Coronavirus Sars-CoV-2/Covid-19 Megathread

[Sheilbh]

I think the key thing here is that for people who have not worked on/with such vaccines before, it can only be an assumption, and the debate is whether such an assumption is justified given the circumstances.

Because the very same British authority/persons in charge of policy held out record-long back in the Spring clinging to their 2011 spreadsheets while this thing engulfed the continent in a very not-usual-flu manner, I can't help being skeptical when they come out and say "yeah well this is a brand new thing but the old thing could totally be delayed so obvs. this can be delayed as well even though the very people who invented it say it shouldn't".

I agree with all that. I think it is reasonable/justified given the circumstances - so sticking to the manufacturer's schedule (which they will of course defend for liability reasons) while watching the share of positive tests triple in a month is a bit like clinging to the 2011 spreadsheets.

And the vaccination schedule is authorised by another body of the great and the good who've not had any covid recommendations to make yet

[garbon]

Sounds like we will have to wait and see:

https://news.sky.com/story/covid-19-extending-gap-between-coronavirus-jab-doses-creates-small-risk-of-escaped-mutant-variant-whitty-12180180

The issue has been raised by former World Health Organisation (WHO) director Anthony Costello, who wrote on Twitter: "If we assume that over the next 12 weeks 12-20 million people get one dose of a vaccine and are told or believe it gives 90% protection what % will actually go for a second jab?

"We might assume second dose coverage is at best 70%. That means between 4 and 6.7 million people might have fading protection.

"Will the risk of creating a vaccine resistant mutant in this group of people, which could spread rapidly to 7 billion people around the world, outweigh the benefits of 6000 deaths prevented."

Florian Krammer, a microbiology professor at the Icahn School of Medicine, also tweeted: "If virus circulation is low, the 12 week window might not be a big problem.

"But if virus circulation is sky high (like right now in the UK), it is not a good idea."

[DGuller]

Hopefully the wider short term vaccination will lower the R enough so that it dies down on its own, then it's going to be a less urgent matter to catch everyone up on full immunity.

[Sheilbh]

Incidentally - an update on the latest about the new UK strain:

Viral mutations may cause another 'very, very bad' COVID-19 wave, scientists warn
By Kai KupferschmidtJan. 5, 2021 , 3:05 PM

For COVID-19 researchers, the new year brings a strong sense of déjà vu. As in early 2020, the world is anxiously watching a virus spread in one country and trying to parse the risk for everyone else. This time it is not a completely new threat, but a rapidly spreading variant of SARS-CoV-2. In southeastern England, where the B.1.1.7 variant first caught scientists' attention last month, it has quickly replaced other variants, and it may be the harbinger of a new, particularly perilous phase of the pandemic.

"One concern is that B.1.1.7 will now become the dominant global variant with its higher transmission and it will drive another very, very bad wave," says Jeremy Farrar, an infectious disease expert who heads the Wellcome Trust. Whereas the pandemic's trajectory in 2020 was fairly predictable, "I think we're going into an unpredictable phase now," as a result the virus' evolution, Farrar says.

The concern has led some countries to speed up vaccine authorizations or discuss dosing regimens that may protect more people rapidly. But as the new variant surfaces in multiple countries, many scientists are calling for governments to strengthen existing control measures as well. U.K. Prime Minister Boris Johnson announced tough new restrictions on 4 January, including closing schools and asking people not to leave their homes unless strictly necessary. But other countries have hesitated. "I do feel like we are in another situation right now where a lot of Europe is kind of sitting and looking," says virologist Emma Hodcroft of the University of Basel. "I really hope that this time we can recognize that this is our early alarm bell, and this is our chance to get ahead of this variant."

In announcing the U.K. restrictions, Johnson said the new variant is between 50% and 70% more transmissible. But researchers have been careful to point out uncertainties. Cases have soared in the United Kingdom over the past month, but the rise occurred while different parts of the country had different levels of restrictions and amid changes in people's behavior and regional infection rates in the run-up to Christmas—"a complex scenario" that makes it hard to pinpoint the effect of the new variant, says evolutionary biologist Oliver Pybus of the University of Oxford.

Yet evidence has rapidly increased that B.1.1.7's many mutations, including eight in the crucial spike protein, do enhance spread. "We're relying on multiple streams of imperfect evidence, but pretty much all that evidence is pointing in the same direction now," says Adam Kucharski, a modeler at the London School of Hygiene & Tropical Medicine. For instance, an analysis by Public Health England showed about 15% of the contacts of people infected with B.1.1.7 in England went on to test positive themselves, compared with 10% of contacts of those infected with other variants.

If other countries that have detected B.1.1.7 also see it surge, it will be "the strongest evidence we will have," Pybus says. In Ireland, where infections have risen rapidly as well, the variant now accounts for a quarter of sequenced cases. And data from Denmark, which leads the European Union in the sequencing of SARS-CoV-2, aren't reassuring either. Routine surveillance there has picked up the variant dozens of times; its frequency went from 0.2% of sequenced genomes in early December to 2.3% 3 weeks later. "We have had what looks like a poster child example of exponential growth these last 4 weeks in Denmark," says genomicist Mads Albertsen of Aalborg University. The numbers are still too low to draw strong conclusions, Albertsen cautions, but if the trend continues it will be a clear sign that many countries may face the same problems as the United Kingdom. "We should start preparing ourselves for the fact that this is happening elsewhere," Hodcroft says.

The lack of evidence—so far—that the new variant makes people sicker is little consolation. Increased transmissibility of a virus is much more treacherous than increased pathogenicity because its effects grow exponentially, Kucharski says. "If you have something that kills 1% of people but a huge number of people get it, that's going to result in more deaths than something that a small number of people get but it kills 2% of them."

If the U.K. estimates of a 50% to 75% increase in the virus' reproduction number, or R, hold true, "keeping the virus from spreading has become a lot harder," says Viola Priesemann, a physicist at the Max Planck Institute for Dynamics and Self-Organization who has been modeling the pandemic and the effects of nonpharmaceutical interventions, such as physical distancing and school closures. "In Germany, you would need two big additional measures to keep the reproduction number below 1," Priesemann says.

Isolating patients and tracing, quarantining, and testing their contacts is one part of any attempt at doing so; those measures alone can reduce R from about 2 to about 1, Priesemann has shown for Germany. But that effect breaks down when case numbers reach a critical threshold and public health authorities are overwhelmed, which means tougher measures now can help contain the spread of the new variant later. "It's yet another reason to go for very low numbers," says Priesemann, who co-authored a December 2020 letter to the The Lancet calling for Europe to adopt a joint strategy to bring down infections fast. Hodcroft agrees. "The case has never been stronger," she says. "What's the worst-case scenario here? We overshoot and we get cases so low that we can get rid of a lot of restrictions."

Curtailing infections sharply has the added benefit of reducing the chances for the virus to evolve even further. Already other variants have emerged, notably one called 501Y.V2 in South Africa, that are just as worrying as B.1.1.7, Farrar adds. "It is essentially a numbers game: The more virus is circulating, the more chance mutants have to appear," he says. In the long term, mutations could arise that threaten the efficacy of vaccines.

It's dispiriting to feel like the world is back where it was in early 2020, says epidemiologist William Hanage of the Harvard T.H. Chan School of Public Health. "But we have to stop this virus. ... Fatalism is not a nonpharmaceutical intervention."

There's a really scary chart in there comparing UK to EU new cases - and that can't all be Christmas. It'll be worth keeping an eye on Denmark because they definitely have cases of the UK strain. But the figures in Ireland are striking - they re-opened in a big way for Christmas - but I suspect it's likely the UK strain is there and that must be a factor - I don't think I've seen figures like this at any point before:

[Sheilbh]

So this is good news - WHO have said that it looks like the new South African variant is unlikely to be an issue for the vaccines which was a fear. It is still more transmissible.

Edit: In less good news with the UK variant - the Netherlands have identified a cluster of 50 cases including 30 in a primary school.

There's also a new report from Denmark - who are key for understanding this in continental Europe because of the amount of sequencing they do. They have found that this strain is growing and estimate it's growing 70% faster than other variants. They basically think they are where the UK was in early November (and it only really took off here in late November) and expect the UK strain to become the dominant strain by mid-February. Their recommendation is that "it is crucial to turn the epidemic curve around and get the reproduction number significantly below 1 in the coming weeks, so that the infection rates are as low as possible when cluster B.1.1.7 becomes the dominant virus in mid-February."

They think that if thet can get the R below 0.7 that could keep the new variant from spreading. Their models on R numbers above that show that it will continue to spread. But their case numbers are still declining and the UK variant numbers are still low so if they're strict enough now (and same probably goes for the rest of Europe) it maybe could be stopped from growing, but everywhere needs a lockdown that is strict and long enough to get numbers very, very low indeed.

[viper37]

I don't really understand how it is more contagious than the "original" strain?

Is it more resistant to alcohol and soap and warm water?  Is it spreading faster after infections?  Is it "alive" longer outside of the human body than the original one?

Any kind of scientific publication on that would be appreciated.

[Zanza]

I don't really understand how it is more contagious than the "original" strain?

Is it more resistant to alcohol and soap and warm water?  Is it spreading faster after infections?  Is it "alive" longer outside of the human body than the original one?

Any kind of scientific publication on that would be appreciated.

There are multiple mutations in the spike protein, which allows B.1.1.7 to enter human cells easier than other varieties of SARS CoV 2.

[Sheilbh]

There are multiple mutations in the spike protein, which allows B.1.1.7 to enter human cells easier than other varieties of SARS CoV 2.

I'm not sure if this is related but I think there's also some evidence that it has a higher viral load so presumably people "emit" more?

Edit: Also it seems like some of the red tape is being got rid of - the NHS are now removing the requirement for everyone delivering vaccines to do fire safety and preventing radicalisation training It's a start.

[celedhring]

I don't really understand how it is more contagious than the "original" strain?

Is it more resistant to alcohol and soap and warm water?  Is it spreading faster after infections?  Is it "alive" longer outside of the human body than the original one?

Any kind of scientific publication on that would be appreciated.

There are multiple mutations in the spike protein, which allows B.1.1.7 to enter human cells easier than other varieties of SARS CoV 2.

I'm an idiot on these matters, but if the virus is already trying to enter your cells, aren't you already infected? This would just increase the viral load, making it more likely you'll get a bad case of it?

[garbon]

I don't really understand how it is more contagious than the "original" strain?

Is it more resistant to alcohol and soap and warm water?  Is it spreading faster after infections?  Is it "alive" longer outside of the human body than the original one?

Any kind of scientific publication on that would be appreciated.

There are multiple mutations in the spike protein, which allows B.1.1.7 to enter human cells easier than other varieties of SARS CoV 2.

I'm an idiot on these matters, but if the virus is already trying to enter your cells, aren't you already infected? This would just increase the viral load, making it more likely you'll get a bad case of it?

You can also spread more viral particles as there is more to shed.

[mongers]

New record high death toll in the UK reported today 1162 deaths. 

[alfred russel]

Guys, I feel like covid is finally closing in on me....

I guess I'm in quarantine because my indoor climbing buddy from Tuesday night thinks he may have picked it up. Which means we can't go visit my fiance's grandparents on Saturday, who just recovered from covid. And she can't go to swim practice tomorrow night, although of the 6 people people on her team only 1 other person hasn't had covid (her coach has also had covid). Last weekend we were climbing (outside) with a couple that were making their first trip outside after recovering from covid.

[alfred russel]

My girlfriend doesn't seem to be grasping quarantining. We normally go to the climbing gym Tuesday and Thursday nights. "So I guess we can't go climbing tonight. Quarantine sucks, there is nothing to do. I have an idea! I have passes to a yoga studio; lets go to a yoga class!" 

[The Brain]

Is it Yoga Berra's? That place is hilarious.

[alfred russel]

Is it Yoga Berra's? That place is hilarious.

Nobody goes there anymore. It is too crowded.