Open AccessAdaptive Susceptible-Infectious-Removed Model for Continuous Estimation of the COVID-19 Infection Rate and Reproduction Number in the United States: Modeling Study
Author(s) -
Mark B. Shapiro,
Fazle Karim,
Guido Muscioni,
Abel Saju Augustine
Publication year - 2021
Publication title -
jmir. journal of medical internet research/journal of medical internet research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.446
H-Index - 142
eISSN - 1439-4456
pISSN - 1438-8871
DOI - 10.2196/24389
Subject(s) - covid-19 , basic reproduction number , epidemic model , reproduction , estimation , infectious disease (medical specialty) , pandemic , virology , biology , computer science , medicine , outbreak , environmental health , genetics , disease , population , engineering , systems engineering , pathology
Background The dynamics of the COVID-19 pandemic vary owing to local population density and policy measures. During decision-making, policymakers consider an estimate of the effective reproduction number R t , which is the expected number of secondary infections spread by a single infected individual. Objective We propose a simple method for estimating the time-varying infection rate and the R t . Methods We used a sliding window approach with a Susceptible-Infectious-Removed (SIR) model. We estimated the infection rate from the reported cases over a 7-day window to obtain a continuous estimation of R t . A proposed adaptive SIR (aSIR) model was applied to analyze the data at the state and county levels. Results The aSIR model showed an excellent fit for the number of reported COVID-19 cases, and the 1-day forecast mean absolute prediction error was <2.6% across all states. However, the 7-day forecast mean absolute prediction error approached 16.2% and strongly overestimated the number of cases when the R t was rapidly decreasing. The maximal R t displayed a wide range of 2.0 to 4.5 across all states, with the highest values for New York (4.4) and Michigan (4.5). We found that the aSIR model can rapidly adapt to an increase in the number of tests and an associated increase in the reported cases of infection. Our results also suggest that intensive testing may be an effective method of reducing R t . Conclusions The aSIR model provides a simple and accurate computational tool for continuous R t estimation and evaluation of the efficacy of mitigation measures.