key: cord-0331316-hqvjvpkr
authors: Ryu, S.; Kim, D.; Lim, J.-S.; Ali, S. T.; Cowling, B. J.
title: Changes in the serial interval and transmission dynamics associated with the SARS-CoV-2 Delta variant in South Korea
date: 2021-08-20
journal: nan
DOI: 10.1101/2021.08.18.21262166
sha: e09930bdbf65b689fec2a446a2d8c8194c872e47
doc_id: 331316
cord_uid: hqvjvpkr

We estimated the mean serial interval and superspreading potential for the Delta variant SARS-CoV-2. As the Delta variant increased in prevalence, the mean serial interval declined from 4.0 to 2.5 days. However, the risk of superspreading events was similar, as 25% to 27% of cases seeded 80% of all transmission.

July 2021-24 July 2021 and Period 2: 25 July 2021-14 August 2021). The serial interval represents the time between symptom onset of successive cases in a transmission chain (3).

We examined a subset of confirmed COVID-19 cases with symptom onset dates during our study period and reconstructed the transmission pairs by identifying the infector and infectee from the available information on the epidemiological links. Based on 3271 transmission pairs (out of a total 5063 pairs) having the date of symptom onset for both infector and infectee, the overall mean and standard deviation of the serial interval estimate were 3.22 Figure 1A ).

To identify the potential changes in Delta variant SARS-CoV-2 transmissibility, we estimated the time-varying effective reproductive number (ܴ ௧ ), which defines the mean number of secondary infectious cases generated from a typical primary infectious case at time t ( Figure 1B and C). We estimated ܴ ௧ using the EpiEstim package in R (5). Enhanced social distancing measures included limiting gathering sizes to 4 people nationwide were implemented from 19 July 2021 (6). However, we identified that the estimated ܴ ௧ was sustained above 1 during the study period ( Figure 1C ).

For SSE analysis, we calculated the number of secondary cases for each individual from the transmission pairs and fitted the data into a negative binomial distribution (7) (Appendix). The two parameters of the distribution represent the reproduction number (ܴ) and overdispersion parameter (݇), respectively. The estimated ݇ of Period 1 and Period 2 was 0.75 (95% CrI: 0.67, 0.85) and 1.01 (95% CrI: 0.87, 1.17), which corresponded to an expected proportion of cases responsible for 80% of secondary cases of 25% (95% CrI: 24%, . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

The copyright holder for this preprint this version posted August 20, 2021. ; https://doi.org/10.1101/2021.08.18.21262166 doi: medRxiv preprint 26%) and 27% (95% CrI: 26%, 28%) ( Figure 2 ).

We estimated that the serial interval distribution of SARS-CoV-2 was shortened as the Delta was becoming predominant. This is consistent with other recent studies describing the faster spread of the Delta variant compared to other SARS-CoV-2 strains (8, 9). The changes in the implementation of public health measures such as contact tracing and isolation of COVID-19 patients would have affected the serial interval, transmissibility and superspreading potential (3, 4). However, the South Korean public health authority has consistently implemented strategies for active case finding and the immediate isolation of laboratory-confirmed COVID-19 patients and exposed individuals using digital QR codes since 10 June 2020 (10) (Appendix). Therefore, the impact of enhanced case isolation against the serial interval of SARS-CoV-2 is likely limited. Furthermore, restricting large gathering had likely reduced the superspreading potential. However, as the ܴ ௧ was above 1 during most of the study period, this social distancing measure was insufficient to control the transmission of SARS-CoV-2.

Our study has some limitations. First, in our analysis, we did not consider the impact of COVID-19 vaccinations. Though only about 7% of transmission pairs used in this study were linked with older adults (≥ 65 years of age), who might have received COVID-19

vaccinations. The vaccination program has not yet been extended to the public below 55 years of age as of early August 2021. Second, we did not consider the increased amount of travel as the study period covered summer holidays. However, enhanced social distancing was consistently implemented nationwide during the study period. Third, we retrieved online case reports, which could have some inaccuracies in the information. However, the daily . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review)

The copyright holder for this preprint this version posted August 20, 2021. ; https://doi.org/10.1101/2021.08.18.21262166 doi: medRxiv preprint

South Korea reports record daily infections as Delta variant drives surge: Reuters

COVID-19 update as of 3