COVID-19 outbreak trends in South Africa: A comparison of Omicron (B.1.1.529), Delta (B.1.617.2), and Beta (B.1.351) variants outbreak periods

Abstract

Objectives: We provided COVID-19 outbreak trends in South Africa during the Omicron (B.1.1.529), Delta (B.1.617.2), and Beta (B.1.351) variants outbreak periods from November 2020 to March 2022.

Methods: We used the time series summary data of the COVID-19 outbreak for South Africa available in the COVID-19 data repository created by the Center for System and Science and Engineering at Johns Hopkins University and the Our World in Data database by the University of Oxford from January 2020 to March 2022. We used the joinpoint regression model with a data-driven Bayesian information criterion method for analyzing the outbreak trends. In addition, we used density ellipses and partition modeling on the outbreak data.

Results: During the Omicron outbreak period, COVID-19 cases in South Africa significantly jumped by 4.7 times from December 01 to December 08, 2021. The average daily growth rate of incidence peaked at 23,000 cases/day until December 16, 2021, which was 18.6 % higher than the peak growth during the Delta outbreak period. South Africa experienced peak growth in COVID-19 cases with 18,611 cases/day (January 04 to January 14, 2021) during the Beta outbreak period and with 19,395 cases/day (July 01 to July 11, 2021) during the Delta outbreak period. Density ellipsoid showed a significant correlation between daily cases and daily death count during the Beta and Delta outbreak period which was not prominent in the Omicron outbreak period. Comparatively higher daily death tolls were reported in days with a recovery rate of less than 89.1 % and 91.9 % in the Beta and Delta outbreak period respectively. The backlog counts may be one of the reasons for the significant increase in daily death tolls during the Omicron period.

Conclusions: During the Omicron period, COVID-19 cases peaked growth was 18.6 % higher than the peak growth during the Delta outbreak period. Despite that fact, growth in death trends in the Omicron outbreak period was found low which might be due to the low mortality rate and case fatality proportion. The emergence of the Omicron variant once again reminds us that- "no one is safe until everyone is safe".

Keywords: Beta (B.1.351); COVID-19; Delta (B.1.617.2); Joinpoint regression analysis; Omicron (B.1.1.529); South Africa.