Probabilistic approximation of effective reproduction number of COVID-19 using daily death statistics

Abstract

The effective reproduction number ( R ) which signifies the number of secondary cases infected by one infectious individual, is an important measure of the spread of an infectious disease. Due to the dynamics of COVID-19 where many infected people are not showing symptoms or showing mild symptoms, and where different countries are employing different testing strategies, it is quite difficult to calculate the R , while the pandemic is still widespread. This paper presents a probabilistic methodology to evaluate the effective reproduction number by considering only the daily death statistics of a given country. The methodology utilizes a linearly constrained Quadratic Programming scheme to estimate the daily new infection cases from the daily death statistics, based on the probability distribution of delays associated with symptom onset and to reporting a death. The proposed methodology is validated in-silico by simulating an infectious disease through a Susceptible-Infectious-Recovered (SIR) model. The results suggest that with a reasonable estimate of distribution of delay to death from the onset of symptoms, the model can provide accurate estimates of R . The proposed method is then used to estimate the R values for two countries.

Analysis of Key Factors of a SARS-CoV-2 Vaccination Program: A Mathematical Modeling Approach

“…The aim is to test the impact of the inoculation rate and efficacy of the vaccine under two different SARS-CoV-2 virus transmission rate scenarios. As it has been mentioned before, there are a lot of uncertainties in the transmission rates for different regions and they vary over time depending on official and unofficial non-pharmaceutical interventions [ 42 , 83 , 101 , 102 , 104 , 154 , 157 ]. However, the approach used here allows us to understand the impact of inoculation rate and vaccine efficacy under two different transmissions of the SARS-CoV-2 virus environments.…”

Analysis of key factors of a SARS-CoV-2 vaccination program: A mathematical modeling approach

“…The aim is to test the impact of the inoculation rate and efficacy of the vaccine under two different SARS-CoV-2 virus transmission rate scenarios. As it has been mentioned before, there are a lot of uncertainties in the transmission rates for different regions and they vary over the time depending on official and unofficial non-pharmaceutical interventions [40, 55, 85, 93, 120, 25, 75]. However, the approach used here allows us to understand the impact of inoculation rate and vaccine efficacy under two different transmission of the SARS-CoV-2 virus environments.…”

A Convex Optimization Solution for the Effective Reproduction NumberRt

“…Menendez 27 shows that Cori et al 10 method can be reproduced effectively using the ratio between the incidence at time t and the value at half the serial interval. Na et al 28 propose a probabilistic methodology where they predict the number of daily new infections from the daily death count. They base their quadratic programming approach on the probability distribution of delays associated with symptom onset and death reporting.…”

“…Na et al . 28 propose a probabilistic methodology where they predict the number of daily new infections from the daily death count. They base their quadratic programming approach on the probability distribution of delays associated with symptom onset and death reporting.…”