Detection and frequency of the C.1.2 mutated SARS-Cov-2 lineage in SA

30 August 2021

The Network for Genomics Surveillance in South Africa (NGS-SA, www.ngs-sa.org), 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), has been monitoring changes in SARS-CoV-2, the virus which causes COVID-19, since March 2020.

C.1.2 Lineage

In May 2021, we detected a mutated group of related SARS-CoV-2 viruses in South Africa which we called the C1.2 lineage. C.1.2 has been detected in all provinces in South Africa at relatively low frequency (up to ~2% of genomes) from May to August 2021. This lineage possesses mutations within the genome that have been seen in other SARS-CoV-2 variants of interest (VOI) or variants of concern (VOC) but also other mutations which are novel.

The World Health Organization and the South African National Department of Health were alerted in July to circulation of this lineage. Lastly the NGS-SA is continuing to monitor the frequency of this lineage and tests to assess the functional impacts of these mutations are underway. Thus far the virus has not fulfilled the WHO criteria for VOC or VOI. 

How do the Beta or Delta variants differ from the C.1.2 lineage?

While the C.1.2 lineage shares a few common mutations with the Beta and Delta variants, the new lineage has a number of additional mutations.

What are the implications? Will these mutations affect vaccine effectiveness, disease outcome and transmissibility?

SARS-CoV-2, like all viruses, mutates with time, with mutations that afford the virus some kind of advantage being selected for in recent infections. While some of the mutations in the C.1.2 lineage have arisen in other SARS-CoV-2 variants of concern or variants of interest, we are being cautious about the implications, while we gather more data to understand virus of this lineage

Based on our understanding of the mutations in this variant, we suspect that it might be able to partially evade the immune response, but despite this, that vaccines will still offer high levels of protection against hospitalization and death.

We expect new variants to continue to emerge wherever the virus is spreading. Vaccination remains critical to protect those in our communities at high risk of hospitalization and death, to reduce strain on the health system, and to help slow transmission. This has to be combined with all the other public health and social measures, so we advise the public to remain vigilant and continue to follow COVID-19 protocol by: ensuring good ventilation in all shared spaces, wearing masks (which cover your nose, mouth and chin), washing or sanitizing your hands and surfaces regularly, and keeping 1.5m distance from others as much as possible. These non-pharmaceutical interventions are still proven to prevent the spread of all SARS-CoV-2 viruses.

Will these mutations affect test sensitivity?

The mutated lineage from specimens tested in over 100 specimens from testing labs in all provinces in South Africa so it is unlikely PCR test sensitivity is affected.   

These PCR tests typically detect at least two different SARS-CoV-2 targets, which serves as a backup in the case of a mutation arising in one.

Issued by the NICD, 31 August 2021