Impact of SARS-CoV-2 variants of concern on Covid-19 epidemic in South Africa

Abstract

The Covid-19 pandemic has resulted in immense suffering throughout the world, with over 250 million cases and over 5 million Covid-19-related deaths reported by 9 November 2021. South Africa has the highest burden of Covid-19 in Africa, accounting for 34% of all cases and 41% of all reported Covid-19 deaths on the continent (Africa CDC COVID-19 Dashboard, 2021). By 1 November 2021, South Africa had reported more than 2.9 million Covid-19 cases and over 89,000 Covid-19 deaths (COVID-19 Corona Virus South African Resource Portal, 2020), with substantial cases and deaths due to the Beta variant in the second wave and to the Delta variant in the third wave. Given the importance of variants in determining what the waves of infection look like, the future trajectory of the SARS-CoV-2 epidemic in South Africa will be largely dependent on viral variants. The fi rst case of Covid-19 in South Africa was reported on 5 March 2020 by a traveller who had recently returned from Italy. Although mitigation measures, such as a national lock-down and border closures, initially kept Covid-19 cases low, there was a steady increase in cases as restrictions eased. In the fi rst wave, the average daily Covid-19 cases peaked at 12,583 in mid-July 2020, driven principally by variants with the D614G mutation. The second wave began in late November 2020 and the average daily Covid-19 cases peaked at 19,042 in January 2021. By mid-May 2021, the country once again began experiencing a surge in cases, reaching a peak of 19,958 in July 2021 in the country ’ s