Understanding variants of SARS-CoV-2

As concerns about a possible third wave gain momentum, so have concerns about whether vaccines will provide good protection against the variants. So what are the facts? Viruses are constantly changing, and this includes SARS-CoV-2, the virus that causes Covid-19. All viruses mutate, but three variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have raised particular concerns globally. These include:

  • B.1.1.7, first identified in the UK;
  • P.1, first identified in Brazil; and
  • B.1.351, first identified In South Africa and which experts have advised has been the dominant variant in circulation during our second wave.

What are variants?

When a virus replicates or makes copies of itself, it sometimes changes. These changes are called “mutations” and are a natural phenomenon that supports its survival. A virus with one or several new mutations is referred to as a “variant”. Viruses accumulate mutations over time and often these disappear. Some mutations, however, prove advantageous to the survival of the virus and how it behaves, which could result in greater transmission (faster spread though the population) or faster replication (more virus that can take root in a host, possibly resulting in more severe disease or faster spread).

How are variants identified?

This new variant of the virus was discovered through routine genomic surveillance of SARS-CoV-2 performed by a network of laboratories around the country (Network for Genomic Surveillance South Africa, NGS-SA). The new variant has been identified in almost 200 samples collected from over 50 different health facilities in the Eastern Cape, Western Cape and KwaZulu-Natal. This new variant is different from the original virus because it has multiple mutations (changes) in the spike protein – this is the very important part of the virus that binds to the receptor on the cells inside our body and that is also the main target for many of the antibodies produced during infection or after vaccination. Work is being done to understand what effect these mutations have on the behaviour of the virus and our body’s response to it, particularly whether it makes the virus spread more easily, whether it might lead to more severe Covid-19, and whether the virus can evade our immune response.

Do variants impact how effective vaccines are?

The mutation of viruses is not a new phenomenon to scientists. However, there are differences in how quickly these mutations develop and whether these mutations render vaccines ineffective, a concept described by scientists as “vaccine escape”. A common example is the flu virus, which mutates very rapidly and requires re-vaccination every year. The virus that causes pertussis, also known as whooping cough, mutates more slowly, so re-vaccination is not required annually. Scientists are still studying the SARS-CoV-2 virus and it is only over time that we will be able to confirm how quickly the virus mutates and what this will mean for re-vaccination.

From a local clinical trial, scientists were able to conclude that the Astra/Zeneca vaccine did not show protection against mild to moderate Covid-19 due to the B.1.351 variant, which resulted in government halting the roll-out of this vaccine. Experts continue to debate whether this vaccine might still be beneficial in terms of protection against severe disease and hospitalisation.

In the meantime, though, pharmaceutical companies are at work to adapt available vaccines to be effective against variants identified, similar to our experience with the flu vaccines that are adapted every year.

Vaccination is a proven method to prevent viruses from spreading and thus reduces the risk of further mutation and variants. It is therefore important that we remain focused on having as many people vaccinated as possible, and as quickly as possible.