Here we go again. CoVID 2.0?

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K Graham
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Here we go again. CoVID 2.0?

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Markets are crashing as a new variant has been reported in South Africa. They're saying it could be immune to current vaccines.
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Re: Here we go again. CoVID 2.0?

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¯\_(ツ)_/¯
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MeDotOrg
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Re: Here we go again. CoVID 2.0?

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When Covid first landed, I thought the virus would run a course similar to the 1918 flu pandemic, but humanity is far more interconnected than we were in 1918. It's hard to see light at the end of the tunnel.
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Re: Here we go again. CoVID 2.0?

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K Graham wrote:
Fri Nov 26, 2021 12:42 pm
Markets are crashing as a new variant has been reported in South Africa. They're saying it could be immune to current vaccines.
Markets will do what they will. We need a lot more data before it is sensible to come to even a provisional conclusion as to what the public health significance of this variant is. Meanwhile, learn to live calmly with ignorance for a while. It can be done!

One thing it certainly is not is a reason to abstain from getting vaccinated.

Here is a quick look, as of this moment from a good source of serious science journalism:

B.1.1.529: How dangerous is the new variant found in South Africa?
There are many open questions about the new variant of SARS-CoV-2 detected in South Africa. Here's what we know so far

A new variant of SARS-CoV-2, known as B.1.1.529, with an unusually high number of mutations has been detected in South Africa and appears to have triggered a recent surge in cases there.

When was B.1.1.529 first identified?

It was first detected on 23 November in South Africa using samples taken between 14 and 16 November. Joe Phaahla, South Africa’s health minister, said yesterday that he believes the variant is behind an exponential daily rise in covid-19 cases across the country in recent days. Yesterday, the UK Health Security Agency (HSA) designated it a variant under investigation, triggering travel restrictions for people travelling to the UK from South Africa, Botswana, Lesotho, Eswatini, Zimbabwe and Namibia. The World Health Organization had listed B.1.1.529 as a variant under monitoring, but its Technical Advisory Group on SARS-CoV-2 Virus Evolution has now advised changing it to a variant of interest. The WHO has now named it Omicron after the Greek letter.

What is happening in South Africa?

National daily cases have gone from 274 on 11 November to 1000 a fortnight later. While the rate of growth has been fast, absolute numbers are still relatively low compared with the UK, which saw 50,000 cases on 26 November. More than 80 per cent of South Africa’s cases are currently in the country’s Gauteng province. All of the 77 cases sequenced in the province between 12 and 20 November were identified as being caused by the variant. The estimated reproduction number, the average number of people that an individual is likely to infect, is almost 2 in Gauteng compared with nearly 1.5 nationally.

What do B.1.1.529’s mutations tell us?

The variant has a “very unusual constellation of mutations”, says Sharon Peacock at the University of Cambridge. There are more than 30 mutations in the spike protein, the part of the virus that interacts with human cells. Other mutations may help the virus bypass our immune systems, make it more transmissible and less susceptible to treatments, according to the HSA. But the body notes that “this has not been proven”.

What the mutations mean is currently theoretical and based on experience of past mutations of SARS-CoV-2 rather than lab tests. Wendy Barclay at Imperial College London says “we don’t really know” if it will reduce the effectiveness of vaccines. Nonetheless, she adds that, in theory, the number of changes across the antigenic sites on the variant’s spike means the effectiveness of antibodies produced by covid-19 vaccines would be compromised.

Mutations on a part of the virus known as the furin cleavage site are similar to those seen in the alpha and delta variants, which could help the variant spread more easily. Barclay says “it’s very biologically plausible” that B.1.1.529 has greater transmissibility than delta.

The mutations also mean that the new variant is likely to be more resistant to antibody treatments such as those developed by Regeneron, which have been shown to save lives. “That is really a cause for concern,” says Barclay. One small bright spot is that, to date, there are no signs that the variant causes more severe disease.

How far has it spread?

Genomic sequencing has found the variant in South Africa, Botswana and Hong Kong. There are also reported cases in Israel, apparently originating from a traveller from Malawi, and in Belgium, from someone who had travelled from Egypt. UK health secretary Sajid Javid said it is “highly likely” that the variant has spread to other countries. No cases have been detected in the UK yet, where about a fifth of positive cases are sent for genomic sequencing. Even in countries with low levels of sequencing, there may be some early warning signs, because the variant is linked to a mutation called S-gene dropout, which is picked up by PCR tests, says Jeffrey Barrett at the Wellcome Sanger Institute in Hinxton, UK.

How have other places responded?

The UK and EU have both imposed restrictions on people travelling from countries in southern Africa, with Javid saying the variant is of “huge international concern”.

Is it a given that this will outcompete the delta variant?

We don’t know. “We don’t have definitive evidence at the moment that this is more transmissible, but there are hints there that it may be,” says Peacock, pointing to the growth in South Africa and the higher R number in Gauteng. Some earlier variants have failed to get a toehold in certain countries because of the competition from other variants: beta hasn’t become established in the UK, for example, while alpha spread from Europe but never reached high levels in South Africa. “If this variant is not as transmissible as delta that would be good news for sure,” says Barrett.

What can I do?

All the usual measures of social distancing, handwashing, mask-wearing, getting vaccinated and having a booster shot still apply. The emergence of such a potentially worrying variant is, however, a reminder of the risk of uneven vaccination rates globally – only 24 per cent of people are fully vaccinated in South Africa – and why helping low and middle-income countries access vaccines is important.

How much do we really know about this variant?

Most of our knowledge is from the Network for Genomic Surveillance in South Africa, and the South African government, both of which have been praised by researchers for acting fast to share information on the variant. But there is more that we don’t know than we do. Tulio de Oliveira at Stellenbosch University, South Africa, said yesterday that the full significance of the variant’s mutations “remain uncertain.” Peacock adds: “It’s important to stress how much we don’t know this new variant.“
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Re: Here we go again. CoVID 2.0?

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Covid Omicron 2019


Coming soon to a theater near you
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Re: Here we go again. CoVID 2.0?

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People are already at work on the virus:

BioNTech says it could tweak Covid vaccine in 100 days if needed
Company says it will know in two weeks whether current Pfizer jab is effective against Omicron variant


mRNA vaccines are by their nature a flexible weapon, and can be retargeted once you have had a good look at the new enemy. But re-jigging may not be necessary - we shall see in a couple of weeks. Meanwhile we continue to take precautions as always.

BioNTech says it could produce and ship an updated version of its vaccine within 100 days if the new Covid variant detected in southern Africa is found to evade existing immunity.

The German biotechnology company is already investigating whether the vaccine it developed with US drugmaker Pfizer works well against the variant, named Omicron, which has caused concern due to its high number of mutations and initial suggestions that it could be transmitting more quickly.

The company says it will know in two weeks whether its current vaccine is likely to be sufficiently effective against the B.1.1.529 variant, now named Omicron by the World Health Organization, based on lab-based experiments.

Omicron: everything you need to know about new Covid variant
Read more
If required, BioNTech said it is poised to tweak its vaccine to match it more closely to the new variant.

“Pfizer and BioNTech have taken actions months ago to be able to adapt the mRNA vaccine within six weeks and ship initial batches within 100 days in the event of an escape variant,” the company said in a statement.

The US company Moderna said it was testing three existing Covid-19 vaccine booster candidates against the Omicron variant, and that it would develop a new variant-specific booster against it.

“From the beginning, we have said that as we seek to defeat the pandemic, it is imperative that we are proactive as the virus evolves. The mutations in the Omicron variant are concerning and for several days, we have been moving as fast as possible to execute our strategy to address this variant,” said Stéphane Bancel, Moderna’s chief executive.

Other vaccine teams, including Johnson & Johnson, also confirmed on Friday that they were testing the effectiveness of their vaccines against the new variant to assess whether updates were likely to be required. AstraZeneca said it is already conducting research in Botswana and Eswatini, where the variant has been identified, to collect real-world data on how the Oxford/AstraZeneca vaccine performs against the new variant.

At the moment, concerns about a decline in protection are theoretical based on the very high number of mutations – double that seen in Delta – on the spike protein that the vaccine targets.

Human immune systems make a variety of antibodies that target several different places on the spike, so even if one bit of the spike changes, a vaccine will still typically work well.

However, in B.1.1.529, nearly all the sites that antibodies target are different, and so scientists are particularly concerned this version could turn out to be an “escape variant”.

Prof Wendy Barclay, a virologist at Imperial College London, said the emergence of the variant made it even more crucial for people to access existing vaccines and have second and third doses. “Sometimes quantity [of antibodies] can compensate for the lack of match,” she said. “That is the only vaccine that’s available to us at the moment. We need to make that work as best as we can.”

Vaccines based on mRNA, such as the BioNTech/Pfizer and Moderna vaccines, are thought to be the easiest to alter. But most companies have been preparing for the eventuality of a so-called escape variant and have ambitious timeframes for distributing an updated vaccine, if deemed medically necessary and commercially feasible.

So far, vaccines have held up well against new variants, such as Beta and Delta, but the emergence of these variants served as practice runs.

BioNTech/Pfizer and AstraZeneca are already running clinical trials on tweaked vaccines and discussing with regulators what new evidence would be needed to support their approval.

“Pfizer and BioNTech … have begun clinical trials with variant-specific vaccines (Alpha and Delta) to collect safety and tolerability data that can be provided to regulators as part of the blueprint studies in the event of an needed variant-specific vaccine,” the companies said in a statement.

Johnson & Johnson, which has developed a single-shot Covid vaccine and is selling it on a not-for-profit basis, like AstraZeneca, said: “We are closely monitoring newly emerging Covid-19 virus strains with variations in the Sars-CoV-2 spike protein and are already testing the effectiveness of our vaccine against the new and rapidly spreading variant first detected in southern Africa.

“We remain steadfast in the benefit the Johnson & Johnson Covid-19 vaccine will provide to millions around the world.”
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Re: Here we go again. CoVID 2.0?

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MeDotOrg wrote:
Fri Nov 26, 2021 4:59 pm
When Covid first landed, I thought the virus would run a course similar to the 1918 flu pandemic, but humanity is far more interconnected than we were in 1918. It's hard to see light at the end of the tunnel.
Thanks for the fact based, non sensationalized overview. The more people are infected, the more chances of new variants. What will they be like? Spin the prize wheel. This is a very good reminder that the Pandemic has to be over everywhere before it is over anywhere.

In the meantime, get your shots, wear your mask, wash your hands, all that stuff.
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Re: Here we go again. CoVID 2.0?

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drumdude wrote:
Fri Nov 26, 2021 8:05 pm
Covid Omicron 2019


Coming soon to a theater near you
Is Omicron part of the Marvel Universe?
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Re: Here we go again. CoVID 2.0?

Post by Res Ipsa »

MeDotOrg wrote:
Sat Nov 27, 2021 3:30 am
drumdude wrote:
Fri Nov 26, 2021 8:05 pm
Covid Omicron 2019


Coming soon to a theater near you
Is Omicron part of the Marvel Universe?
Wait! I thought the next Greek letter was “neu.” I guess being able to talk about the new neu variant was too much to hope for.

Omicron? Phhhhb
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Re: Here we go again. CoVID 2.0?

Post by Moksha »

I imagine China, with its strict epidemiological policies, will be able to manage the virus. If even more virulent than current COVID 19 variants, it will probably ravage the United States (which will resist efforts of containment on the basis of freedom to spread contagion).
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