Asked and answered: Six things you need to know about the new Covid variant in South Africa

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  • A variant of the new coronavirus was recently identified in SA
  • Mutations in viruses can change how they behave
  • The new variant, while more transmissible, is not more severe

South Africa’s department of health gathered the country’s best and brightest for a virtual briefing on Monday evening. Here scientists presented the latest findings on a variant of the new coronavirus - called 501Y.V2.

This variant was first identified in South Africa in 2020 by a genomics team led by the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal.

Following the December announcement of the new variant, researchers have been working to answer key questions about what this means for South Africa’s epidemic.

Monday evening’s two-hour presentation sought to share what they’ve learnt. 

In the discussion, the country’s Covid braintrust shared what this variant means for South Africans, new figures on the impacts of 501Y.V2 on the healthcare system and plans for future studies.

If the technical briefing left you scratching your head then this summary is for you.

The answers to these six questions will tell you everything we know - and what we still don’t - about the 501Y.V2 variant currently spreading through South Africa.

1. What is a variant?

Viruses change over time as they spread and replicate. These changes are called mutations, Richard Lessels, an infectious diseases specialist, explained. Mutations can be classified as variants or strains - which classification is followed, is largely a matter of scientific convention and consensus.

Tulio de Oliveira, a bioinformatician, explained that the naming conventions for the new coronavirus were adopted at the early stages of the virus’ spread.

The international scientific community chose to classify the virus in terms of variants and lineages - these are changes which “live for a short time and that could be controlled with normal interventions”, de Oliveira said during the briefing’s question and answer section. 

The term strain is usually used to classify bacteria, de Oliveira added. Viruses can be called strains too, but this is less common. Normally, something is called a strain if the changes to its structure are long-lasting.

Since it is too early to tell what the current mutations mean for SARS-CoV-2 or how long they will last, the better terminology to use at the moment is variant.

The key takeaway on Covid terminology is: we shouldn’t call this ‘the South African variant’.

This fairly recent change in naming practices is done to avoid placing blame or creating stigma around the country that first identified a virus. Instead, stick to calling the new variant 501Y.V2. After all, a novel coronavirus by any other (country) name would be incorrect. 

For more find our explainer on variants and mutations here

2. Is the 501Y.V2 variant more infectious?

Lessels explained that some mutations in viruses could have a functional significance - these are changes which affect how the virus behaves. One such change is how efficient the virus is at spreading.

Unfortunately, the 501Y.V2 variant is 50% more transmissible than the previous variants of Covid-19. How do we know this? Maths.

Salim Abdool Karim, the co-chair of South Africa’s ministerial advisory committee on Covid-19, explained that it took 107 days in the first wave for the Western Cape to reach its first 100 000 cases of SARS-CoV-2 infection (SARS-CoV-2 is the virus that causes Covid-19).

It only took 54 days for the province to get to the same number of cases in the second wave. 

KwaZulu-Natal took 254 days to reach 100 000 cases in the first wave compared to 33 days in the second wave.

3. Is this new variant more severe?

Plainly put, no.

Abdool Karim said that a comparative look at the first 100 000 cases recorded during South Africa’s first and second waves gave us a similar proportion of hospital admissions. 

Mary-Ann Davies, a health medicine specialist responsible for epidemiology and surveillance at the Western Cape’s department of health, explained how data from public sector patients helped scientists reach this conclusion.

The Western Cape started seeing cases of the new variant roundabout mid-October and November 2020. A large proportion of the province’s COVID-19 cases from this period onwards were assumed to be 501Y.V2 infections and signposted the start of the second wave.

Davies and her team found that in both waves:

  • Between 70 to 80% of people admitted to hospital had comorbidities;
  • About 90% of Covid patients who died had comorbidities; and
  • The age pattern in the proportion of Covid cases and deaths remained the same.   

All of this comes together to suggest that 501Y.V2 isn’t any more severe when compared to older variants of the virus.

As Davies brings home: “What we see is that the risk of death when we take into account age and comorbidities, and the number of admissions that hospitals are experiencing, is no different between the upsurge of wave one and the upsurge of wave two, which would suggest that this new variant is not causing more severe disease.”

4. Can you get re-infected with the variant?

Re-infection refers to someone testing positive for a virus 90 days after being disease or virus free, explained Koleka Mlisana, the executive manager at South Africa’s National Health Laboratory Services.

This happens when your body’s immune response - the way it recognises and fights against foreign bodies, like viruses - is either inadequate or short-lived Mlisana said.

Using data from South Africa’s Covid tests, scientists looked to see if there were any cases of people testing positive for the virus twice, with a minimum 90-day interval between the tests. As of 6 January, the data showed that there were 4 000 cases like this, Mlisana said.

This suggests that re-infections are possible.

Mlisana added that the second wave had seen an increasing number of re-infections - this is likely due to the higher case numbers overall being seen in the country’s second wave. But, according to this analysis, the proportion of re-infections has remained relatively constant across both the first and second waves in South Africa.

This suggests that the risk of re-infection is the same for the new and older variant. 

The caveat? It’s still early days.

“Bear in mind, we’re only talking a month, so far,” Mlisana cautioned. “So this is an area that we need to look at very closely. In fact, we are going to continue to monitor this data and look to see whether there’s any change.”  

However, a study published on the online journal, biorxiv, on January 19 (a day after the health department’s briefing), of which the National Institute for Communicable Diseases’ (NICD) Penny Moore was an author, found that the antibodies in the blood samples from half the people that researchers tested - who had all previously had Covid-19 - didn’t protect them against 501Y.V2.

“This suggests that they may no longer be protected from re-infection,” the NICD said on its website. It is therefore important that people who have previously had Covid-19 continue to adhere to public health measures such as wearing masks, regular washing or sanitising of hands, cleaning of surfaces and social distancing.

Learn more about different research study designs in Bhekisisa’s epidemiology 101 resource

5. Will vaccines be able to protect you from getting infected with the new variant?

It’s too soon to tell.

The short, unsatisfactory answer is that we just don’t have enough information to fully answer this yet.

Several scientists are working on trying to answer this question, but at this point there just isn’t enough information to know for sure, cautioned Abdool Karim.

Why is this a concern?

Antibodies are our bodies’ first line of defence against most foreign invaders, like viruses. These proteins can help our bodies identify and ward off infections from a virus - this is called immunity.

Antibodies form one part of this immunity, as they help our bodies to recognise the structure of a virus and flag it as something that needs to be destroyed. Vaccines work by triggering this kind of response, even if you have not previously been infected with a virus. But the current Covid vaccines that we have, train your body to recognise a part of the virus that is changing in the new variants being identified around the world.

The worry is that antibodies from the original virus won’t be able to recognise these new variants, which is something we are seeing in labs, explained Alex Sigal, a virologist at the Africa Health Research Institute.

A study published as a preprint (in other words, not peer reviewed) on the online journal medRxiv on January 21, found that the 501Y.V2 variant can indeed escape antibodies generated from previous infection. This means that antibodies from people who were infected with previous variants may not work well against 501Y.V2. 

Another preprint, published on January 19 on biorxiv showed that the antibodies that people’s bodies produce after receiving mRNA vaccines (the type of jabs produced by Pfizer/BioNTech and Moderna) was slightly less effective — “by a small, but significant margin” — against engineered viruses with three of the key mutations in the variant identified in South Africa.

Moore study’s results concurred with the above findings suggesting that the antibodies elicited by vaccines could potentially be ineffective against 501Y.V2.  This however doesn’t mean current vaccines don't elicit some immune response in our bodies to the new coronavirus variants, like 501Y.V2. That’s because, while antibodies are the first line of defence, they aren’t the only weapon our body has against viruses.

As Sigal explained, vaccines stimulate different types of immunity and are more complex than simply looking at how antibodies respond to these variants in a lab setting.

Sigal concluded: “The problem here is that the vaccines were designed for the previous variants. Now we don’t know what’s going to happen and vaccines are very complex and can elicit a lot of different types of immunity. So what results we have now are not indicative that the vaccines will not work.” 

Read more about Covid vaccine front runners here

6. Should South Africa change its Covid vaccine rollout plans?

“No,” stated Abdool Karim. “Not at this stage. Not with the evidence we have at this point.” 

He said that the best course to follow is sticking to the planned roll-out.

This is partly because the available Covid vaccines are amongst the most effective for any disease. The leading candidates, developed by Pfizer and Moderna, have a reported efficacy of 95%, which is incredibly high and on par with the measles vaccine (one of the world’s most effective jabs).

These highly effective vaccines will help South Africa reduce incidents of clinical illness and hospitalisation - something which is critical as the new variant continues to put increased pressure on the country’s healthcare system.

The road ahead is long, challenging and filled with unknowns, but these aren’t reasons “for us to hesitate to use a vaccine that saves lives”, cautioned Abdool Karim.

More on South Africa’s COVID vaccine rollout strategy

This story was produced by the Bhekisisa Centre for Health Journalism. Sign up for the newsletter.

*This article was updated on 22 January 2021 to reflect new information on 501Y.V2.

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