POST 215. November 26, 2021. CORONAVIRUS. Dr. Fauci on the new South African variant: “It’s not going to be possible to keep this infection out of the country. The question is: Can you slow it down?”

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“Dr Susan Hopkins, the chief medical adviser to the UK Health Security Agency, said the R value, or effective reproduction number, of the B.1.1.529 variant in the South African province of Gauteng, where it was first found, was now 2 – a level of transmission not recorded since the beginning of the pandemic, before restrictions began to be imposed. For an R of anything above 1, an epidemic will grow exponentially.” (A)

“Scientists in South Africa have identified a new coronavirus variant with a worrisome combination of mutations that experts fear could make it more transmissible and allow it to evade immune protection — including the protection generated by vaccines.

Experts are scrambling to learn more about the variant, known by its scientific name B.1.1.529 and called Omicron by the World Health Organization. Right now, there are more open questions than firm answers. And although scientists have expressed significant early concern over the variant — the WHO designated it as a “variant of concern” on Friday — they have cautioned that they are still seeking critical information about it.

One reminder: There have been a series of variants that have caused initial alarm, only to prove largely unimportant in the course of the pandemic.

Scientists in South Africa detected the lineage on Monday, according to the country’s National Institute for Communicable Diseases, and rang the alarm bell for the world. Researchers in Botswana and Hong Kong also posted sequences publicly, and other cases have since been reported in Belgium and Israel. The variant is likely in other countries, but researchers just haven’t picked it up yet.

It’s not clear where the variant actually emerged. It could be that South Africa and Botswana saw it early because they have strong genetic sequencing networks.

On Friday afternoon, the United States joined other countries in imposing travel restrictions from those two countries, as well as Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique, and Malawi, effective Monday.

Why is it causing concern? Several reasons.

For one, it appears to be outcompeting other variants in South Africa — including the extremely transmissible Delta variant — and fast. It’s starting to drive cases up in that country, which has already had several massive waves in its epidemic. Some possible explanations are that it’s a better spreader than even Delta, that it can cause infections in people who are protected at higher rates, or some combination of the two.

But beyond the epidemiological landscape in South Africa, scientists are concerned because of the number and variety of mutations B.1.1.529 acquired — what Sharon Peacock, the director of the Covid-19 Genomics UK Consortium, called a “very unusual constellation of mutations.” Some mutations have been previously seen in other variants and are associated with increased transmissibility and the ability to get around immune protection.

Scientists can’t predict how different mutations will behave when combined, but of particular worry to scientists is that the virus has some 32 mutations in its spike protein, which is what vaccines teach our immune system to recognize and target.

The variant “has a very high number of mutations with a concern for predictive immune evasion and transmissibility,” said Tulio de Oliveira, director of the Centre for Epidemic Response and Innovation, who helped identify the variant in South Africa.” (B)

“Researchers in South Africa are racing to track the concerning rise of a new variant of the SARS-CoV-2 coronavirus that causes COVID-19. The variant harbours a large number of the mutations found in other variants, including Delta, and it seems to be spreading quickly across South Africa.

A top priority is to follow the variant more closely as it spreads: it was first identified in Botswana earlier this month and has since turned up in a traveller arriving in Hong Kong from South Africa. Scientists are also trying to understand the variant’s properties, such as whether it can evade immune responses triggered by vaccines and whether it causes more or less severe disease than other variants do.

“We’re flying at warp speed,” says Penny Moore, a virologist at the University of the Witwatersrand in Johannesburg, South Africa, whose lab is gauging the variant’s potential to dodge immunity from vaccines and previous infections. There are anecdotal reports of reinfections and of cases in vaccinated individuals, but “at this stage it’s too early to tell anything”, Moore adds.

“There’s a lot we don’t understand about this variant,” Richard Lessells, an infectious-diseases physician at the University of KwaZulu-Natal in Durban, South Africa, said at a press briefing organized by South Africa’s health department on 25 November. “The mutation profile gives us concern, but now we need to do the work to understand the significance of this variant and what it means for the response to the pandemic.”..

Researchers also want to measure the variant’s potential to spread globally — possibly sparking new waves of infection or exacerbating ongoing rises being driven by Delta.” (C)

“The World Health Organization said a heavily mutated version of the virus that causes Covid-19 poses a possible increased risk of reinfection.

The WHO named the strain omicron and labeled it a variant of concern.

South African scientist Tulio de Oliveira said in a media briefing that the variant contains more than 30 mutations to the spike protein, the component of the virus that binds to cells.

South African scientist Tulio de Oliveira said in a media briefing held by the South Africa Department of Health on Thursday that the variant contains a “unique constellation” of more than 30 mutations to the spike protein, the component of the virus that binds to cells. This is significantly more than those of the delta variant.

Many of these mutations are linked to increased antibody resistance, which may affect how the virus behaves with regard to vaccines, treatments and transmissibility, health officials have said.

De Oliveira said the variant contains around 50 mutations in total. The receptor binding domain, the part of the virus that first makes contact with cells, has 10 mutations, far greater than just two for the delta Covid variant, which spread rapidly earlier this year to become the dominant strain worldwide.

This level of mutation means it’s possible that it came from a single patient who could not clear the virus, giving it the chance to genetically evolve. The same hypothesis was proposed for the alpha Covid variant.” (D)

“Officials also expressed concern that the mutation could result in immune evasion and enhanced transmissibility of the virus, but added it is too early to tell what kind of impact the mutations will have on vaccine efficacy. More studies also need to be conducted to understand the clinical severity of the variant compared to previous variants, officials said.

“The full significance of this variant remains uncertain and the best tool we have is still the vaccines,” De Oliveira said. He added that lab studies still need to be carried out to test vaccine and antibody evasion.”” (E)

“The US will restrict travel from South Africa and seven other southern African countries to try to contain a new coronavirus variant spreading there.

From Monday, only US citizens and residents will be allowed to travel from the region.

This follows a similar flight ban imposed by the EU earlier on Friday.

The World Health Organization (WHO) declared the new variant to be “of concern”, naming it Omicron.

US officials said flights from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi will be blocked, mirroring earlier moves taken by EU Member States. It will come into effect on Monday.

In a statement, President Joe Biden called the move a “precautionary measure” taken until more is known about the variant.” (F)

“By imposing the travel restrictions, the administration will not stop the virus from coming to the United States; in fact, experts said, it may already be here. But it can give health officials and pharmaceutical companies time to determine whether the current vaccines work against the new variant — and if not, to create new vaccines that do.

“It’s going to buy us some time,” Dr. Fauci said. “It’s not going to be possible to keep this infection out of the country. The question is: Can you slow it down?”

Dr. Fauci said the new variant has about 30 mutations, and roughly 10 of them are on a part of the virus that is associated with transmissibility and immune protection. That suggests the virus may be more transmissible and may escape the current vaccines “to an extent yet to be determined.”

He said there had been some breakthrough infections among those who had recovered from the Delta variant, and among those who were vaccinated.

But at the same time, he said, scientists do not know the severity of the infections caused by the new variant. It is entirely possible that it spreads more quickly but causes less severe disease.

“You don’t want to say don’t worry, and you don’t want to say you’ve got to worry yourself sick, because we’re gathering information rapidly,” he said, adding, “Even though the numbers are still small, the doubling time is pretty rapid and the slope of the increase is really rather sharp.”

Biden administration officials said they were continuing to work with health officials in other countries to learn more about the variant.

“Restricting travel is going to slow its coming, not stop it from coming,” said Dr. Ezekiel Emanuel, chair of the department of medical ethics at the University of Pennsylvania and an adviser to the president during his transition. “The fact that it’s coming here is inevitable. The environment in which it comes may not be inevitable. We can alter the environment.”

Mr. Biden said on Friday that the rise of the Omicron variant was another reason for vaccinated Americans to get boosters and unvaccinated Americans to get inoculated — a point Dr. Fauci echoed. And Mr. Biden said the development should push the international community to donate more vaccines to nations suffering from a lack of access or poor vaccination rates.

Michael Osterholm, an infectious disease expert at the University of Minnesota who also advised Mr. Biden during his transition, said the administration had little choice on implementing the travel ban.

But Dr. Osterholm said it could take time before scientists know if the current vaccines are effective against the variant, and how transmissible it is. One way to figure that out is through laboratory studies, which will take several weeks, he said. Another way is to follow breakthrough cases in people who are already vaccinated, which could take months.” (G)

“Is it more transmissible?

Will existing vaccines work against it?

What about existing drugs?

Will the variant cause more severe Covid?

Can the vaccines be tweaked and how long could that take?”  (H)

• A.What do we know about the new ‘worst ever’ Covid variant?, Andrew Gregory, Tom Ambrose and Haroon Siddiquehttps, https://www.theguardian.com/world/2021/nov/25/what-do-we-know-about-the-new-worst-ever-covid-
• B.Heavily mutated coronavirus variant puts scientists on alert, by Ewen Callaway, https://www.nature.com/articles/d41586-021-03552-w
• C.What’s known and unknown about Omicron, the coronavirus variant identified in South Africa, by Andrew Joseph, https://www.statnews.com/2021/11/26/whats-known-and-unknown-about-the-coronavirus-variant-identified-in-south-africa/
• D.A heavily mutated Covid variant emerges in southern Africa: Here’s what we know so far, by Elliot Smith, https://www.cnbc.com/2021/11/26/covid-variant-emerges-in-south-africa-heres-what-we-know-so-far.html
• E.A new Covid-19 variant could show immune evasion and enhanced transmissibility, South African scientists warn, By David McKenzie and Ghazi Balkiz, https://www.cnn.com/2021/11/25/world/covid-variant-south-africa-immune-evasion-transmissibility/index.html
• F.Covid: US joins EU in restricting flights from S Africa over new coronavirus variant, https://www.bbc.com/news/world-59427770
• G.Covid Live Updates: Biden Moves to Restrict Travel from Southern Africa  , by Zolan Kanno-Youngs and Sheryl Gay Stolberg, https://www.nytimes.com/live/2021/11/26/world/covid-vaccine-boosters-variant?referringSource=articleShare#:~:text=Covid%20Live%20Updates,Sheryl%20Gay%20Stolberg
• H.Omicron: everything you need to know about new Covid variant, by Hannah Devlin, https://www.theguardian.com/world/2021/nov/26/vaccine-resistant-what-scientists-know-new-covid-variant