Calculation of transmission dynamics parameters and prediction of epidemic size in infectious disease outbreak—based on software R

  Objective  Taking the COVID-19 data of the United States as an example, using software R to calculate of the serial interval (SI), basic reproduction number (R₀), effective reproduction number (Re), doubling time and the number of COVID-19 using software R to provide a reference for the future epidemic response.

  Methods  The daily incidence of COVID-19 in the United States from February 27, 2020 to November 30, 2020, and the SIs of 170 pairs of primary infection cases and and secondary infection cases in the two epidemics in the United States were collected. The “fitdistrplus” package bootstrap method was used to fit the “gamma” distribution of the SI to obtain the mean and standard deviation. Based on the obtained SI, four methods including exponential growth (EG), maximum likelihood (ML), sequential Bayesian estimation (SB), and time-dependent reproduction number (TD) were used to calculate R₀. The R₀ with the best fitting effect based on R² was selected. The doubling time was converted based on the exponential growth rate of the EG method. The “EpiEstim” package was used to calculate Re. The SEIARD model was used to estimate the incidence of COVID-19 in the United States without any intervention, using the “deSolve” and “FME” packages.

  Results  After the fitting of the gamma distribution of SIs of 170 pairs of primary infection cases and secondary infection cases, the SI was =4.78 (95%CI: 4.27−5.31) and the sd was =3.56. The fitted R₀ of EG, ML, SB and TD methods were 2.31 (95%CI: 2.30−2.31), 1.96 (95%CI: 1.95−1.97), 3.01 (95%CI: 2.53−3.55), 3.07 (95% CI: 2.20−4.22), the R² were 0.95, 0.73, 0.99, 0.96, respectively. The doubling time was 3.75 days (3.74−3.77 days). The SEIARD model estimated that all people in the United States would be infected by May 31, 2020 without intervention measures, and no cases would be reported by June 7, 2021, with a total of 5 502 466 deaths.

  Conclusion  The use of software R can quickly calculate the transmission dynamics parameters such as R₀ and predict the size of the epidemic, which is useful in outbreak management.