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 (2 Dec 2022), with an additional 32 genomes since the last report.

In summary:

  • Sequencing update
    • All provinces have sequences for September, and all provinces except the Eastern Cape have sequences for October.
    • Gauteng, Western Cape, Limpopo, Mpumalanga, Northern Cape and North West have sequences for November.
  • Variant of Concern Omicron in South Africa
    • Omicron continued to dominate in September (98%), October (98%) and November (100%).
    • Omicron BA.5 and sub-lineages were dominant in September (78%), October (90%) and currently make up 91% of November data.
    • BA.2.75.* was detected at a low prevalence (≤1%) in September, October and November.
    • XAY was detected in September and October at a low prevalence (≤2%).
    • BQ.1 and sub-lineages have been detected in September, October and November
      • September (1%) – BQ.1*: n=1 in the Northern Cape, n=6 in the Western Cape, n=1 in Gauteng
      • October (5%) – BQ.1*: n=2 in KwaZulu-Natal, n=14 in Gauteng, n=24 in the Western Cape, n=1 in the Northern Cape, n=1 in the Mpumalanga
      • November (12%) – BQ.1*: n=9 in the Western Cape, n=7 in Gauteng, n=1 in the Northern Cape
    • XBB has been detected in October and November
      • October (1%): n=2 in Gauteng, n=3 in the Western Cape
      • November (4%): n=4 in Gauteng, n=2 in the Western Cape
  • Delta detected at low frequency until July, and once in October.

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (2 Dec 2022)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (31 DEc 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (24 DEc 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (17 DEc 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (10 DEc 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (8 DEc 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (3 DEc 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (1 DEc 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (26 Nov 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (19 Nov 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (12 Nov 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (05 Nov 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (29 Oct 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (22 Oct 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (15 Oct 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (08 Oct 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (30 Sept 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (27 Sept 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (17 Sept 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (9 Sept 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (1 Sept 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (27 Aug 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (19 Aug 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (12 Aug 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (5 Aug 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (29 July 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (19 July 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (12 July 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (7 July 2021)

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (1 July 2021)