EXPERT REACTION: Could South Africa’s new, mutated variant be worse than Delta? (preprint*)

Very little data is currently available on the C.1.2 variant; we are awaiting further studies to characterise it.  

Originating in South Africa, its geographical spread has so far been limited and it has caused relatively few infections.  

As long as there are new infections with SARS-CoV-2, the virus will evolve. New variants will emerge and it is important to monitor them. However, not every variant survives, and many die out despite containing mutations which might suggest otherwise. 

C.1.2 contains key mutations within the spike gene seen in other variants of concern, such as Alpha and Beta. Compared to the original Wuhan variant, these mutations could increase the virus's transmissibility but we don't know how it compares to Delta in this regard. Vaccinations will still provide a high degree of protection from the disease, but variants may slightly reduce the ability of antibodies generated by vaccination to prevent symptomatic disease.   

SARS-CoV-2 continues to mutate as we continue to provide it with many chances to spread freely and continuously among its favoured host - us!.

This latest preprint from scientific and medical experts in South Africa highlights a new group of SARS-CoV-2 viral variants that cluster under the name of C.1.2. The study describes this viral variant's genetic features but doesn't give us new evidence about signs and symptoms of COVID-19, the incubation period, serial interval, viral load, transmission efficiency, immune response or ongoing vaccine effectiveness.

Even in South Africa, this virus comprises just 2 per cent of the known SARS-CoV-2 variants spreading there. This is despite more virus genome sequencing occurring there now than ever before. Approximately 100 sequences exist worldwide since the viruses were first discovered approximately three months ago.

We will learn more about C.1.2 in time, but as yet we have no real indication that this most recently popularised variant should be an urgent cause of concern. We do know the viruses harbour some mutations that may be a cause for concern when viewed individually. How the constellation of mutations interacts in the final viral package and once in humans though, is unclear. The World Health Organization and a world full of genomic experts will maintain vigilance. As yet, this hasn't; been characterised as a variant of interest (VOI), the step preceding a possible classification as a variant of concern (VOC;https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/).  

In the meantime - we can get fully vaccinated to protect ourselves from serious disease due to infection by any SARS-CoV-2 variant. We can wear a mask to reduce the risk of infecting others and ourselves and we can stay distant from others and work hard to avoid sharing the same air as those who might be infected. All of these steps combine to help keep us as safe as we can be from this latest airborne virus.

The New C.1.2 South African variant. A Potential cause for concern?

Scientists in South Africa are monitoring a new coronavirus variant with an unusually high mutation rate, and whose frequency has gradually increased in recent months. The variant, known as C.1.2., was flagged last week by the KwaZulu-Natal Research and Innovation and Sequencing Platform in a preprint study that has yet to be peer reviewed. Most of South Africa’s coronavirus cases are currently caused by the Delta variant (first detected in India).

How different is this new variant from Delta?

This new C.1.2. variant caught scientists’ attention because its mutation is almost twice as fast as observed in other global variants including the current predominant Delta. It has since spread to most provinces in South Africa, as well as a handful of other countries in Africa, Europe, Asia and Oceania, according to the research, which is still awaiting peer review. 

Why is there a concern?

Scientists are concerned about the variant because of how quickly it has mutated: it is between 44 and 59 mutations away from the original virus detected in Wuhan, making it more mutated than any other WHO-identified Variant of Concern or Variant of Interest. It also contains many mutations which have been associated with increased transmissibility and a heightened ability to evade antibodies in other variants, the scientists said, though they occur in different mixes and their impacts on the virus are not yet fully known. 

Should we be worried?

From the published preprint, it is evident that C.1.2. may have more immune evasion properties than the prevalent delta variant, based on its pattern of mutations, but the full extent of the fitness and pathogenicity of the new variant is still very much under review. I personally feel that at current stage, people shouldn’t be overly concerned about C.1.2. yet, as it was expected that variants with more mutations would emerge later in the pandemic.

Furthermore, C.1.2. still makes up a very small but consistently growing portion of all of South Africa’s cases. It accounted for just 1 per cent of samples in June and 3 per cent in July, versus 67 per cent of samples in June and 89 per cent in July for the delta variant. 

There has been much concern expressed in the social media and the mainstream media about the C.1.2 variant just discovered in South Africa. However, it is too early to determine whether or not it is likely to create major problems or indeed even take over from the Delta variant.

Similar concerns were expressed about the Iota variant first detected in New York, and that was swiftly overtaken by the Delta variant. At the moment, C.1.2 is not even a Variant of Interest, let alone a Variant of Concern. So, I think that we should remain calm, let the excellent South African virologists do their work, and watch carefully what happens over the next few weeks.

Unfortunately, the identification of a new COVID-19 variant is not a surprise. As this virus infects and replicates in hundreds of millions of persons globally, it will evolve and adapt.

These adaptations in the viral genome give the virus an advantage; to replicate faster and to avoid the immune system. This current finding of a new variant that may be more infectious than the Delta variant underscores that we must increase our vaccination rates here in Australia and globally. The race continues between vaccines and variants.

While we continue to see high numbers of cases of COVID-19 with ongoing surveillance for genetic changes, new variants will continue to be detected as we know viruses mutate or evolve over time.

Initially termed variants of interest, these variants can become variants of concern if we establish that the changes detected confer properties to the virus that make it a bigger problem than it already is, such as increases in transmission or reduced effectiveness of vaccines for example.

This new variant, termed C.1.2, certainly has some changes in its genetic code that give it the potential to become a variant of concern, particularly where some of the mutations are, in that there are multiple in the spike protein. It is also the variant that has changed the most of the variants detected so far when compared with the original strain, although this is not in itself surprising given it is what we would in many ways expect over time.

It has not yet been established whether this variant does indeed have any of the properties that will make it a variant of concern, investigations into this are ongoing. The discussion around this new variant should reinforce why it is so important to continue to do what we can to reduce the global burden of this virus, most notably striving for high vaccine coverage worldwide, but also to remain vigilant with respect to basic infection control strategies including the use of hand hygiene, social distancing, masks and having high rates of testing and isolating of positive cases wherever practical.

If a new variant is detected that does truly evade protection from existing vaccines, then this is not necessarily the doomsday scenario some are concerned it may be. Most of the leading vaccine manufacturers are prepared for such an eventuality and can generate a new vaccine to address a new variant if or when this is required in a relatively short space of time.

The need to cover for new variants may be one of many reasons boosters are used in the future, but at this point in time it is simply too soon to know if this variant, C.1.2, has any of the properties that will make it a variant of concern and if it is, exactly how big a problem it may be.