, resilience of the environment, and arrangement of medical resources. In order to analyze the impact of COVID-19 on people’s lives, activities, and the natural environment, this paper investigates the spatial and temporal characteristics of Nighttime Light (NTL) radiance and Air Quality Index (AQI) before and during the pandemic in mainland China. The monthly mean NTL radiance, and daily and monthly mean AQI are calculated over mainland China and compared before and during the pandemic. Our results show that the monthly average NTL brightness is much lower during the quarantine period than before. This study categorizes NTL into three classes: residential area, transportation, and public facilities and commercial centers, with NTL radiance ranges of 5–20, 20–40 and greater than 40 (nW· cm − 2 · sr − 1 ), respectively. We found that the Number of Pixels (NOP) with NTL detection increased in the residential area and decreased in the commercial centers for most of the provinces after the shutdown, while transportation and public facilities generally stayed the same. More specifically, we examined these factors in Wuhan, where the first confirmed cases were reported, and where the earliest quarantine measures were taken. Observations and analysis of pixels associated with commercial centers were observed to have lower NTL radiance values, indicating a dimming behavior, while residential area pixels recorded increased levels of brightness after the beginning of the lockdown. The study also discovered a significant decreasing trend in the daily average AQI for mainland China from January to March 2020, with cleaner air in most provinces during February and March, compared to January 2020. In conclusion, the outbreak and spread of COVID-19 has had a crucial impact on people’s daily lives and activity ranges through the increased implementation of lockdown and quarantine policies. On the other hand, the air quality of mainland China has improved with the reduction in non-essential industries and motor vehicle usage. This evidence demonstrates that the Chinese government has executed very stringent quarantine policies to deal with the pandemic. The decisive response to control the spread of COVID-19 provides a reference for other parts of the world. 
    more » « less
  5. null (Ed.)
    Development of strategies for mitigating the severity of COVID-19 is now a top public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions. We developed an individual-based model for COVID-19 transmission in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan. The calibrated model was used to simulate different intervention scenarios and estimate the impact of different interventions on outbreak size and workday loss. The use of high-efficacy facial masks was shown to be able to reduce infection cases and workday loss by 80% (90% credible interval (CrI): 73.1–85.7%) and 87% (CrI: 80.0–92.5%), respectively. The use of social distancing alone, through reduced contacts between healthcare workers, had a marginal impact on the outbreak. Our results also indicated that a quarantine policy should be coupled with other interventions to achieve its effect. The effectiveness of all these interventions was shown to increase with their early implementation. Our analysis shows that a COVID-19 outbreak in a hospital's non-COVID-19 unit can be controlled or mitigated by the use of existing non-pharmaceutical measures. 
    more » « less