Credit NICD
#16,379
One week ago today the South African NICD (National Institute of Communicable Diseases) issued the first alert (see South African NICD Statement On B.1.1.529 Variant) on what is now known as the Omicron Variant of Concern.
While researchers are still trying to determine it actual threat, public health agencies around the world are already on alert (see ECDC: Updated Threat Assessment Brief on COVID Omicron (B.1.1.529) - Dec. 2nd) and some nations have restricted travel or even closed their borders (see Japan: Prime Minister's Statement On Closing Borders To Non-Nationals).
Although Delta remains the dominant strain globally, the recent surge in South Africa (see below) suggests that Omicron can successfully compete with - and likely outperform - that COVID juggernaut.
After months of Delta dominating the COVID landscape, during the month of November Omicron was the overwhelming leader among sequenced samples by the NICD.
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 December 2021.
Highlights include:
- New B.1.1.529 (21K) lineage has been designated Variant of Concern Omicron
- Earliest detection in South Africa: 8 November, Gauteng
- Omicron dominates November sequencing data at 74% of genomes (n=183/249). Sequencing is ongoing to determine prevalence of Omicron in other provinces.
- Omicron has now been detected in 19 countries worldwide
- More information can be found at https://www.nicd.ac.za/frequently-asked-questionsfor-the-b-1-1-529-mutated-sars-cov-2-lineage-in-south-africa/
- Delta variant dominated in all provinces until end October
- The Delta sub-lineages vary by province
- C.1.2 lineage detected in all provinces of South Africa with prevalence of <4% of genomes per month
