Experts Identify New COVID Variation in South Africa – What’s Known So Far

As a team of South African researchers, we have identified a new line of SARS-CoV-2, the virus that causes COVID-19. A lineage represents a genetically distinct virus population with a common ancestor. This virus may be classified as a variant in the future, based on heavily modified properties, but first we need to understand it better. Our findings to date are set out in a non-pre-peer-reviewed paper.

The new lineage, which has been given the name C.1.2, has been found in all provinces of the country. Although it shares some mutations with other variants, it is different in some respects.

Viruses are constantly mutating. Sometimes the mutations have an additional benefit for the virus, such as increased transmissibility. But often mutations do nothing good for the virus. So more mutations don’t always mean problems for us, the host.

Much is still unknown for C.1.2. For example, it is too early to say whether these mutations will affect the transmissibility or efficacy of the vaccine.

The Network for Genomics Surveillance in South Africa has been monitoring changes in SARS-CoV-2 since March 2020. South Africa was one of the first countries in the world to introduce systematic and coordinated genomic surveillance, sequencing the genomes of SARS-CoV-2 from patient samples representative of different geographic regions and over time.

The findings have provided insight into how and when SARS-CoV-2 was introduced into the country and its early spread. The network has also sequenced virus genomes to identify newly developing viral lines of particular interest.

Later in 2020, the network discovered what is now called the Beta variant of concern and more recently observed, in near real time, the arrival and rapid “acquisition” of the Delta variant in South Africa.

What is known and what is not known?

We select patient samples from diagnostic labs across the country and perform sequencing to analyze the virus genomes. We then compare these sequences with the sequences we have seen before and elsewhere. It is very similar to the game where you see the difference between almost identical images.

We play the difference on the spot with SARS-CoV-2. When we find a lot of differences – or differences in certain particularly important places like the peak of the virus – we pay special attention. Then we look at how often we see this particular virus and where – in one region of the country or in multiple regions, just in South Africa or also in other parts of the world. We are also checking to see if it increases over time, which could indicate that it is replacing previous versions of the virus.

When we sequence the virus and compare it to other SARS-CoV-2 viruses, it is assigned a name based on the most similar virus. Then we look at the virus and the virus it matches to see how similar they are. If we see many differences, that could be an indication of a new lineage.

In May 2021, we first discovered a mutated group of related SARS-CoV-2 viruses in South Africa that has been given the C.1.2 lineage. So far, from May to August 2021, C.1.2 has been detected in all provinces. Yet it occurs at a relatively low frequency and although we see small increases over time in this lineage, they remain very low.

This lineage possesses mutations in the genome that have been observed in other SARS-CoV-2 variants.

The network warned the World Health Organization (WHO) and the South African National Ministry of Health about this lineage in July. The two months between our initial discovery and notification stem from the lengthy process of sequencing and analysis. In addition, mutated viruses appear from time to time, but many disappear again. So we had to keep an eye on this particular instance to see if it would be detected in other regions. It wasn’t until we started detecting it in other provinces and when it was reported from other countries as well that we felt we had enough evidence to suggest a new lineage.

The surveillance network continues to monitor the frequency of the lineage across the country and is helping other African countries do the same. Tests are also underway to assess the functional impact of the mutations it harbors – for example, how well do antibodies in people previously vaccinated or infected neutralize the new virus, how well it multiplies in cell cultures compared to other viruses. variants, and so on.

The virus does not yet meet the WHO criteria to be classified as a variant of interest or concern. An interesting variant has genetic changes that affect important virus characteristics (transmissibility, disease severity, immune, diagnostic or therapeutic escape) and epidemiological effects that indicate a risk to global public health. A variant of concern is the worst category – it is a variant with proven increased transmissibility and/or virulence and/or decreased effectiveness of public health or medical devices such as vaccines, therapies and tests.

Delta is a prime example of a variant of concern that quickly dominated the epidemic worldwide and caused major waves in many countries, including those with advanced vaccine rollouts.

The C.1.2 lineage shares a few common mutations with all other variants of concern, including the beta, lambda, and delta variants. But the new lineage has some additional mutations.

The implications

We are still collecting more data to understand the impact of this lineage on transmissibility and on vaccines.

SARS-CoV-2, like all viruses, mutates over time, usually in a way that gives the virus some benefit. Some of the mutations in the C.1.2 lineage originated in other SARS-CoV-2 variants of interest or concern. But we still don’t have a complete picture. Characterizing its properties requires a combination of ongoing thorough monitoring (especially to see if it might displace the current prevailing delta variant) and laboratory studies.

Based on our current understanding of the mutations in this particular lineage, we suspect it may partially evade the immune response. Despite this, our opinion, based on what we now know, is that vaccines still provide a high degree of protection against hospitalization and death.

We expect that new variants will emerge wherever the virus spreads. Vaccination remains critical to protecting those in our communities at high risk of hospitalization and death, reducing pressure on the health system and slowing transmission. This should be combined with all other public health and social measures.

We therefore advise the public to remain vigilant and to continue to follow the COVID-19 protocol by including good ventilation in all shared areas and wearing masks that cover the nose, mouth and chin. These non-pharmaceutical interventions have still been shown to prevent the spread of SARS-CoV-2 regardless of the variant.

We also believe that the mutated lineage is unlikely to affect the sensitivity of PCR assays. These tests typically detect at least two different parts of the SARS-CoV-2 genome, which serves as a backup in the event of a mutation in one of them. Studies are underway to assess any implications for diagnostic testing.

Why vigilance is necessary?

The Network for Genomic Surveillance in South Africa connects the National Health Laboratory Service and private COVID-19 testing labs with academic sequencing centers. This collaboration allowed South African experts to quickly generate and analyze sequence data to inform regional and national responses.

At the end of August 2021, the delta variant accounted for more than 90% of the sequences in southern Africa. But virus evolution is ongoing, as long as the virus can spread from person to person, multiply and be passed on. It is therefore necessary to continue to monitor its evolution, to detect new problematic properties at an early stage and to take countermeasures where possible.

Written by:

Prof. dr. Wolfgang Preiser – Head: Department of Medical Virology, Stellenbosch University Cathrine Scheepers – Senior Medical Scientist, University of the Witwatersrand Jinal Bhiman – Chief Medical Scientist at National Institute of Communicable Diseases (NICD), National Institute of Communicable Diseases Marietjie Venter – Head : Program for zoonotic, occupational and respiratory virus, professor, department of medical virology, University of Pretoria Penny Moore – Reader and DST/NRF SARChI Chair of Virus-Host Dynamics, National Institute for Communicable Diseases, CAPRISA Research Associate, University of the Witwatersrand Tulio de Oliveira – Director: KRISP – KwaZulu-Natal Research and Innovation Sequencing Platform, University of KwaZulu-Natal

Disclosure Statement

Prof. dr. Wolfgang Preiser receives funding from the South African Medical Research Council and other scientific funders. He is a member of the South African Ministerial Advisory Committee on COVID-19 Vaccines (VMAC).

Jinal Bhiman receives funding from South African National Ministry of Health as part of COVID-19 emergency response; a collaboration agreement between the National Institute for Communicable Diseases of the National Health Laboratory Service and the United States Centers for Disease Control and Prevention; the African Society of Laboratory Medicine (ASLM) and Africa Centers for Disease Control and Prevention through a Bill and Melinda Gates Foundation sub-award; the British Foreign, Commonwealth and Development Office and Wellcome; the South African Medical Research Council and the South African Department of Science and Innovation; the UK Department of Health and Social Care, managed by the Fleming Fund and implemented under the auspices of the SEQAFRICA project. She is affiliated with the National Institute for Communicable Diseases and the University of the Witwatersrand; and is a member of the World Health Organization’s Technical Advisory Group on Viral Evolution.

Marietjie Venter receives funding from the National Research Foundation of South Africa; The European Union program (LEAP-Agri); the BMBF (the German Federal Ministry for Education and Research); and National Health Laboratory Services Research Foundation for Unrelated Research. She is currently employed by the University of Pretoria. She acted as a temporary advisor to the WHO. The views expressed here are those of the author and do not reflect those of the funders or employer.

Penny Moore receives funding from the National Research Foundation, the South African Medical Research Council and the US National Institutes of Health.

Tulio de Oliveira does not work for, consult, hold shares in or receive funding from any company or organization that would benefit from this article, and has not disclosed any relevant affiliations outside of their academic appointment. It is supported by funding from the South African Medical Research Council and the Department of Science and Innovation.

Cathrine Scheepers does not work for, consult, hold stock in, or receive funding from, any company or organization that would benefit from this article, and has not disclosed any relevant affiliations outside of their academic tenure.

This article was first published in The Conversation.