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 (01 March 2024) 

In summary:

Sequencing update

  • November sequences (n=261) and December sequences (n=116) are from all provinces except the Northern Cape. January sequences (n=82) are from the Western Cape, Mpumalanga, Eastern Cape, North West and Gauteng, and February sequences (n=22) are from the Western Cape.

Variant of Concern Omicron in South Africa

  • BA.2.86 was dominant at 56% of sequences in November, 60% in December, 51% in January and was not detected in February, although based on a small number of sequences.
  • JN.1 constituted 5% of November sequences, 18% of December sequences, 39% of January sequences and 86% of February sequences.
  • XBB.1.16 was detected in November (2%), December (1 %) and January (1 %), and was not detected in February sequences.
  • EG.5.1.* lineage (clade 23F) was detected at a prevalence of 3% in November, 3% in December and 1% in January.
  • Nine sequences of newly designated BA.2.87.1 lineage have been detected in SA in September-December 2023. No new sequences have been detected since December 2023.
  • Recombinant XDD.1.1 (EG.5.1.1 and JN.1.1) has been detected in Gauteng (n=1) and the Western Cape (n=7). It has a cumulative prevalence of <0.5% worldwide.

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (01 March 2024)

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)