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 Note: Going forward, this SARS-CoV-2 NGS-SA report will no longer be generated. However, circulating SARS-CoV-2 lineages will continue to be monitored and will be reported in the Weekly Respiratory Pathogens Surveillance Report.
Please see below the NGS-SA report (09 Septrmber 2024)
In summary:
Sequencing update
Testing for SARS-CoV-2 throughout the whole country is very low, and as a result few specimens are being submitted for sequencing.
SARS-CoV-2 detections remain stable from systematic testing from sentinel syndromic surveillance (WEEKLY RESPIRATORY PATHOGENS SURVEILLANCE REPORT WEEK).
Variant of Concern Omicron in South Africa
The JN.1 lineage is the dominant lineage, accounting for 54% of sequences in May, 44% in June and 56% in July. BA.2.86 lineages (parent lineage of JN.1) continue to be detected, but have declined in prevalence.
Variants under monitoring (VUM) KP.2 (n=18) and KP.3 (n=8), have been detected in Gauteng, Limpopo, Mpumalanga and the Western Cape between February and July. Both VUMs have increased in prevalence in the recent months.
Recombinant XDD.1.1 (EG.5.1.1 and JN.1.1) has been detected in Gauteng (n=6) and the Western Cape (n=22). It has a cumulative prevalence of <0.5% worldwide.
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (14 DECEMBER 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (01 DECEMBER 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (17 november 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (03 november 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (20 October 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (06 October 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (08 SEPTEMBER 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (25 AUGUST 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (11 AUGUST 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (14 DECEMBER 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (01 DECEMBER 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (17 november 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (03 november 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (20 October 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (06 October 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (08 SEPTEMBER 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (25 AUGUST 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (11 AUGUST 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (30 June 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (15 June 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (2 June 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (19 May 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (5 May 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (21 April 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (14 April 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (31 March 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (24 March 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (17 March 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (10 March 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (3 March 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (24 Feb 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (17 Feb 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (10 Feb 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (3 Feb 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (27 Jan 2023)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (23 Dec 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (15 Dec 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (9 Dec 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (2 Dec 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (25 Nov 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (18 Nov 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (11 Nov 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (4 Nov 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (28 Oct 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (21 Oct 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (14 Oct 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (7 Oct 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (30 Sep 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (23 Sep 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (16 Sep 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (9 Sep 2022
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (2 Sep 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (26 Aug 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (19 Aug 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (12 Aug 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (5 Aug 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (29 July 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (22 July 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (15 July 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (24 June 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (17 June 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (10 June 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (3 June 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (27 May 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (20 May 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (13 May 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (6 May 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (29 April 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (22 April 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (14 April 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (8 April 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (1 April 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (18 Mar 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (11 Mar 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (4 Mar 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (25 Feb 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (18 Feb 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (11 Feb 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (4 Feb 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (28 Jan 2022)
SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (21 Jan 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)
