‘We have to be alert, not alarmed’ says KRISP director about B.1.617 variant identified in India

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  • The SARS-CoV-2 variant detected in India has not been identified in SA, health minister Zweli Mkhize confirmed this week
  • Still, we have to focus on maintaining NPIs and avoiding social gatherings, two experts say 
  • They also stressed the importance of scaling up vaccination, testing, contact tracing, and isolation

Covid-19 cases continue to overwhelm hospitals in India as the country deals with a new coronavirus variant, known as B.1.617. Meanwhile, South Africans need to “keep calm and keep focused”.

These are the words of Professor Tulio de Oliveira, director of KRISP, who told Health24 that although the variant hasn’t been detected in South Africa, our behaviour is still central to the transmission of the virus and how fast it spreads.

Trying to 'overcompensate'

“History normally repeats itself. If you’ll remember, our second wave was caused by a much more transmissible variant (501Y.V2), but it was also caused at a time – the end of November and December 2020 – when people were trying to go back to normality.

"They were almost trying to overcompensate for the time they had lost with social gatherings,” he said.

B.1.617 has already been identified in more than 30 countries, said de Oliveira, including the UK. Last month, India was added to the UK's "red list" of places from which travel is banned in order to prevent the spread of the virus. The country has the second-highest case numbers in the world, after the US, and nearly 235 000 lives have been lost.

Health Minister Zweli Mkhize said on Wednesday that there were no direct flights from India, and that the country is "currently on high alert to screen passengers and test those who require further assessment", News24 reported.

Calling it the ‘double mutant’ is a misnomer

The B.1.6.7 variant has been dubbed the “double mutant” in several reports worldwide, but according to de Oliveira, this label is incorrect and misleading since the variant has more than two mutations.

“When it was called the double mutant, it’s because they were talking about two mutations at the receptor-binding domain (RBD) located on the spike protein of the coronavirus. That is one of the most important regions of the virus.”

The spike protein is responsible for viral attachment, fusion and entry, explains ProteoGenix.

De Oliveira added: “If we’re going to use that terminology, then the variant we discovered in South Africa would be considered a triple mutant as it has three mutations at the RBD. And that’s why that was not the best way to describe it. It gives the impression that the B.1.617 had twice as many mutations as the other variants, which is untrue.”

De Oliveira, who is also a member of the WHO Virus Evolution group, explained that B.1.617 is currently considered a variant of interest. The World Health Organization (WHO) classifies variants into one of two groups: variants of concern (VOC) and variants of interest (VOI).

VOC vs VOI

A VOC is one that is suspected to either be more contagious than the original virus variant, cause more severe disease, or escapes vaccine-induced protection. A VOI, on the other hand, can become a VOC if evidence emerges that it has one or more of these characteristics.

At the moment, VOCs include:

  • B.1.1.7, or 501Y.V1, first discovered in the UK
  • B.1.351, or 501Y.V2, first discovered in South Africa
  • P.1, or 501Y.V3, first detected in travellers from Brazil
  • B.1.427, first discovered in Southern California 
  • B.1.429, also first discovered in Southern California

What do we know about the variant?

While there is anecdotal evidence that the variant is responsible for India's catastrophic second wave, scientists caution that the data is inconclusive and that it’s unclear how much it’s contributing directly to the surge in cases. Instead, it is possible that other factors may explain the outbreak, such as super spreader events.

The variant appears to be responsible for around 50% of cases in India's most populated region, which would suggest higher transmissibility.

De Oliveira weighed in: “We don’t yet know if the second wave is due to the process of the variant itself, or if it’s because of the way that India returned to normality with mass religious gatherings, political rallies, and even cricket matches. The beginning of their second wave was associated with massive migration and public gatherings.”

Professor Willem Hanekom, director of the Africa Health Research Institute (AFRI) told Health24 that there are preliminary results (mentioned on Twitter by Professor Ravindra Gupta, an AHRI Faculty member and a Professor of Clinical Microbiology at the Cambridge Institute for Therapeutic Immunology and Infectious Diseases), that suggest that having two mutations in the RBD of the spike protein does not make this variant more infectious in the laboratory, or allows it to grow faster in the lab, or less able to be neutralised by plasmas (blood products) from previously infected or vaccinated people.

By contrast, the 501Y.V1 variant has already spread to over 100 countries, while the variant dominating infections in South Africa has been identified in 70 countries, said de Oliveira.

“Unfortunately that’s the nature of the virus. It’s almost impossible to avoid its introduction into countries,” he explained, and stressed that he's more concerned about the variant in SA, which is responsible for the majority of infections.

Banning travellers from individual countries won’t work

One thing history has taught us is that banning travellers from a country generally doesn’t avoid the introduction of a new virus variant, said de Oliveira, referring to the example of the US restricting entry from China in 2020, which did nothing to prevent the virus from entering the country. This was because the virus had already spread to other countries, leading to case numbers quickly shooting upward in the US.

“Introductions of variants will happen, but with very strong and diligent testing, contact tracing, and isolation, you can control the spread in a country,” he said. “Of course, transmission is a very big problem, but the biggest problem is severe disease and death – and that’s why we need to urgently increase vaccination, especially in the advanced age groups and in people with comorbidities,” he cautioned.

Hanekom also explained: "Travel restrictions are important – but targeting India alone makes no sense, as variants that we should be worried about are in multiple settings, including many countries that can travel to South Africa.

"A more comprehensive approach may be warranted – focusing on reliable test results of passengers before boarding elsewhere – and perhaps again testing when persons land in South Africa. These rapid tests that would be used at entry are antigen tests – and they are not 100% sensitive. We know that. However, this additional testing may contribute to controlling import of virus from elsewhere."

More than 300 000 healthcare workers in SA have been vaccinated with the single-dose Johnson & Johnson jab. News24 reported that the remaining 75% of the country’s healthcare workers would have to be inoculated by 17 May, as that’s when Phase 2, open to people aged 60 and older, is set to begin.

SA's third wave is imminent

The B.1.617 variant may not yet be in South Africa, but we already have 501Y.V2, which is likely more infectious, said Hanekom.

"My point is that we don’t 'need' another variant for our third wave to happen. So far, although we have had a massive epidemic and although there are some SA communities where it appears that more than 50% of people have been infected, this is not enough for community (herd) immunity from natural infection. Therefore, we are at risk of a third wave at any time.

"Numbers are increasing in the Northern Cape, Free State, North West and Gauteng. This wave is imminent. Expansion of this kind of epidemic happens due to either human (behaviour) factors or viral factors – at the moment, the former appear responsible, and not a new variant," he added. 

The take-home message 

“The main take-home message is that we have to be on alert, but we shouldn’t be alarmed,” said de Oliveira.

More than 10 introductions of other variants, including the 501Y.V1 have been detected in South Africa, and while scientists and the government are focused on increasing the public health response, de Oliveira urged that we need to focus on the main variant in the country.

“To be honest, I would be much more worried about the 501Y.V2 than the variant in India because we have a much stronger connection to 501Y.V2, which is causing the majority of infections in South Africa.”

The new variant, however, may be a good wake up call for South Africa.

“We have to keep calm because panic doesn’t help. And we must maintain our non-pharmaceutical interventions [hand washing, wearing a face mask, and physical distancing], and strengthen testing; contact tracing; isolation; quarantining – not only for travellers, but for every person experiencing Covid infection in the country – and, of course, increase vaccination,” he said.

Hanekom echoed this stance, saying: "We need to follow NPIs. It is by far the most important, and we are becoming a bit too relaxed now in SA, I think."

Update: The department of health confirmed on 8 May 2021 that four cases of the B.1.617 variant was detected in South Africa, News24 reported.

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

READ | Moderna’s experimental booster shot protects against variants first discovered in SA and Brazil

READ | Older adults who get Pfizer, Moderna jab 94% less likely to be hospitalised for Covid-19 – study

READ | Why South Africa stopped making vaccines

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