A highly mutated virus variant for Covid-19 is circulating in Mzansi. While it has been detected at low rates, the country has seen a gradual increase in detection rates month to month.
The National Institute for Communicable Diseases (NICD) issued an alert on the C.1.2 lineage on Monday, saying that it had been detected in all provinces.
This lineage possesses mutations that have been seen in other SARS-CoV-2 variants of interest (VOI) and variants of concern (VOC).
The NICD said it was monitoring the situation closely. “It is doing to some extent what Delta did at the beginning of the second wave. It’s impossible [to predict how it will spread]. It’s crystal ball stuff and we’ve learnt not to predict what variants do. We are watching it carefully, we are counting the number of genomes, we are counting where the genomes are,” the NICD’s professor Penny Moore said in a press briefing.
Labs are testing vaccine’s efficacy against C.1.2
The NICD said that several labs in the country were now assessing the efficacy of vaccines against C.1.2, the SABC reports.
“What that entails, is taking blood from people who have been vaccinated and from people who have been infected with Covid-19.”
“We grow the virus C.1.2 in a lab and we test the antibodies from those people against the virus to assess that. Protection from severe disease is mediated by a separate arm of the immune system: T-cells.
“T-cells are much more tolerant of mutations. T-cells maintain almost all their activity against the variants that we have so far. This is the reason that despite the various mutations in this variant, the vaccines that we have will still protect against severe disease,” added Moore.
A brief history of C.1.2
In May 2021 the Network for Genomics Surveillance in South Africa (NGS-SA) detected a mutated group of related SARS-CoV-2 viruses in South Africa, which it dubbed the C.1.2 lineage.
The World Health Organization (WHO) and the South African national department of health were alerted in July to the circulation of this lineage. 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 WHO criteria for a virus of interest to be placed on a higher-alert tier as a virus of concern.
The NGS-SA is comprised of the NICD, the National Health Laboratory Service (NHLS), the Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP) and the Universities of Cape Town (UCT), Stellenbosch (SUN), the Free State (UFS), Pretoria and the Witwatersrand (WITS).
Frequently asked questions about the variant:
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 several additional mutations, said the NICD.
What are the implications? Will these mutations affect vaccine effectiveness, disease outcome and transmissibility?
SARS-CoV-2, like all viruses, mutates with time. Mutations afford the virus some kind of advantage, 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, the NICD said it is being cautious about the implications while they gather more data to understand virus of this lineage
“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 hospitalisation 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 hospitalisation and death, to reduce strain on the health system and to help slow transmission.”
Will these mutations affect test sensitivity?
The mutated lineage from specimens tested in over 100 specimens from abs in all provinces in South Africa, so it is unlikely that 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.
Mzansi’s vaccination status
According to the department of health, the country has now distributed 12 289 478 vaccines, translating to 9 252 975 people who have received at least one dose of vaccination. A total of 5 818 291 people are now fully vaccinated.