Dataset Information

Estimation of the serial interval and basic reproduction number of COVID-19 in Qom, Iran, and three other countries: A data-driven analysis in the early phase of the outbreak.

ABSTRACT: The outbreak of COVID-19 was first reported from China, and on 19 February 2020, the first case was confirmed in Qom, Iran. The basic reproduction number (R0 ) of infection is variable in different populations and periods. This study aimed to estimate the R0 of COVID-19 in Qom, Iran, and compare it with that in other countries. For estimation of the serial interval, we used data of the 51 confirmed cases of COVID-19 and their 318 close contacts in Qom, Iran. The number of confirmed cases daily in the early phase of the outbreak and estimated serial interval were used for R0 estimation. We used the time-varying method as a method with the least bias to estimate R0 in Qom, Iran, and in China, Italy and South Korea. The serial interval was estimated with a gamma distribution, a mean of 4.55 days and a standard deviation of 3.30 days for the COVID-19 epidemic based on Qom data. The R0 in this study was estimated to be between 2 and 3 in Qom. Of the four countries studied, the lowest R0 was estimated in South Korea (1.5-2) and the highest in Iran (4-5). Sensitivity analyses demonstrated that R0 is sensitive to the applied mean generation time. To the best of the authors' knowledge, this study is the first to estimate R0 in Qom. To control the epidemic, the reproduction number should be reduced by decreasing the contact rate, decreasing the transmission probability and decreasing the duration of the infectious period.

SUBMITTER: Aghaali M

PROVIDER: S-EPMC7300937 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Estimation of the serial interval and basic reproduction number of COVID-19 in Qom, Iran, and three other countries: A data-driven analysis in the early phase of the outbreak.

Aghaali Mohammad M Kolifarhood Goodarz G Nikbakht Roya R Saadati Hossein Mozafar HM Hashemi Nazari Seyed Saeed SS

Transboundary and emerging diseases 20200616 6

The outbreak of COVID-19 was first reported from China, and on 19 February 2020, the first case was confirmed in Qom, Iran. The basic reproduction number (R<sub>0</sub> ) of infection is variable in different populations and periods. This study aimed to estimate the R<sub>0</sub> of COVID-19 in Qom, Iran, and compare it with that in other countries. For estimation of the serial interval, we used data of the 51 confirmed cases of COVID-19 and their 318 close contacts in Qom, Iran. The number of c ...[more]

PMID: 32473049

Similar Datasets

Project description:Estimating the basic reproduction number of a pandemic and the changes that appear on this value over time provide a good understanding of the contagious nature of the virus and efficiency of the controlling strategies. In this paper, we focus on studying the basic reproduction number (R0) for two important variants of COVID-19 pandemic in Iran: Alpha and Delta variants. We use four different methods, three statistical models and one mathematical model, to compute R0: Exponential Growth Rate (EGR), Maximum Likelihood (ML), Sequential Bayesian (SB), and time-dependent SIR model. Alpha variant of COVID-19 was active in Iran from March 10, 2021 until June 10, 2021. Our computations indicate that total R0 of this variant according to EGR, ML, SB, and SIR model is respectively 0.9999 (95% CI: 0.9994-1), 1.046 (95% CI: 1.044-1.049), 1.06 (95% CI: 1.03-1.08), and 2.79 (95% CI: 2.77-2.81) in the whole active time interval. Moreover, during the time interval from April 3, 2021 to April 9, 2021 in which this variant was in its exponential growth in Iran, R0 of Alpha variant in Iran according to SB, EGR, ML, and SIR model is respectively 2.26 (95% CI: 2.04-2.49), 2.64 (95% CI: 2.58-2.7), 11.38 (95% CI: 11.28-11.48), and 12.13 (95% CI: 12.12-12.14). Delta variant was active in Iran during the time interval from June 22, 2021 until September 22, 2021. Our computations show that during the time interval from July 3, 2021 to July 8, 2021 in which this variant was in its exponential growth in Iran, R0 of Delta variant in Iran according to SB, EGR, ML, and SIR model is respectively 3 (95% CI: 2.34-3.66), 3.1 (95% CI: 3.02-3.17), 12 (95% CI: 11.89-12.12), and 23.3 (95% CI: 23.19-23.41). Further, total R0 of Delta variant in Iran in the whole active time interval according to EGR, ML, SB, and SIR model is respectively 1.042 (95% CI: 1.04-1.043), 1.053 (95% CI: 1.051-1.055), 0.79 (95% CI: 0.63-0.95), and 5.65 (95% CI: 5.6-5.7). As the results show Delta variant was more severe than Alpha variant in Iran. Chasing the changes in R0 during each variant shows that the controlling strategies applied were effective in controlling the virus spread.

Dataset Information

Estimation of the serial interval and basic reproduction number of COVID-19 in Qom, Iran, and three other countries: A data-driven analysis in the early phase of the outbreak.

Publications

Estimation of the serial interval and basic reproduction number of COVID-19 in Qom, Iran, and three other countries: A data-driven analysis in the early phase of the outbreak.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets