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.

This report is based on data collected up to 1 July 2022. 

Highlights include:

Variant of Concern Omicron in South Africa

  • Dominates 2022 sequencing data at >98% of genomes.
  • While BA.1 was the predominant lineage in January (55%), BA.2 dominated in February (86%) and March (78%).
  • Omicron lineages BA.4 and BA.5 increased in prevalence in March (16%), and together are dominant in April (73%), May (94%) and June (96%).
  • BA.2.12.1 was detected in South Africa at low prevalence in May and June (<1%)
  • Low frequency of previously circulating variants such as Delta still detected in recent data.

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