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 14 January 2022. 

Highlights include:
Variant of Concern Omicron

  • Detected in 139 countries and dominating globally
  • Split into three lineages based on different mutational profiles: BA.1 (21K), BA.2 (21L), BA.3 (remains in 21M with parent lineage B.1.1.529 as does not meet
    requirements for new clade)
  • New sub-lineage has been designated: BA.1.1. This contains lineage-defining BA.1.1 + spike:R346K

South Africa:

  • Dominated November sequencing data at 86% of genomes (n=1252/1579) and
    December sequencing data at 99% of genomes (n=1361/1377)
  • Limited sequence data for January shows continued dominance of Omicron
    (n=58/59)
  • BA.1 dominant in SA, with BA.2 increase recently observed and to be confirmed by
    additional data

Low frequency of previously circulating variants such as Delta and C.1.2 still detected in
recent data

SARS-CoV-2 GENOMIC SURVEILLANCE UPDATE (14 Jan 2021)

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

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)