New COVID-19 variant identified in SA


Health Minister Dr Zweli Mkhize on Friday announced that a variant of the SARS-COV-2 Virus (COVID-19) – currently termed the ‘501.V2 Variant’ –  has been identified by genomics scientists in South Africa.

Mkhize said a genomics team, led by the Kwazulu-Natal Research Innovation and Sequencing Platform, or KRISP, has sequenced hundreds of samples from across the country since the beginning of the pandemic in March. They noticed that a particular variant has increasingly dominated the findings of the samples collected in the past two months.

In addition, clinicians have been providing anecdotal evidence of a shift in the clinical epidemiological picture- in particular noting that they are seeing a larger proportion of younger patients with no co-morbidities presenting with critical illness. The evidence that has been collated, therefore, strongly suggests that that the current second wave we are experiencing is being driven by this new variant.

Explaining the findings, Professor Salim Abdool Karim said the second wave is showing some early signs that it is spreading faster than the first wave.

“It is still very early but at this stage, the preliminary data suggests that the virus that is now dominating in the second wave is spreading faster than the first wave. It is not clear if the second wave has more or less deaths, in other words, the severity is still very unclear. We would expect it to be a less severe virus, but we do not have clear evidence at this point. We have not seen any red flags looking at our current death information,” he said.

“We had all of these different strains routinely spreading in South Africa during our first wave and subsequently. What became quite different that we did not expect is the rapid way in which this variant has become dominant in South Africa.

This particular virus has three mutations on the receptor-binding domain, which is the actual part of the virus that attaches to the human cell. One of the interpretations of these changes is that it increases the affinity for the ACE2 receptor. The other two mutations possible add some potential antibody escape but the full implications of the combination of the three mutations still need to be understood in more detail.”

Karim said the new variant has increased viral loads in the body.

“When we look at this new variant, the CT score is lower than the other viruses that have been spreading during our first wave. It means that the amount of virus in the swab is higher. A lower score means a higher amount of virus: we refer to that as the viral load. When we do a swab, we are getting a lot more virus in these patients that have the 501.V2 virus,” he said.

“The higher viral load in these swabs may translate to a higher efficiency of transmission. If there’s higher transmissibility, it may translate to a higher R0 (the number of additional people one patient may infect). While the other viruses are still transmitting, this virus is spreading so much faster that when we take swabs it is the dominant variant that we see. This may translate into a second wave that may have many more cases than the first wave.

We do know that it is an unusual variant. It has been reported in other countries, including the UK, Australia and several others. In our country, we are finding between 80 and 90% of the virus is this 501.V2 mutant.”

He said there are still many issues that need to be investigated.

“We don’t know where it came from and we don’t know why it formed. We found the first in Nelson Mandela Bay, but we don’t know if it originated in Nelson Mandela Bay. It is too early to tell if it is more severe.”

Concluding the briefing, Mkhize said that while this mutation is a cause for concern, there is no reason to panic.

“We appeal to all the media and medical and scientific community to focus on the facts and avoid entering into speculation or issue unproven statements and generate panic and disinformation. This research underlines the need for all of us all to loyally adhere to the practice of non-pharmaceutical interventions which work as effectively in any pandemic of this nature including COVID-19 as we have known it and is just as effective to a mutant variant of the same virus,” he said.

“Nothing will beat the rigid implementation of wearing of masks, use of hand sanitizer and washing with soap and distancing. Many countries experienced a second wave that was more severe than first – even where no mutations were reported.

He said there is no evidence to suggest a need to change in clinical treatment and patient management of COVID-19 in the second wave to date and that this discovery does not necessitate additional restrictive measures.