Coronavirus Sars-CoV-2/Covid-19 Megathread

[Razgovory]

I'm going to admit, I'm not that comfortable with direct payments like this.  I benefit more than most since I have so little money and I'm not a deficit hawk like Yi, but still...  I'm particularly worried that both Democrats and Republicans have the Senate race in Georgia in mind when they passed this bill.  I don't like even the hint that Congress is passing out free money to affect an election.


I know, this is an emergency, and I don't have any better ideas.  It just doesn't feel right.

[Sheilbh]

The new strain is already out there and may explain at least some of the additional difficulties that various countries have faced with the second wave. Horse, stable door, bolted .... blah blah blah

The government should not have kept this secret for so long.

I don't think it's been kept secret - Starmer's statement included the line that the government knew since September (which I've seen doing the rounds online) but from what I understand that's not true. September is the earliest sample with this strain.

From Science Magazine:

Mutant coronavirus in the United Kingdom sets off alarms but its importance remains unclear
By Kai KupferschmidtDec. 20, 2020 , 5:45 PM

On 8 December, during a regular Tuesday meeting about the spread of the pandemic coronavirus in the United Kingdom, scientists and public health experts saw a diagram that made them sit up straight. Kent, in the southeast of England, was experiencing a surge in cases, and a phylogenetic tree showing viral sequences from the county looked very strange, says Nick Loman, a microbial genomicist at the University of Birmingham. Not only were half the cases caused by one specific variant of SARS-CoV-2, but that variant was sitting on a branch of the tree that literally stuck out from the rest of the data. "I've not seen a part of the tree that looks like this before," Loman says.

Less than two weeks later, that variant is causing mayhem in the United Kingdom and elsewhere in Europe. Yesterday, U.K. prime minister Boris Johnson announced stricter lockdown measures, saying the strain, which goes by the name B.1.1.7, appears to be better at spreading between people. The news led many Londoners to leave the city today, before the new rules take effect, causing overcrowded railway stations. Also today, the Netherlands, Belgium, and Italy announced they were temporarily halting passenger flights from the United Kingdom. The Eurostar train between Brussels and the British capital will stop running at midnight tonight for at least 24 hours.

Scientists, meanwhile, are hard at work trying to figure out whether B.1.1.7 is really more adept at human-to-human transmission—not everyone is convinced yet—and if so, why. They're also wondering how it evolved so fast. B.1.1.7 has acquired 17 mutations all at once, a feat never seen before. "There's now a frantic push to try and characterize some of these mutations in the lab," says Andrew Rambaut, a molecular evolutionary biologist at the University of Edinburgh.

Researchers have watched SARS-CoV-2 evolve in real time more closely than any other virus in history. So far, it has accumulated mutations at a rate of about 1 to 2 changes per month. That means many of the genomes sequenced today differ at around 20 points from the earliest genomes sequenced in China in January, but many variants with fewer changes are also circulating. "Because we have very dense surveillance of genomes, you can almost see every step," Loman says.

But scientists have never seen the virus acquire more than a dozen mutations seemingly at once. They think it happened during a long infection of a single patient that allowed SARS-CoV-2 to go through an extended period of fast evolution, with multiple variants competing for advantage.

One reason to be concerned, Rambaut says, is that among the 17 are eight mutations in the gene that encodes the spike protein on the viral surface, two of which are particularly worrisome. One, called N501Y, has previously been shown to increase how tightly the protein binds to the ACE2 receptor, its entry point into human cells. The other, named 69-70del, leads to the loss of two amino acids in the spike protein and has been found in viruses that eluded the immune response in some immunocompromised patients.

A fortunate coincidence helped show that B.1.1.7 (also called VUI-202012/01, for the first "variant under investigation" in December 2020), appears to be spreading faster than other variants in the United Kingdom. One of the PCR tests used widely in the country, called TaqPath, normally detects pieces of three genes. But viruses with 69-70del lead to a negative signal for the gene encoding the spike gene; instead only two genes show up. That means PCR tests, which the U.K. conducts by the hundreds of thousands daily and which are far quicker and cheaper than sequencing the entire virus, can help keep track of B.1.1.7.

In a press conference on Saturday, chief science advisor Patrick Vallance said that B.1.1.7, which first appeared in a virus isolated on 20 September, accounted for about 26% of cases in mid-November. "By the week commencing the 9th of December, these figures were much higher," he said. "So, in London, over 60% of all the cases were the new variant." Boris Johnson added that the slew of mutations may have increased the virus's transmissibility by 70%.

Christian Drosten, a virologist at Charité University Hospital in Berlin, says that was premature. "There are too many unknowns to say something like that," he says. For one thing, the rapid spread of B.1.1.7 might be down to chance. Scientists previously worried that a variant that spread rapidly from Spain to the rest of Europe—confusingly called B.1.177—might be more transmissible, but today they think it is not; it just happened to be carried all over Europe by travelers who spent their holidays in Spain. Something similar might be happening with B.1.1.7, says Angela Rasmussen, a virologist at Georgetown University. Drosten notes that the new mutant also carries a deletion in another viral gene, ORF8, that previous studies suggest might reduce the virus's ability to spread.

But further reason for concern comes from South Africa, where scientists have sequenced genomes in three provinces where cases are soaring: Eastern Cape, Western Cape, and KwaZulu Natal. They identified a lineage separate from the U.K. variant that also has the N501Y mutation in the spike gene. "We found that this lineage seems to be spreading much faster," says Tulio De Oliveira, a virologist at the University of KwaZulu Natal whose work first alerted U.K. scientists to the importance of N501Y. (A preprint of their results on the strain, which they are calling 501Y.V2, will be released on Monday, De Oliveira says.)

Another worry is that B.1.1.7 could cause more severe disease. There is anecdotal evidence that the South African variant may be doing that in young people and those who are otherwise healthy, says John Nkengasong, director of the Africa Centres for Disease Control and Prevention. "It's concerning, but we really need more data to be sure." The African Task Force for Coronavirus will convene an emergency meeting to discuss the issue on Monday, Nkengasong says.

Still, B.1.177, the strain from Spain, offers a cautionary lesson, says virologist Emma Hodcroft of the University of Basel. U.K. scientists initially thought it had a 50% higher mortality rate, but that turned out to be "purely messy, biased data in the early days," she says. "I think that is a very strong reminder that we always have to be really careful with early data." In the case of N501Y, more young people may be getting sick because many more are getting infected; Oliveira says some recent post-exam celebrations in South Africa have turned into superspreading events. Studies in cell culture and animal experiments will have to show how a virus with several or all of the mutations carried by the new variant compares with previous variants, says Drosten.

Getting definitive answers could take months. But Ravindra Gupta, a virologist at the University of Cambridge has made a start. The 69-70del mutation appeared together with another mutation named D796H in the virus of a patient who was infected for several months and was given convalescent plasma to treat the disease. (The patient eventually died.) In the lab, Gupta's group found that virus carrying the two mutations was less susceptible to convalescent plasma from several donors than the wildtype virus. That suggests it can evade antibodies targeting the wildtype virus, Gupta wrote in a preprint published this month. He also engineered a lentivirus to express mutated versions of the spike protein and found that the deletion alone made that virus twice as infectious. He is now conducting similar experiments with viruses that carry both the deletion and the N501Y mutation. The first results should appear just after Christmas, Gupta says.

Does it occur elsewhere?

The ban on flights from the United Kingdom that other countries are imposing "is pretty extreme," says Hodcroft. But it does give countries time to think about putting any additional measures in place to deal with passengers from the United Kingdom, she says: "I would hope that most countries in Europe are thinking about this."

But scientists say B.1.1.7 may already be much more widespread. Dutch researchers have found it in a sample from one patient taken in early December, Dutch health minister Hugo de Jonge wrote in a letter to Parliament today. They will try to find out how the patient became infected and if there are related cases. Other countries may well have the variant as well, says epidemiologist William Hanage of the Harvard T.H. Chan School of Public Health; the United Kingdom may just have picked it up first because that country has the most sophisticated SARS-CoV-2 genomic monitoring in the world. Many countries have little or no sequencing.

The evolutionary process that led to B.1.1.7 may also occur elsewhere. With vaccines being rolled out, the selective pressure on the virus is going to change, meaning variants that help the virus thrive could be selected for, says Kristian Andersen, an infectious disease researcher at Scripps Research. The important thing in the coming months will be picking up such events, says Andersen.  "Whatever enabled the B.1.1.7 lineage to emerge is likely going on in other parts of the world", he says. "Will we be able to actually detect it and then follow up on it? That, to me is one of the critical things."

Kai Kupferschmidt
Kai is a contributing correspondent for Science magazine based in Berlin, Germany. He is the author of a book about the color blue, published in 2019.

[Admiral Yi]

Oh I am aware. I would want $1,000 a month for the duration of the crisis.

But it is some crumbs. Sometimes a few crumbs can make a difference.

People on unemployment are getting 1,200/month in addition to their unemployment.  People not on unemployment are presumably getting their wages.

[Sheilbh]

The area I love in has been in four different tiers/lockdown levels in the last four weeks

[Richard Hakluyt]

Thanks for that Sheilbh; looks like the government is in the clear on "keeping the variant secret".

Do you always love in only a specific area btw; or is that a temporary measure due to coronavirus?

[Sheilbh]

Do you always love in only a specific area btw; or is that a temporary measure due to coronavirus?

 

Edit:

Thanks for that Sheilbh; looks like the government is in the clear on "keeping the variant secret".

Yes. I think they've done what they should which is once they're aware of it letting people know - including from what I've read informing the WHO etc. And I think other countries have behaved sensibly in closing borders (just like we did with Denmark during the zombie mink incident).

I was very anti-border closures in the first wave because I just didn't see that it would have an impact given how the world is connected. But it's clear it's a big part of the success in APAC countries. Epidemiologists were also very negative about the idea in the first wave (though I'd note they were also negative on the idea of masks and lockdowns in January-February so......) and now are all saying it can play a part, although they worry now that countries could be incentivised to cover things up if they think their neighbours might close the borders. Personally I think the benefits outweight that risk.

Edit: It's pathological, Johnson's inability to just deliver bad news/get ahead of things. Sir Patrick Vallance the chief scientific advisor, stood next to him it's likely that cases especially of the new strain will grow and "it's likely that measures will need to be increased in some places in due course and not reduced".  Johnson's message: "continue to shop normally"

[garbon]

Yes. I think they've done what they should which is once they're aware of it letting people know - including from what I've read informing the WHO etc. And I think other countries have behaved sensibly in closing borders (just like we did with Denmark during the zombie mink incident).

I was very anti-border closures in the first wave because I just didn't see that it would have an impact given how the world is connected. But it's clear it's a big part of the success in APAC countries. Epidemiologists were also very negative about the idea in the first wave (though I'd note they were also negative on the idea of masks and lockdowns in January-February so......) and now are all saying it can play a part, although they worry now that countries could be incentivised to cover things up if they think their neighbours might close the borders. Personally I think the benefits outweight that risk.

Edit: It's pathological, Johnson's inability to just deliver bad news/get ahead of things. Sir Patrick Vallance the chief scientific advisor, stood next to him it's likely that cases especially of the new strain will grow and "it's likely that measures will need to be increased in some places in due course and not reduced".  Johnson's message: "continue to shop normally"

I don't really get this. Given that it has already spread past the UK border (as evidenced by logically it would because it has been around since September and it has already started being spotted in multiple countries - Europe and Australia), it feels like the cat is already out of the bag.

[Sheilbh]

I don't really get this. Given that it has already spread past the UK border (as evidenced by logically it would because it has been around since September and it has already started being spotted in multiple countries - Europe and Australia), it feels like the cat is already out of the bag.

I agree and that's why I didn't get border closure in the first wave. But I suppose if it's still small in those countries then it can be found (especially because by luck this strain can be spotted by current tests and doesn't require gene sequencing) so you can probably track and trace domestic cases plus quarantine for those people and stop new cases from South-East England.

And the most successful countries like New Zealand, Australia, Japan, South Korea and Taiwan have been pretty militant on border controls - it seems like that is an important part of how they've stopped the spread of covid.

[Richard Hakluyt]

The Guardian has rounded up some European health experts who think that the increased transmissibility of the new variant is not yet proven :

https://www.theguardian.com/world/2020/dec/21/european-experts-urge-caution-over-new-covid-mutation-uk

Let's hope their scepticism is not misplaced.

[Barrister]

And the most successful countries like New Zealand, Australia, Japan, South Korea and Taiwan have been pretty militant on border controls - it seems like that is an important part of how they've stopped the spread of covid.

It seems to me those countries all have something in common that explains how they're able to be "militant on border controls"...

[Valmy]

Oh I am aware. I would want $1,000 a month for the duration of the crisis.

But it is some crumbs. Sometimes a few crumbs can make a difference.

People on unemployment are getting 1,200/month in addition to their unemployment.  People not on unemployment are presumably getting their wages.

Ok so everybody is getting big unemployment checks or their wages then why is there an economic crisis at all? People have tons of money to spend, why are we pumping hundreds of billions we don't have into the economy after trillions we didn't have earlier this year? Why is there an eviction crisis? Why have an eviction moratorium at all if everybody has plenty of cash either through their work or through unemployment?

Honest questions I keep hearing about economic disaster with huge numbers of businesses shutting their doors forever and millions about to be cast out of their homes so I am puzzled by your rosy diagnosis. What's actually going on Yi? Is everybody either getting the help they need or still getting good employment?

I am just getting big cognitive dissonance but hey I am in Austin Texas where, sure we have homelessness (yeah where are those people's wages and big unemployment checks? Surely if that was accurate there would not be very many homeless people...), but generally the economy is always doing well here so I don't know. Maybe all the doom and gloom is just media sensationalism.

[Sheilbh]

The Guardian has rounded up some European health experts who think that the increased transmissibility of the new variant is not yet proven :

https://www.theguardian.com/world/2020/dec/21/european-experts-urge-caution-over-new-covid-mutation-uk

Let's hope their scepticism is not misplaced.

Yeah - though I'd note that the NERVTAG minutes that have been released of their 18 December meeting said they had "moderate confidence that VUI-202012/01 demonstrates a substantial increase in transmissibility compared to other variants". Today Vallance said NERVTAG had met again and the minutes would be released in course, but he also said "the conclusion was that experts have high confidence in the fact that this is transmitting more readily."

I think there's a bit of politics in this in that they don't trust the UK (and I think there was something similar with the vaccine approval - which has since been reversed now that it's been approved elsewhere). I don't think it helps when you've got respectable media voices like Lionel Barber, former editor of the FT, saying "it's pretty clear" the government "egged up the transmissibility of the new strain" - while presenting zero evidence for that.

Separately - it definitely feels like something else is going on in the Tier 4 areas where this strain is most prevalent and I don't think that can be fully explained by general relaxation/mingling:


This is why I think we probably need Tier 4 everywhere now and it makes sense for neighbours/other countries to close their borders to most travel. It doesn't look like a normal rate of growth even as % of tests - it's scarily steep.

It seems to me those countries all have something in common that explains how they're able to be "militant on border controls"...

Sure but that also applies to the ROTW dealing with the UK, no?

From what I understand it's also the case with south-east Asia - Thailand, Cambodia and Vietnam have all been very successful in repressing covid and all been strict on border control.

[Admiral Yi]

Ok so everybody is getting big unemployment checks or their wages then why is there an economic crisis at all? People have tons of money to spend, why are we pumping hundreds of billions we don't have into the economy after trillions we didn't have earlier this year? Why is there an eviction crisis? Why have an eviction moratorium at all if everybody has plenty of cash either through their work or through unemployment?

Honest questions I keep hearing about economic disaster with huge numbers of businesses shutting their doors forever and millions about to be cast out of their homes so I am puzzled by your rosy diagnosis. What's actually going on Yi? Is everybody either getting the help they need or still getting good employment?

I am just getting big cognitive dissonance but hey I am in Austin Texas where, sure we have homelessness (yeah where are those people's wages and big unemployment checks? Surely if that was accurate there would not be very many homeless people...), but generally the economy is always doing well here so I don't know. Maybe all the doom and gloom is just media sensationalism.

Moving the goal posts a bit there.  600 to start plus 300 extra per week not being crumbs is not the same thing as no restaurants, bars, and retail establishments suffering from lack of business.

People have been short on rent at least in part because the last stimulus top up ran out a while ago.  The new stimulus will presumably alleviate that problem.

[Admiral Yi]

Bill has 300 billion for small businesses too.  Didn't see that first time.

[Valmy]

Moving the goal posts a bit there.  600 to start plus 300 extra per week not being crumbs is not the same thing as no restaurants, bars, and retail establishments suffering from lack of business.

People have been short on rent at least in part because the last stimulus top up ran out a while ago.  The new stimulus will presumably alleviate that problem.

I am not moving the goal posts. I thought we were in a serious economic crisis and people were suffering. $600 is a pretty small amount if there is the widespread suffering that has been reported. Supposedly there is this big homelessness problem and only a eviction moratorium is the only thing keeping about 20 million people from being thrown out of their homes.

You just posted, without comment or context:

People on unemployment are getting 1,200/month in addition to their unemployment.  People not on unemployment are presumably getting their wages.

So naturally such a big statement against this alarmist narrative causes me to question my sources. Am I out of touch? Is everybody actually doing fine? What is Yi trying to say?

So what you were getting at was that $600 plus the unemployment increase is not peanuts? Ok well why didn't you just say so?

I think we can both agree it is really needed and I will restate I hope it helps struggling families.