Estimation of Effective Reproduction Number for a COVID-19 Outbreak Caused by SARS-CoV-2 Omicron Variant of Concern in Shenyang, China

Background/Objective: Since reported firstly in November 2021, Severe Acute Respiratory Syndrome Coronavirus2(SARS-CoV-2) Omicron Variant of Concern (VoC) has spread worldwide at an unprecedented speed. However, scholars have different research results on the transmissibility of this VoC. This study was to estimate the communication power of SARS-CoV-2 Omicron VoC through calculating the time-varying effective reproduction number Re(t) using an outbreak data in Shenyang, China to, as well as to provide data support for other scholars to carry out further transmissibility research of SARS-CoV-2 Omicron VoC.Methods: The daily incidence data of COVID-19 outbreak during March 5 and April 25 in Shenyang, China was downloaded from the Nationwide Notifiable Infectious Diseases Reporting Information System (NIDRIS). The infector-infectee pair was identified through epidemiological investigation and analysis. Then make a list of series interval(SI) distribution and a table of generation time(GT) distribution for each infector-infectee pair. Convert series interval in SI list to generation time distribution through 'est.GT' function included in 'R0' package. At last, estimate Re(t) by R Package 'EpiEstim' based on bayesian framework through parameter and non parameter method respectively.Results: 1134 infections were found in this outbreak with 20 confirmed cases and 1124 asymptomatic infections. 54 infector-infectee pairs were identified and form a SI list, but only 15 infector-infectee pairs were included in the GT table at last. The generation time distribution converted from series interval in SI list met the best fitting distribution of LogNorm distribution with mean = 2.84 and sd = 2.22. Re(t) calculated by parameter method and nonparametric method all peaked on March 17 with a value of 2.58 and 2.54, Re(t) calculated by parameter method decreased to less than 1 on March 29 then remained less than 1, Re(t) calculated by the nonparametric method decreased to less than 1 on March 28 then remained less than 1. There was no statistical difference in Re(t) distribution calculated by the two methods (t = 0.001, P = 0.999).Conclusions: It was reasonable to calculate Re (t) through parameter method in which the SI list was converted into GT distribution by 'est.GT' function in the 'R0' package when we did not have access to generational time distribution of infection-infectee pair data.Funding Information: This work was not supported by any funding.Declaration of Interests: The authors declare that they have no conflict of interest.Ethics Approval Statement: Not applicable.