Tracking and controlling the spatiotemporal spread of SARS-CoV-2 Omicron variant in South Africa

Background: South Africa is the focus of the current epidemic caused by Omicron. Understanding the spatio-temporal spread of Omicron in South Africa and how to control it is crucial to global countries. Methods: To explore the spatiotemporal spread of Omicron in 9 provinces in South Africa, a province-level geographic prediction model of COVID-19 symptom onset risk, is proposed. Results: It has been found that i) The spatiotemporal spread was relatively slow during the first stage and following the emergence of Omicron in Gauteng. The spatial spread of Omicron accelerated after it had become the dominant variant, and continued to spread from Gauteng to the neighboring provinces and main transport nodes. ii) Compared with current Alert Levels 1-4 in all provinces, the imposition of lockdown in the high-onset-risk Gauteng together with the Alert Level 1 in other 8 provinces, was found to more effectively control the spread of Omicron in South Africa. Moreover, it can reduce the spread of the Omicron epidemic in the provinces where main international airports are located to other parts of the world. iii) Due to declining vaccine efficiency over time, even when the daily vaccination rates in each province increased by 10 times, the daily overall onset risk was only reduced by 0.34%-7.86%. Conclusions: Our study has provided a comprehensive investigation concerning the spatiotemporal dynamics of Omicron and hence provided scientific findings to enable a contribution which will assist in controlling the spatiotemporal spread of Omicron by integrating the prevention measures and vaccination.