TRACKING SARS-COV-2 VARIANTS
All viruses, including SARS-CoV-2, the virus that causes COVID-19, change over time. Most changes have little to no impact on the virus’ properties. However, some changes may affect the virus’s properties, such as how easily it spreads, the associated disease severity, or the performance of vaccines, therapeutic medicines, diagnostic tools, or other public health and social measures.
The Network for Genomics Surveillance in South Africa (NGS-SA), which includes the National Institute for Communicable Diseases (NICD), KRISP at the University of KwaZulu-Natal (UKZN), University of Cape Town (UCT), Stellenbosch University (SUN), the University of the Free State (UFS), the University of Pretoria, the University of the Witwatersrand (WITS) and the National Health Laboratory Service (NHLS), continue to monitor and assess the evolution of SARS-CoV-2.
Please see below the updated NGS-SA report (22 September 2023),
- July sequences (n=58) are from the Eastern Cape, KwaZulu-Natal, Gauteng, Mpumalanga, and the Western Cape.
August sequences (n=93) are from Gauteng, Limpopo, Mpumalanga, North West and the Western Cape.
September sequences (n=18) are from the Western Cape.
Variant of Concern Omicron in South Africa
- Omicron dominated in July (100%), August (100%), and September (100%), although the number of sequences
from September are small (n=18)
- XBB.1.5 constituted 38% of July, 30% of August and 28% of September sequences
- XBB.1.16 has been detected in July (17%), August (15%), and September (22%)
- XBB.1.9.* (newly designated clade 23D) was detected in sequences from July (16%), August (10%) and September
- Eleven sequences of the EG.5.1.* lineage (newly designated clade 23F) have been detected in Gauteng (n=1) and
the Western Cape (n=10) in July (n=7), August (n=2), and September (n=2)
- Eighteen sequences of the BA.2.86 lineage have been detected in Gauteng (n=9), Mpumalanga (n=5), Western
Cape (n=2) and North West (n=2), in July (n=2) and August (n=16)