2 METHODOLOGY
Real-time RT-PCR results were obtained from the Seegene Medical Foundation. The assays used were divided into different periods. In the early stages, emergency use assays (Allplex™ 2019-nCoV (SARS-CoV-2) Assay, E, RdRP, N gene target (February 7, 2020 to December 13, 2020)) were used, and official assays (Allplex™ SARS-CoV-2 Assay,E, RdRP/S, N gene target (December 14, 2020 to January 31, 2022)) were used thereafter. The data was of upper airway samples collected from February 2020 to January 2022 from the collected specimens, Ct values from a total of 296,347 specimens that tested positive withRdRp/S as the target gene were used. The daily median Ct values were computed to determine the time series trends, and the category-specific distributions of Ct values were also examined. In addition, Ct values were compared against the number of new cases and Rt trends to determine their associations. Data for new cases and Rt were obtained from the Korea Disease Control and Prevention Agency (KDCA) for the period between January 20, 2020 (date of index case) to January 2022.
Time series trends and associations were analyzed for the total time and by four COVID-19 waves. The COVID-19 waves were defined by the KDCA; the first, second, and third waves were primarily mass outbreaks in a particular region, while the fourth wave was characterized by community-wide outbreaks facilitated by contacts throughout the community. The first wave is from January 20, 2020 to August 11, 2020. There was a total of 14,660 confirmed cases (daily average 71.5), and the fatality rate—defined as the ratio of confirmed cases to number of deaths—was 2.1%. The major routes of infection were a religious facility and health care facility in a non-metropolitan area. The second wave was from August 12, 2020 to November 12, 2020. There was a total of 13,280 confirmed cases (daily average 142.8), and the fatality rate was 1.66%. During this wave, small and medium-sized outbreaks occurred in religious facilities and demonstrations in the metropolitan area. The third wave was from November 13, 2020 to July 6, 2021. There was a total of 133,600 confirmed cases (daily average 566.1), and the fatality rate was 1.16%. Mass outbreaks occurred in correctional facilities, health care facilities, and religious facilities primarily in the metropolitan area. The fourth wave was from July 7, 2021 to January 31, 2022. There was a total of 684,068 confirmed cases (daily average 3,273.1), and the fatality rate was 0.69%. New patients were concentrated in the metropolitan area and large cities, and the cases surged markedly compared to previous waves due to several factors, including the diminished vaccine effectiveness, domination of the Delta variant, and emergence of the Omicron variant (Yang et al., 2022)
For the association analysis, we applied a time lag between Ct values and new cases and Rt for a detailed analysis of the two indices. The data were analyzed using the SAS 9.4 software (SAS Institute, Inc.).