Our study partner The National Institute For Communicable Diseases Of South Africa, which worked with us on the Cough Check study, has said that:
Omicron has been the dominant variant in South African since it emerged in November 2021. In the beginning of the omicron wave, BA.1 (the original omicron) was the dominant lineage, and remained dominant through January 2022 (NICD, 2022).
Omicron BA.2 started increasing in the proportion of the South African population it infected in December 2021 and was dominant by February 2022 (NICD, 2022).
Omicron BA.3 never became dominant, but has been continually detected a low levels (see NICD press release, 2022; NICD, 2022).
BA.4 and BA.5 have increased in prevalence in SA, and as of 29 April 2022 to the 4th of May when this statement was released by the NICD, together make up the majority of genomes found amongst COVID patients tested in South Africa (NICD, 2022).
BA.4 and/or BA.5 have been confirmed in seven provinces in South Africa (Eastern Cape, Gauteng, KwaZulu-Natal, Limpopo, Mpumalanga, North West and Western Cape) in samples collected between 1 January 2022 and 20 April 2022 (Tegally et al., 2022).
In Gauteng and KwaZulu-Natal, BA.4 and BA.5 have rapidly replaced BA.2, and are responsible for approximately 60-75% of sequenced cases by the week starting 18 April 2022 (Tegally et al., 2022).