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

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

Viruses mutate all the time. Sometimes the mutations result in an added benefit for the virus, such as increased transmissibility. But often mutations don’t do anything beneficial for the virus. So more mutations do not always mean trouble for us, its host.

For C.1.2, a lot is still unknown. For example, it’s too early to tell whether these mutations will affect transmissibility or vaccine efficacy.

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 globally to introduce systematic and coordinated genomic surveillance, sequencing genomes of SARS-CoV-2 from patient samples representative of different geographic regions and over time.

Its findings have provided insights into how and when SARS-CoV-2 was introduced into the country, and into its early spread. The Network has also been sequencing virus genomes to identify newly developing viral lineages of particular concern.

Later in 2020 the network detected what is now called the Beta variant of concern and more recently observed, almost in real-time, the arrival and rapid “take-over” of the Delta variant in South Africa.

What’s known, and what’s not known

We select patient samples from diagnostic laboratories throughout the country and perform sequencing to analyze the virus genomes. We then compare these sequences to those seen before and elsewhere. It’s very much like the game where you spot the difference between nearly identical pictures.

We’re playing spot the difference with SARS-CoV-2. When we find many differences – or differences in certain particularly important places like the spike of the virus – we pay special attention. We then look to see how often we see this particular virus and where – in one region of the country or in multiple regions, only in South Africa or also in other parts of the world. We also monitor whether it increases over time, which would suggest that it is replacing previous versions of the virus.

When we sequence the virus and compare it to other SARS-CoV-2 viruses it gets assigned a name based on the closest matching virus. We then look at the virus and the one that it matches to see how similar they are to each other. If we see a lot of differences that could be an indication of a new lineage.

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

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

The network alerted the World Health Organisation (WHO) and the South African National Department of Health to this lineage in July. The two months between our first discovery and the notification comes from the lengthy process of sequencing and analysis. In addition, mutated viruses appear from time to time – but many disappear again. Therefore we needed to monitor this particular one to see if it would be detected in additional regions. Only when we started detecting it in other provinces and when it was reported also from other countries did we feel we had sufficient evidence to suggest a new lineage.

The surveillance network is continuing to monitor the frequency of the lineage across the country, and helping other African countries do the same. Also, tests to assess the functional impact of the mutations it harbors are under way – for example, how well do antibodies in people who have been vaccinated or infected previously neutralise the new virus, how well does it multiply in cell cultures compared to other virus variants, and so on.

The virus has not yet fulfilled the WHO criteria to be classified as a variant of interest or variant of concern. A variant of interest has genetic changes affecting important virus characteristics (transmissibility, disease severity, immune, diagnostic or therapeutic escape) and epidemiological impacts suggesting a risk to global public health. A variant of concern is the worst category – it’s a variant with proven increased transmissibility and/or virulence and/or decreased effectiveness of public health or medical tools such as vaccines, therapeutics, and tests.

Delta is a good example of a variant of concern that rapidly came to dominate the epidemic globally, causing major waves in many countries including those with advanced vaccination roll-out programs.

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 a number of additional mutations.