Spatiotemporal prevalence of COVID-19 and SARS-CoV-2 variants in Africa

Li-Ping Gao ^1* Canjun Zheng ² Ting-Ting Tian ² Alie Brima ³ Michael K Abdulai ³ Xiao Kang ² Cao Chen ² Dong-Lin Liang ² Qi Shi ² Zhi-Guo Liu ² Xiao-Ping Dong ²

• ¹ National Institute for Viral Disease Control and Prevention (China CDC), Beijing, China
• ² Chinese Center For Disease Control and Prevention, Beijing, China
• ³ Sierra Leone China Friendship Hospital, Freetown, Sierra Leone

The COVID-19 pandemic has caused significant public health and socioeconomic crisis across Africa, however, the prevalent patterns of COVID-19 and the circulating characteristics of SARS-CoV-2 variants on the continent remain insufficiently documented. In this study, national data on case numbers, incidences, mortalities, the circulation of SARS-CoV-2 variants, and key health indexes from Jan 2020 to Dec 2023 were collected from several official or professional sources. The prevalent profiles and circulating features of SARS-CoV-2 across African continent, its five regions and all African countries were analyzed. Four major waves of epidemic were observed, closely associated with the introduction of the early SARS-CoV-2 strain (1st wave) and the emergence of specific variants, including VOC (variants of concern) Alpha, Beta, VOI (variants of interest) Eta (2nd wave), VOC Delta (3rd wave), and VOC Omicron (4th wave). SaTScan analysis identified four large spatiotemporal clusters, affecting varying numbers of countries. A significant portion of countries (50 out of 56) reported their first case during Feb and Mar 2020, predominantly involving individuals with confirmed cross-continental travel histories, mainly from European. In total, 12 distinct SARS-CoV-2 VOCs and VOIs were identified, among which VOCs Omicron, Delta, Beta, Alpha, and VOI Eta were the most prevalent. Unlike the dominance of VOC Delta during the 3rd wave and Omicron during the 4th wave, VOC Alpha was comparatively scarce in the Southern region but more common in other four regions, while Beta predominated in the Southern region and Eta in the Western region during the 2nd wave. Relatively higher case incidences and mortalities were reported in the Southern and Northern Africa regions. Spearman rank correlation and Geographically Weighted Regression (GWR) analyses of COVID-19 incidences against health indexes in 52 African countries, indicating that countries with higher national health expenditures and better personnel indexes tended to report higher case incidences. This study provides a comprehensive overview of the COVID-19 pandemic in Africa. Strengthening the capacity of health institutions across African countries is crucial for the timely and accrual detection of new variants SARS-CoV-2 and, consequently, for preparedness against future COVID-19 pandemics and other potential infectious diseases outbreaks.