SA’s potential Covid-19 variant of interest 'a signal that the pandemic is not over' - expert

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  • The C.1.2 lineage shares a few common mutations with Beta and Delta, but has a number of additional mutations. 
  • Scientists in the country are continuing to monitor its spread and test the effectiveness of antibodies against it in the lab. 
  • The co-author of the study, Dr Richard Lessells, said people needed to continue to vaccinate and follow Covid-19 protocols.

The potential variant of interest that was identified by scientists in South Africa raises looming questions, including whether it could increase transmission of the Covid-19 virus and evade immune protection from natural infection or vaccination.

Known as C.1.2, it was first detected in May 2021 and had spread across the majority of the provinces in the country, although it appeared to account for a small number of cases, Health24 recently reported. It has also spread to seven other countries across Africa, Europe, Asia and Oceania.

It was important to highlight the lineage of C.1.2, given its concerning number of mutations, according to the researchers whose study was published in a preprint server in August 2021. Mutations refer to individual changes in the virus's genetic code.

The variant evolved from PANGO C.1, one of the lineages that dominated South Africa's first wave of infections.

But, as concerning as it was, C.1.2 had not yet fulfilled the World Health Organisation's (WHO) criteria for a variant of interest (VOI) or a variant of concern (VOC), as scientists still needed more information about it in order to determine whether it should be classified under one of the two categories, co-author of the study, Dr Richard Lessells, told Health24.

Lessells is a leading infectious diseases expert involved in surveillance for Covid-19 variants.


Emerging variants of the SARS-CoV-2 virus are classified as VOI or VOC. The former receives the classification if it has undergone genetic changes that may allow it to transmit more easily; cause more severe illness; or reduce the effectiveness of vaccines or treatments, among other factors.

When there is increased evidence of it fulfilling at least one of the above criteria, it is elevated to a VOC, such as the Delta variant which is currently dominating infections in South Africa.

Many mutations

Compared to C.1, the new variant had "mutated substantially", the authors wrote. It is also more mutations away from the original virus first detected in Wuhan, China, than any other of the four VOI or four VOC identified so far.

"[C.1.2] is different from Beta and Delta that have dominated the second and third waves," said Lessells.

However, it did share many of the same mutations as the VOC - it was just a different mix of those mutations, he added.

These additional properties may mean that C.1.2 has enhanced transmissibility or the ability to partially evade immunity by natural infection or vaccination. This is why the team decided to flag their findings and believe it is a variant that needs to be monitored actively.

Number of mutations not important

Each new variant brings growing unease along with it, and since C.1.2 has multiple mutations within the spike protein, the findings of the study has led to concern. 

But the number of mutations should not cause worry, said Lessells.

"As we go on in this pandemic, and as new variants pop up, each new one that pops up will have more mutations than the last one, because more time has elapsed and the virus had more time to evolve. So, the number of mutations is not really a helpful thing to differentiate," he added.

Rather, the critical aspect was the specific pattern, or combination of mutations, as that would determine the behaviour of the virus, said Lessells. And that is what the researchers still need to work out in the context of C.1.2.

What might have driven C.1.2’s emergence?

Discovering the new variant was unexpected, as the "parent lineage", C.1, was last detected in January 2021 in South Africa.

Lessells said he believed its emergence could be due to one of two possibilities.

The first is the virus was spreading and evolving in some part of the country, where the team of scientists were not really receiving virus samples that were fed into their genomics surveillance. This means they were not seeing the evolution of the virus.

"And that's possible because we only sequence a very small fraction - less than 1% - of all the cases that happen in South Africa," he said.

The other possibility

The second possibility is that there was accelerated evolution of the virus within an immuno-compromised individual.

Lessells and his colleagues previously reported a case of a patient with HIV, who had a prolonged SARS-CoV-2 infection. Through this patient, they could follow the evolution of the virus.

"We could see some of the mutations develop over time. And we think that that's one way that these variants of concern and interest may come about. In an individual whose immune system is not strong and they're not able to clear the virus, the virus causes a more prolonged infection and evolves inside that person," he said.

Gaining an evolutionary advantage

If the mutated virus started spreading from that individual to other people, it could have an evolutionary advantage in the population, and begin spreading through it, Lessells added. 

"So, we think that that may be the more likely scenario here, and that would explain why we haven't seen it for some time, and then it popped up with all these extra mutations. It's quite plausible."

A similar incident was observed in Boston, the US, in one immunocompromised man who had contracted the virus and was highly infectious for 155 days before he died. In that time, he developed the virus with 20 mutations. 

Scientists globally, therefore, believe that new variants are often brought about by an immunocompromised person who doesn't fight off the virus quickly and allows it to linger in their body for an extended period of time. 

Vaccination for immunocompromised

The above point certainly highlighted the importance of immunosuppresed people being vaccinated, said Lessells.

"But there is also a question of whether some groups of immunosuppressed people would need an extra [booster] dose to give them adequate protection, and that's something that's being discussed here," he added.

Booster doses are already being offered to individuals with compromised immune systems in the US.

South Africa was also home to the largest HIV-positive population worldwide, and it was critical that people with HIV were diagnosed and were on antiretroviral therapy, as this would strengthen the immune system of the individual and "shut off the SARS-CoV-2 process inside the body" should they contract an infection, said Lessells.

Where we are at

As it stands, the researchers will continue to monitor the spread of C.1.2 through their genomic surveillance, and will assess whether the combination of mutations makes it more transmissible than other variants.

"How transmissible it is really depends on continued surveillance, and seeing if [the variant] is increasing in frequency in any one part of the country, or across the country," said Lessells.

The researchers will monitor whether C.1.2 seems to be associated with an increase in cases in a particular area, and whether there is any evidence that it is out-competing the Delta variant in any part of the country. 

"And so we expect each week that we'll have a little bit more information about that and we'll get a better understanding of how it's behaving in the population," he added.

Testing antibodies against C.1.2

Laboratory work is also well underway, where the team is trying to understand whether C.1.2 evades the antibodies from previous Covid-19 infection or vaccination.

"We test the virus against plasma taken from people who've been recently infected or who've recently had the vaccine, and we see how well the virus is neutralised in the laboratory," said Lessells. Results are expected within the next week or two.

Could C.1.2 lead to a fourth wave of cases in SA?

"It's too early to say, but the important point is that any new variant could contribute to a new wave, or to a new prolongation of this wave. As you know, we're not really out of the third wave in some provinces," said Lessells.

"Fundamentally, it's just a reminder that this virus is not going away, however much we would like it to go away, and however much we would like each wave to be the last wave. This virus has different ideas. And this virus is still finding new ways to evolve and potentially to get better at infecting us," he added.

The detection of C.1.2 was also a reminder of how important vaccination was for everyone, said Lessells. "It helps slow the spread of the virus and that's what slows this evolutionary process."

The take-home message

"The key message is that people shouldn't panic, specifically about this C.1.2 variant, but they should be aware that this is a signal, again, that this pandemic is not over, and that we all have to do the right thing in doing what we can to slow the spread of the virus, and to prevent these new variants from emerging," he added.

"And that means getting vaccinated as soon as we can, while still also following all the other public health and social measures that are in place to try and reduce the spread in our communities."

*For more Covid-19 research, science and news, click here. You can also sign up for our Daily Dose newsletter here.

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