Coronavirus Sars-CoV-2/Covid-19 Megathread

[mongers]

In news of Sheilbh's interest, the analysis of sewage from a mountain town in the Pyrenees have bizarrely (or alarmingly) shown a 30% prevalence of the British Covid variant.

So far sequencing of PCR samples had shown rates of around 10% in both the Madrid and Barcelona areas.

It's British homoeopathy, just one drop is enough. 

Isn't the region either side of the Pyrenees somewhat popular with Brit expats, given our woeful travel restriction I'd be unsurprised that lots of my fellow countrymen have been travelling unnecessarily.

[mongers]

Its not a number I normally pay much attention to...
But 2 million currently infected in the UK.
Thats just insane. 3% of the country have corona virus.

I think it's nearer half that or less, as the last figures I saw said 1 in 55 for England, 1 in 110 for Scotland, 1 in 70 for Wales and I believe those figures are from the peak about two weeks ago. 

[celedhring]

It's not connected to ski resorts (which have been closed for a while now, anyway), nor a place foreigners should have interest in going. It is, however, one of the largest Covid hotspots in Catalonia right now. Looking at the available data, some other nearby towns/cities have anomalously large % of the variant.

[Richard Hakluyt]

And I'm sure that if one starts looking there are probably hundreds of variants already, just that few will have true epidemiological significance.

One of our government ministers reckons there are currently 4,000 variants doing the rounds, from the Guardian :

"Vaccine Deployment Minister Nadhim Zahawi told Sky:

It's very unlikely that the current vaccine won't be effective on the variants whether in Kent or other variants especially when it comes to severe illness and hospitalisation.

All manufacturers, Pfizer-Biontech, Moderna, Oxford-AstraZeneca and others are looking at how they can improve their vaccine to make sure that we are ready for any variant - there are about 4,000 variants around the world of Covid now."

[Sheilbh]

Update from Denmark - which captures my worries for the US and Europe really well:

Danish scientists see tough times ahead as they watch more contagious COVID-19 virus surge
By Kai KupferschmidtFeb. 3, 2021 , 2:50 PM

On its face, the curve of COVID-19 infections in Denmark looks reassuring enough. A nationwide lockdown has led numbers to plummet from more than 3000 daily cases in mid-December 2020 to just a few hundred now. But don't be fooled. "Sure, the numbers look nice," says Camilla Holten Møller of the Statens Serum Institute, who heads a group of experts modeling the epidemic. "But if we look at our models, this is the calm before the storm."

That's because the graph really reflects two epidemics: one, shrinking fast, that's caused by older variants of SARS-CoV-2, and a smaller, slowly growing outbreak of B.1.1.7, the variant first recognized in England and now driving a big third wave of the pandemic there. If B.1.1.7 keeps spreading at the same pace in Denmark, it will become the dominant variant later this month and cause the overall number of cases to rise again, despite the lockdown, Holten Møller says. "It is a complete game changer."

The same is likely happening in many countries without being noticed. But a massive virus-sequencing effort has allowed Denmark, a country of 5.8 million, to track the rise of the new COVID-19 variant more closely than any other country. "All eyes are on Denmark right now," says Kristian Andersen, an infectious diseases researcher at Scripps Research who is advising the Danish government. "When it comes to B.1.1.7, is there a way in which ... we can prevent the kind of calamity that we have seen in the U.K. and Ireland, for example?" he asks.

The data aren't reassuring. Danish scientists' best guess is that B.1.1.7 spreads 1.55 times faster than previous variants, Holten Møller says. To keep it from spiraling out of control, the country will have to remain in lockdown—or even add new control measures—until a large part of the population has been vaccinated. That prospect is so unappealing that some epidemiologists say Denmark should consider an alternative: Reopen once the most vulnerable people are vaccinated, even if that means a big new surge in cases.

Denmark reported B.1.1.7 within its borders in December 2020, soon after the United Kingdom put the world on notice, and has since stepped up an already impressive virus-sequencing operation. Mads Albertsen, a bacterial genome researcher at Aalborg University, leads a team that has sequenced virus genomes from more than half of all COVID-19 patients so far this year and hopes to reach 70% soon.

It was clear by early January that B.1.1.7 was roughly doubling in frequency every week, says Lone Simonsen, an epidemiologist at Roskilde University. At that point, Denmark had already closed schools and restaurants; to combat the new threat, the lockdown was tightened by cutting the number of people allowed to gather from 10 to five, for example, and doubling the recommended distance between people from 1 to 2 meters. That helped bring the overall reproductive number (R) to a healthy 0.78, according to the most recent estimate. But B.1.1.7 still has an estimated R of 1.07; in other words, it's growing exponentially. Meanwhile, the share of COVID-19 cases infected with the variant has increased from less than 0.5% in early December 2020 to 13% in late January.


Previous SARS-CoV-2 variants are rapidly declining in Denmark (top), but B.1.1.7 is on the rise (bottom).
(GRAPHIC) V. ALTOUNIAN/SCIENCE; (DATA) STATENS SERUM INSTITUTE

The country could take further steps such as requiring people to work from home when possible and improving contact tracing, which becomes easier as the numbers dwindle. Rolling out rapid tests could also help, and more can be done to encourage patients to isolate, says Michael Bang Petersen, a political scientist at Aarhus University; currently, 15% of those who receive a positive test do not self-isolate.

By doing more, Denmark can still rid itself of B.1.1.7 and avert a third wave, says Andersen, who points out that case numbers are falling in the United Kingdom, where B.1.1.7 now dominates: "It can be done, but it requires a tremendous amount of effort." (He says Denmark should attempt to end its epidemic altogether, New Zealand style, through aggressive measures and border closures.)

Others are not convinced the tide can be turned. The drop in the United Kingdom may partly be due to the fact that so many have been infected already and are no longer susceptible, says Viggo Andreasen, a modeler at Roskilde. At best, Denmark could push R for the variant just below 1, he says, leading to a very slow decline—although better weather by April could help.

So far, the public has accepted the government's message that the lockdown needs to remain in place despite the declining cases, says Petersen, who coordinates a project to study how the government and the public are reacting to the pandemic: "What has been amazing during January is that the numbers have substantially dropped, but at the same time, people have reduced their contacts even further." But that will be hard to sustain as time goes on, he says. "There's a huge pressure on the government to reopen the country," adds Thea Kølsen Fischer, a virologist at the University of Copenhagen. In a small first step, the government is reopening schools for children in first to fourth grade on 8 February.

Simonsen says the cost of extending the lockdown for many more months may prove too high. Instead, Denmark should consider opening as soon as people over age 50 and other vulnerable groups have been vaccinated—an effort that is underway. Reopening might trigger a sharp increase of cases among the unvaccinated, but few would presumably die. At that point, society could start to think of SARS-CoV-2 more like influenza, which also occasionally kills healthy young people, she says: "We don't close down birthday parties for this."

Andreasen disagrees. Accepting a new surge might have been a good strategy before other countries saw variants emerge that appear to partially evade human immunity. More infections raise the risk of further viral evolution, he says. "It's a nasty mix to have a population where half of the population harbors the virus, and the other half is like a big experimental vessel for the virus to learn how to escape immunity."

Letting the virus go would have another downside, says Devi Sridhar, a global health scientist at the University of Edinburgh: More people with mild infections might develop long-lasting health problems. "Given what we know about long COVID and the associated morbidity we might see," Sridhar says, "I just think the risks are high with that."

*Correction, 3 February, 5:20 p.m.: A previous version of this story said half of those who receive a positive COVID-19 test in Denmark don't self-isolate. The correct number is 15%.

[Maladict]

The third wave is already taken as unavoidable here, even with current restrictions kept indefinately.

So, we're opening schools next week, with teachers slated to get their vaccines around summer or later. What could possibly go wrong?

[Sheilbh]

The third wave is already taken as unavoidable here, even with current restrictions kept indefinately.

So, we're opening schools next week, with teachers slated to get their vaccines around summer or later. What could possibly go wrong?

Yeah

In the UK vaccinating teachers as a priority has become a political issue. Part of that is Tory MPs who think if you vaccinate teachers you can re-open schools. But the issue with schools and the new variant isn't that teachers get infected - in the UK teachers do not get covid more than the average across sectors and are far less "at risk" than, say, delivery drivers or shop workers. The issue is instead kids mixing meaning the new variant can skip from household to household.

There's a lot of pressure on re-opening schools but I just don't think it's safe with the new variant, even if it might be okay if we just had the old covid strains.

[celedhring]

I don't know if B117 changes things, but schools opened here in autumn and they have not become the covid hotspots people feared. What's the established science on children spreading covid? (I feel like I've read articles pointing in contradictory directions)

[Tamas]

I guess what'll happen (and to be fair probably should happen) is get enough vulnerable people vaccinated to avoid overloading the hospitals then gradually open up and let it wash through the population, taking all of us who can't fight it.

[Sheilbh]

I don't know if B117 changes things, but schools opened here in autumn and they have not become the covid hotspots people feared. What's the established science on children spreading covid? (I feel like I've read articles pointing in contradictory directions)

Yeah so I don't think the science has shifted on this.

Jonathan Van Tam the UK Deputy Chief Medical Officer explained this really well in the press conference last week:
https://news.sky.com/video/covid-19-van-tam-answers-questions-about-schools-and-covid-12200552

Basically it contributes to R rather than being a hotspot or a risk for children or teachers.

[Sheilbh]

I guess what'll happen (and to be fair probably should happen) is get enough vulnerable people vaccinated to avoid overloading the hospitals then gradually open up and let it wash through the population, taking all of us who can't fight it.

It depends when. The first 4 vulnerable groups for vaccination in the UK account for 80% of the mortality, but the full 9 priority groups account for 99% of the mortality in the UK.

I think it is difficult to argue that we have full restrictions if that mortality rate is far lower - especially with schools which I think should be the thing we always look to re-open first. I also think consent would break down pretty quickly. But I think we will still need to have some restrictions to try and keep the R down while the rest of the population are being vaccinated to avoid the risk of a new variant emerging and also that even if the mortality rate is lower the non-vulnerable groups can still end up needing hospitalisation/putting pressure on the NHS.

Of course we could also lift restrictions for people 3 weeks after they've been vaccinated so it'll be like that episode of The Simpsons were all the old people are out in the streets all night playing  and causing mayhem

Edit: Also in UK covid noise a teenager filmed himself shouting at Chris Whitty (the Chief Medical Officer) that he's a liar and just abusing him on the street. It went viral with people being outraged. The teens mother said she saw the video and has now confiscated his Playstation Which seems proportionate because I was worried we were on the cusp of a cat-bin-lady witch-hunt

Edit: And good news from vaccines minister - 90% of the over 80s and almost 90% of the over 75s have been vaccinated and around 50% of the 70-75s. Which is great because obviously those are the highest risk groups but it also suggests that take-up is really high in these groups which is very positive.

Edit: And finally an update on care homes. 99% of care homes have been visited and 90% of care home residents vaccinated - which suggests a very high take up

[Agelastus]

Edit: And finally an update on care homes. 99% of care homes have been visited and 90% of care home residents vaccinated - which suggests a very high take up

Yep, my mother had her first shot a couple of weeks ago.

Although the fact that Corby has the second highest rate of cases in England is a tad worrying.

[Sheilbh]

Oh glad to hear your mum got her jab - I need to checkup on some relatives. No update on my dad but his age-group has mostly been done in the South-West so I'm curious

[Syt]

Austrian government is considering isolating Tyrol from the rest of Austria and neighboring countries.

After last year's mismanagement (Ischgl & Co. where tourism continued unabated despite warnings and first cases, and the virus was spread by tourists throughout Europe), the state government insisted, "We've done everything right!"

Now, despite the lockdown, there's numerous hotels in Tyrol that found workarounds for having tourists, e.g. those people renting rooms claiming to be looking for work, ski slopes are fully operating with questionable security concepts, and several clusters of the British and South African mutations cropping up, plus signs that a Tyrolean strain is emerging. Let's not even talk about vaccinations going to mayors and their families, owners of ski lifts, etc. rather than doctors or the elderly. Local authorities seem unwilling to go after any of these cases.

There's (unverified) reports that they're behind on testing (and reluctant to test) which makes their numbers look better than they are. There have been calls for two mass testing events over the next seven days, but locals say there's a lot of pressure to not attend those, to avoid talking to experts or outside investigators and journalists who are just engaging in Tyrol bashing.

Meanwhile, the state government insists that they're "doing everything right", that they're monitoring the situation, but that there's no reason to be as alarmed as the rest of the country is about what's happening in Tyrol.

Tyrol's main business is tourism. It permeates all society - many families rent out guest rooms for tourists, there's the big and small hotels and proprietors of the ski slopes and ski lifts, not few of which are also local politicians, mayors etc. There's many small communities where everyone knows everybody and who stick together against "outsiders." The rest of Austria is increasingly of the opinion that the only thing that matters to Tyroleans is MOAR TOURSIM, like when a few years ago one resort announced plans to remove two mountain peaks to make room for MOAR SLOPES and MOAR HOTELS.

Remains to be seen what happens. The state is run by Chancellor Kurz's party, and while there's anonymous reports that behind closed doors he's extremely pissed at what's happening there, he's been reluctant to call them out in public for fear of alienating voters, and leaves it to his Greens coalition partner who have the health ministry.

A decision about the isolation is expected for Sunday. I expect that it will be avoided by Tyrol promising to be a good boy now (and then to keep doing what they've been doing).

[Admiral Yi]

https://www.youtube.com/watch?v=c31MZU8TuDY

Canadian anti-masker.