Publications
- A leading researcher says testing is already underway to understand the impact of the new variant in vaccinated people.
- It is plausible the new variant will have an impact on transmission protections offered by vaccines, but it is unclear how severe this will be.
- The world moved swiftly to halt travel to southern African countries, led by the UK, despite early evidence the new variant was already present in other parts of Africa and the world.
The world and South Africa will have to wait some weeks before there are answers to key questions around the new B.1.1.529 coronavirus variant first discovered in the country and Botswana.
SA had, as of Friday morning, detected roughly 50 cases of the new variant of the SARS-CoV-2 virus that causes Covid-19. Adding to alarm was a dump of more than 75 000 historic test results by health authorities, of which 18 000 were positive cases, on Monday night.
Data seen by News24 show that some of the positive cases date back to April 2020. In reality, 868 new cases were recorded on Monday.
The latest variant has, according to researchers, shown a "big jump" in evolution, with one researcher telling News24 on Friday that the variant had no links to current variants in circulation, but harked back to the virus that was in communities early in the pandemic.
The news comes amid early signs of rising infections in the capital of Tshwane and Johannesburg, with no definitive link to suggest these cases were predominantly the new variant yet.
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Gauteng recorded 2 172 new cases on Friday, of 2 828 cases nationally.
On Friday afternoon, Health Minister Joe Phaahla labelled the immediate travel bans instituted by various countries, led by the UK, as "unjustified".
A further two cases of the new variant were confirmed in Hong Kong, one in a man who had returned to the country after being in South Africa, the other in a man who stayed in a hotel room across the hall.
Health authorities in Belgium announced on Friday that a woman who had travelled to Egypt, via Turkey, was the country's first confirmed case of the new variant. Another case was discovered in Israel. The person was an Israeli national who had returned home after travelling to Malawi.
News24 understands that, privately, some leading scientists have already started suggesting another hard lockdown for the country, to mitigate the spread of the new variant, which has shown early signs of being as highly transmissible as the Delta variant, which quickly became the dominant strain causing infections around the world.
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These early signs, however, were indications only in a small sample of sequenced tests.
The 50 or so cases of the new variant were detected in 71 Gauteng samples, between 14 and 23 November, suggesting that it has been present already for some time.
The mutations in this variant, designated by the World Health Organisation (WHO) on Friday as Omicron, has concerned researchers because some mutations mirror those seen in previous variants of concern.
The variant has raised concern among scientists because it has more than 30 mutations, including novel mutations - which, while worrying, will assist in identifying people infected with the new variant through normal testing, rather than somewhat delayed sequencing of samples used to detect other variants.
Head start
Dr Richard Lessells, an infectious diseases expert at the University of KwaZulu-Natal, who is part of the KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) team, with Professor Tulio de Oliveira, who announced the new variant on Thursday, said there was sufficient reason to be concerned, but work had already begun on answering important questions posed by the variant.
"It's lot of different things happening simultaneously, and it's really going to be very similar to this time last year with the Beta variant, because we are detecting it first here and in Botswana, we are going to have to lead the scientific response," he told News24 on Friday.
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Lessells said it was different to the Delta variant, in that Delta was first detected in India, which meant much of the science done to understand the Delta variant was done collaboratively around the world.
He explained of the processes underway:
Growing of live virus and the creation of pseudo viruses, essentially viruses made in laboratory conditions to mirror the mutations found in the new virus, would be subjected to neutralisation assays, which would be undertaken at KRISP's labs in Durban, and by Professor Penelope Moore of the University of the Witwatersrand at labs at the National Institute for Communicable Diseases (NICD).
Moore was not immediately available for interviews on Friday.
Lessells explained that the live virus and pseudo virus would be combined with serum, blood drawn from people previously infected with SARS-CoV-2 and from people previously vaccinated.
"You put it [the serum] together with that live virus or the pseudo virus, and you see how well the virus is neutralised, and that gives you a sense how well the antibody response from the vaccines or from a prior infection, how well they still recognise this new variant, and how well they combine and neutralise that new variant," he said.
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Other processes in the laboratories would be to look at how other parts of the immune response, particularly T-cells from vaccination – part of the body's immune response to infections – recognise the new variant.
"The neutralisation takes a few weeks, and the T-cells takes a bit longer, because it is more complex to do in the laboratory. So, these are not things you get results in a couple of days, it's more a couple of weeks and longer," Lessells explained.
"But those have already started this week, so we have got a head start."
Key weapon
This was only one part of the scientific response however.
One type of PCR test, manufactured by Thermo Fisher, was able to detect "signals" in test samples that could assist health authorities to track which samples were the new variant and which were from other, existing variants, predominantly Delta.
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News24 understands that laboratory workers at privately-owned Lancet facilities first noticed the signal in PCR results with these assays, and sequenced the samples first, before approaching the NICD to confirm their results.
"It does help us, although we have a good sequencing network, we do a relatively low volume of sequences. We sequence less than 1 in a 100 of cases which are detected by PCR. But this PCR having this kind of signal means that, with just the PCR, you can say who has this variant and who has just maybe just the Delta variant," Lessells explained.
"Those kind of analyses of understanding the severity of the disease and the transmission are much easier, because you have more data you can use, so you get the answers more quickly than you would if you had to wait to sequence cases," he added.
Professor Glenda Gray, president of the South African Medical Research Council, who also led vaccine trials in the country, said she was confident that current vaccines would work well in preventing severe Covid-19 disease and hospitalisation, even in people infected by the new variant.
She said:
Gray said she was concerned that healthcare workers, who were part of the original Sisonke study earlier this year, had not turned out in their numbers to get a second dose of the Johnson and Johnson vaccine.
"I worry that only 120 000 healthcare workers have stood up and got their second vaccines. What are the other 350 000 people waiting for? Now's the time. We've got some time, and hopefully this will spur them on. There is no evidence that the vaccine we are giving them is inferior," Gray said.
"The vaccine is there, the sites are there. There are over 400 sites in the country, we have 450 000 doses, it's all lined up for them. They need to get into these empty vaccination sites and protect themselves."
South Africa has roughly 16 million doses of vaccines stockpiled, while roughly 35% of those eligible had not yet taken up the opportunity to be vaccinated.
Additional steps
Other work ongoing, according to Lessells, was the linking of key databases of testing, hospitalisation and vaccine data to help the earlier understanding of the variant's ability to transmit, and potentially impact on existing immunity.
It would help researchers gain clear pictures of who was getting infected with the variant, whether it was spreading in vaccinated people, and whether these individuals were only getting mild disease, or falling severely ill.
He added:
He agreed that fully vaccinated people would have a higher level of protection.
"What we have seen so far with these variants of concern is that the vaccine protection against severe outcomes has held up well, but different from the protection against transmission and infection. It's quite plausible, based on the mutation profile we see seeing, that the infection protection will take a bigger hit with this variant than with others," he said.
"But the hope is that the protection against severe disease still holds up strong."
Despite the characteristics of the variant's ability to break through immunity, if at all, or its transmissibility not being immediately clear, several countries moved to restrict travel to and from South Africa and other African countries, including Botswana, eSwatini and Mozambique.
The charge was led by the UK, Germany, Spain and the Philippines on Friday, with Denmark also halting non-essential travel.
The European Union also announced late on Friday it would recommend travel restrictions. This was despite the WHO urging caution around travel curbs.
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