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 (07 June 2024) 

In summary:

Sequencing update

  • Testing for SARS CoV 2 throughout the country is very low, and as a result few specimens are being submitted for sequencing.

  • NGS SA partners are working towards closing the delay to sequencing results during the coming months.

  • Systematic testing from sentinel syndromic surveillance has however not indicated an increase in SARS CoV 2 detections (WEEKLY RESPIRATORY PATHOGENS SURVEILLANCE REPORT WEEK)

Variant of Concern Omicron in South Africa

  • The JN.1 lineage is currently the dominant lineage, accounting for 68% of all sequences in South Africa in February through May. BA.2.86 lineages (parent lineage of JN.1) are also being detected but declining in dominance due to JN.1.

  • Recombinant XDD.1.1 (EG.5.1.1 and JN.1.1) has been detected in Gauteng (n=4) and the Western Cape (n=19) in January through May. It has a cumulative prevalence of <0.5% worldwide.

  • JN.1.11.1.* lineages (specifically KP.1.1 and KP.2) have been detected in Gauteng (KP.2, n=1) and the Western Cape (KP.2, n=2 and KP.1.1, n=2).

  • The KP.2 lineage is currently increasing in prevalence in the USA.

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (07 jUNE 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)