Much to learn about new Covid-19 virus variant detected in SA: It surprised us, scientists say

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  • Scientists say there is still much to learn about the variant, but there is concern, and they are monitoring it.
  • Fortunately, it was detected early, and, they say, it appears there will be an easier way to track it.
  • For now, our best form of protection is vaccination - and to continue with non-pharmaceutical interventions.

In a hastily arranged Covid-19 briefing on Thursday, the Department of Health, as well as scientists from the Network for Genomic Surveillance in South Africa, announced the detection of a new Covid-19 virus variant in South Africa.

While the briefing was suddenly announced, the main topic of the briefing, the detection of the B.1.1.529 variant, was not.

News had already broken about the variant earlier in the day, and a concern already highlighted then was the considerable number of mutations detected.

"This variant … surprised us … [it] has a big jump on evolution," said Professor Tulio de Oliveira who is the director of the KwaZulu-Natal Research Innovation and Sequencing Platform (Krisp). 

South Africa has a large collaborative genomic surveillance network, which involves detecting and researching variants and controlling outbreaks.

Krisp is the principal investigative institute of this network.

De Oliveira added it had many more mutations than scientists expected, especially after a severe third wave, which was driven by the Delta variant.

"Many of the mutations are of concern for immune evasion and transmissibility. We can see the variant potentially spreading very fast… We do expect, unfortunately, to start seeing pressure in the healthcare system in the next few days and weeks."

Greek name will soon be assigned

The World Health Organisation (WHO) classified the B.1.1.529 variant as a variant under monitoring (VUM).

A variant receives this label when it has genetic changes that are believed to affect the virus' characteristics and that may allow it to pose a future risk, the WHO noted.

However, it required "enhanced monitoring and repeat assessment, pending new evidence", it added. 

De Oliveira said a Greek name would soon be assigned to the variant by the WHO.

Variant may be spread across SA

Around 90% of the cases linked to this variant were from Gauteng, he added.

The team is generating data from other provinces.

Another scientist pointed out there were early signs from diagnostic lab tests this variant might already be present in many of the other provinces, although he cautioned this was based on a much smaller number of positive PCR tests.

"The cases are not rising to the same extent in the other provinces, but it gives us concern that this variant might be circulating quite widely in the country," said Dr Richard Lessells, an infectious diseases expert involved in surveillance for Covid-19 variants.

When can results be expected?

According to the team, B.1.1.529 was different from other circulating variants of concern, but the variant also had mutations that were familiar to them and were likely associated with immune escape and increased transmissibility.

But studying this variant was no easy task, said Professor Penny Moore, the South African research chair of Virus-Host Dynamics at Wits University and National Institute for Communicable Diseases (NICD).

Moore and her team are currently assessing the variant's impact on neutralising antibodies, a particular subset of antibodies (derived from natural infection or vaccination) that are able to bind to the virus and stop it from infecting cells.

These antibodies were critical for preventing Covid-19 infection, Moore previously said.

Testing this was "complicated by the number of mutations this variant has", she added, saying: "That makes our lives as scientists somewhat more difficult to try to get there as quickly as possible."

Moore said to get the actual data from the laboratory experiments would likely take a number of weeks.

Immunity: the whole picture

The measurement of antibodies was only one arm of the immune system, she added.

The team is also working to understand the other arms of the immune system within the context of B.1.1.529, including T cells which play a key role in protecting against severe Covid disease. 

Moore said:
To be able to pull all of that data together and to get a coherent understanding of the impact of all of these mutations will take us some time, unfortunately.

In spite of this, she added, based on what the experts knew about the existing mutations, there was a critical need to employ non-pharmaceutical interventions, including physical distancing, wearing a face mask, and avoiding crowded spaces.

"We know that we need to protect ourselves from infection while we wait for the laboratory data," Moore said.

Severity of cases need to be monitored

Lessells said the main factor to keep under careful observation over the next couple of weeks was the severity of Covid-19 cases.

"Often at the beginning of a resurgence, we sometimes get fooled into thinking that everything is [mild cases of the] disease, and that can be because it is initially spreading in the younger age groups.

"So, we have to see as the spread becomes more generalised, whether we're seeing cases of severe disease," he added.

This then has to be tied together with the PCR testing data, genomic data and the vaccination data so officials are able to determine how many hospitalised Covid-19 patients are unvaccinated, partially vaccinated or fully vaccinated.

"It's about pulling all those different strands of data together on a rolling basis," said Lessells.

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

READ | New Covid-19 virus variant detected in SA: What we've learnt so far

READ | Fewer hospital admissions projected for SA’s fourth Covid-19 wave, but bed capacity may be an issue

READ | Covid-19: Scientists monitoring new virus variant detected in SA, Botswana

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