Coronavirus Sars-CoV-2/Covid-19 Megathread

[mongers]

There might be an issue with new South African variant possible not being being defeated by the vaccines; Prof Sir Bell, lead of the Oxford-AstraK programme said it's spike had two significant mutations as compared to the Kent variant that only has one and so it is assumed will still be affected by the vaccines.

[mongers]

Apparently excess mortality analysis by Russia's own statistical agency indicates that three times as many people died of Covid as officially reported.  I guess that wasn't too shocking, their death numbers seemed to make no sense before.  That said, I wonder what story excess death analysis tells us in other countries.

Good news that the Russian statistical agency was able to come clean about this; I half expected Putin to keep the reality suppressed.

I guess it's going so badly outside of Moscow, that to deny it would be laughable and damage the Regime/leaders credibility and take him into Bolsanaro/Trump territory.

As it is, the deputy prime minster is confirming it :

Russia's deputy prime minister has revealed more than 80% of excess deaths this year are linked to Covid-19, which would mean its death toll is three times higher than previously reported.

Excess deaths are the difference between the total number of deaths registered and the average over the previous years for the same period.

Official figures say 55,827 people have died with Covid-19 in Russia.

The deputy prime minister said excess deaths would take that to 186,000.

Countries use different methods when reporting deaths related to the virus, which makes international comparisons difficult.

Russia has been criticised for calculating its official deaths from Covid-19 based on the number of post-mortem examinations that list coronavirus as the main cause of death.

However, this means that other deaths linked to Covid-19, which did not list it as the main cause of death, will not have been included.

The new numbers mean Russia's coronavirus death toll could be the world's third-highest, after the US with 335,000 deaths and Brazil, which has had 192,000, according to a tally by Johns Hopkins University.

Maybe he's being set up as the scapegoat?

[jimmy olsen]

More than 3700 dead on the 29th.
More than 3800 dead on the 30th.

The numbers are so bad.

[Sheilbh]

Still really grim here - the important chart is on the right:


And hospital occupancy is at or near the peak in most places and climbing:


And any impact of Christmas on the numbers is probably still a week away from showing up in the figures - but people who were infected at Christmas are probably now at their most infectious (so hopefully everyone - particularly in Scotland where it's more important than Christmas - stays in over NYE ).

Meanwhile Gavin Williamson's announcement yesterday on schools has me furious. He shouldn't be in office.

In good - or at least hopeful news - Israel now has over 25% of the over 60s vaccinated. Based on estimates by scientists there they expect to see a lower percentage of the 60+ in the critically ill category and it should fall from 70% of the critically ill now to around 20% by the second half of January. Obviously given the risk profile of this disease that's going to be huge if the estimates are correct.

We're nowhere near those levels and there's not enough clear communication on the vaccines yet in terms of how many doses we have, what's been distributed and what's been administered (though I suspect this will improve like the other covid stats) - but I think it does show the way out. Having said that apparently we'll only be delivering the first AstraZeneca vacine on 4 January - I do not know why, given that we've pre-ordered these vaccines, and we know they're all going through the approval process it takes that long. I get there's holidays and stuff but we could use the military for logistics if necessary - I think given everything a week between approval and actually getting it to hospitals and GPs to deliver is ridiculous.

[Sheilbh]

Looks like UK is going to be releasing weekly vaccination data
https://coronavirus.data.gov.uk/details/healthcare

Up to about 950k - which is a start, but we need to go a lot faster. Based on previous releases that will probably be about 600k over 80s and 300k frontline healthcare/care home workers.

Christmas seems to have got in the way (weirdly it didn't for testing). In the week ending 20 December there were about 600k doses administer, it was about half that in the week ending 27 December. Hopefully we can get back to 600k and a lot higher soon.

Edit: Also it looks kind of dystopian but is probably necessary - public spaces in London and other cities are being boarded up/fenced off with a lot of police roaming round to prevent any NYE gatherings - I can't wait to get out of this

Edit:

Smells fishy they're doing this rather than letting retired people doctors in. Somebody is profiting.

So apparently the issue is that - I hope in bureaucratic oversight - the NHS is requiring full up-to-date certificates/training records.

In addition to your general application and the covid specific training certificate you need to upload the following certificates:
Passport or work visa
DBS
Higher education certificate
Conflict resolution training (level 1)
Data security awareness training (level 1)
Equality, diversity and human rights training (level 1)
Fire safety training (level 1)
Health and safety training (level 1)
Introduction to anaphylaxis
Legal aspects of vaccination
Moving and handling training (level 1)
Preventing radicalisation training (level 1)
Recognising and managing anaphylaxis
Resuscitatoin (level 2)
Safeguarding adults (level 2)
Safeguarding children (level 2)

I feel like in the interests of time we could probably streamline the amount of training certificates people need to send through or training they need to attend before they're giving the vaccine. And I imagine mainly working with the over 80s present some pretty unique challenges for both the diversity and preventing radicalisation training

[Sheilbh]

End of an email sent round Royal London Hospital today:


It also mentions that Kent is as bad if not worse. Hospitals in Liverpool and Plymouth are taking patients from Kent and London. It feels like the NHS will be overwhelmed here soon.

[Tamas]

 

I don't understand why we are not in spring-style lockdown yet.

e.g. it's a tiny thing but during the Spring, MOT tests (annual car checks for you dirty foreigners who we are now free to keep off the island) could be postponed. Now you can't, so come next Friday I'll be going to this cosy little garage to have it done because otherwise I won't be able to legally use my car. Feels stupid that while my county has declared an emergency, I am legally forced to do indoor interactions.

[Iormlund]

Same thing here. I waited until I had a few days off to get the car to the garage. Disinfected it afterwards and was more careful than usual for ten or so days (not taking the FFP2 mask off during commute, disinfecting my hands after I left it, etc).

[Josquius]

Hope the peak passes soon. Baby due start of March...

[Sheilbh]

I don't understand why we are not in spring-style lockdown yet.

e.g. it's a tiny thing but during the Spring, MOT tests (annual car checks for you dirty foreigners who we are now free to keep off the island) could be postponed. Now you can't, so come next Friday I'll be going to this cosy little garage to have it done because otherwise I won't be able to legally use my car. Feels stupid that while my county has declared an emergency, I am legally forced to do indoor interactions.

I suppose one other difference from spring is we're all wearing masks indoors

I think the bigger thing is, and I really wish it wasn't like this, we probably can't re-open schools with this new variant on the loose. From what I understand, there's no evidence that kids are more suscepitble or that it is more dangerous for kids but the increase in transmission also affects them and schools are going to cause a lot of spread. The other lockdown stuff will help but I think schools and education are the biggest difference between the spring lockdown and the autumn lockdown.

Obviously the focus needs to be on vaccinating people because from my understanding during spring lockdown the R number went down to 0.6. If the new variant is somewhere between 50-70% more transmissible then even a spring style lockdown might not be enough.

Edit: Incidentally on the bureaucratic headaches with the vaccination program - it feels like there's a fair few changes we could make here pretty easily (without really increasing risk) and this is where we need some sort of national mobilisation/national effort to get people inoculated (especially because I think 30 million by summer is too low a target):

Ministers urged to strip away red tape to hit UK vaccine rollout target
Doctors say 24/7 vaccine centres and recruiting retired health workers could help reach goal
Linda Geddes Science correspondent
Fri 1 Jan 2021 18.13 GMT
Last modified on Fri 1 Jan 2021 23.33 GMT

Red tape should be stripped away to allow retired health workers help the coronavirus vaccine effort and vaccination centres should open around the clock to meet the target of immunising 30 million people by the summer, ministers have been told.

So far, GPs and hospital staff have injected nearly 950,000 people with a first dose of the Pfizer/BioNTech vaccine, and the approval of the Oxford/AstraZeneca vaccine should mean tens of millions more doses will become available in the coming weeks and months.

"This is now a race against time and there isn't a moment to lose," said Jonathan Ashworth, the shadow health secretary. "We need ministers to move heaven and earth to roll out vaccination starting with 2m jabs a week to save lives and hit the government's spring promise of easing restrictions."

GPs have called for greater clarity on the role they're expected to play in delivering these vaccines, stressing that they will be unable to hit the summer target without additional resources.

Despite talk of mass vaccination centres operating at football stadiums and race courses, GPs had been provided with very little information about how these would operate and who would run them, said Prof Martin Marshall, the chair of the Royal College of GPs. "It would be useful to know what the plans are, and it would certainly be useful to know what general practice is expected to deliver," he said.

"If we're going to get 30 million people vaccinated twice in six months, which I think is probably realistic, this can't just be done by general practice. The workforce isn't big enough to allow for that and to deliver business as usual for people who are acutely ill, those with long-term conditions, childhood vaccinations, as well as cervical cancer screening and all that kind of stuff as well."

He called for an urgent conversation about the role that retired medical personnel might play. "We've got tens of thousands of recently retired GPs, physicians, surgeons, nurses who are desperate to come back, even as unpaid volunteers, and they are being desperately put off by the bureaucratic process which is preventing them from doing so," Marshall said.

"Some of these bureaucratic demands are ridiculous, such as the requirement to be certified in fire safety, or preventing radicalisation. There are people who have experience of giving a jab and dealing with anaphylaxis if someone had an allergic reaction, so you don't need to see their O-level certificates or many of the other bits of paperwork they are being asked for."

Others urged the government to draw on expertise from the military and manufacturing supply chains. "Medics do what they are trained to do, but they are not trained to be logisticians," said Dr Bharat Pankhania, an expert in communicable disease at the University of Exeter who was also involved in the response to the 2009 swine flu pandemic. "We need to harness this knowledge and skill that comes from other sectors but which we could easily deploy [to rapidly deliver vaccines]."

A spokesperson for the Ministry of Defence said the military had not yet been approached about assisting in the delivery of Covid vaccines, although about 130 medically qualified military personnel had been placed on standby. "The armed forces have personnel including specialist planners, logisticians and medics, ready to support responses to the outbreak if required," they said.

Another strategy that should be considered was 24/7 vaccine delivery, Pankhania said. "I appreciate that elderly or infirm people can't be immunised at 3am, but there are many fit and healthy people who would willingly go to a place which is well-lit, well-directed, well-run at 3am, because it is better to get the vaccine than not to," he said.

"When you make it a 24/7 operation, you are also giving a clear signal that the government means business, that this is a strategy to get the country back on its feet as fast as possible, but that people must observe infection control practice in the meantime."

My instinct is do all of it Get the military to help on logistics/supply chains - I'd also speak to, for example, Boots - pharmacists do the flu vaccine so they have the infrastructure on the supply chain side and probably could be trained too. Get rid of the requirements for their O-Level statistics or the preventing radicalisation training for retired medical personnel and just get them in (and vaccinated) to help deliver it. We are being too slow and too business as usual - and it's particularly annoying because we've known vaccines were coming for at least the last couple of months and should have been preparing plans for this

[mongers]

Hope the peak passes soon. Baby due start of March...

:gasp:

Congratulations Tyr and Partner. 

[Sheilbh]

Latest data on this new strain in England - it's almost totally out-competed the normal strains in the South-East and totally replaced them there and looks like it's on course to do the same very shortly in the rest of England:


Probably a useful lesson for countries with identified cases - they need to move quickly and strongly if they identify any cases of this strain. It's spread incredibly quickly and widely. Saw an estimate by an American epidemiologist that this strain is probably less than 1% of US cases right now but could become the dominant strain by March

[Iormlund]

Probably a useful lesson for countries with identified cases - they need to move quickly and strongly if they identify any cases of this strain.

It's far too late. The track and trace system was overwhelmed back in July here. If this strain is so competitive there's not much we can do short of another total lockdown. Which probably won't happen unless the ICU units are overflowing with patients as in the first wave.

[Sheilbh]

It's far too late. The track and trace system was overwhelmed back in July here. If this strain is so competitive there's not much we can do short of another total lockdown. Which probably won't happen unless the ICU units are overflowing with patients as in the first wave.

Yeah - I think if countries are finding cases then it's there and given that it seems to be so much more competitive it will probbably become the dominant strain there at some point. There was an update today from Denmark which is the only European country that does more sequencing of tests per capita than the UK - so is in a really good position to monitor this. They've sequenced 11% of their tests since Novermber - overall in that period this strain is about 0.8% of those tests, but if you look at the last week then it's about 2.5% of tests. And there is big regional variations (like the UK) so it's about 7% of samples in one region but still below 1% in others.

The other thing I wonder about is how well other countries will be able to track because we've been very lucky in that one bits of covid the PCR tests here look for is one of the bits affected by this new strain. So, purely by chance, our normal covid PCR test can give an indication of whether it's this strain or not (supported by the slower sequencing). My understanding is that different countries use different PCR tests and they look for different bits of covid so they may not be able to spot it without sequencing. It feels like it might be worth adjusting those tests globally because now we know about it it would be a sort-of canary in the mine.

It's - again - incredible how quickly the scientists are learning about this, but it isn't yet clear how much more transmissible it is. But it is definitely more transmissible and maybe so much that even  a spring style lockdown won't stop its spread it'll just slow it down. I think that's why the focus has to shift to really getting people vaccinated.

I worry this has been slightly lost amid the Plague Island jokes and our government's, let's say, competence issues. I think it's a really worrying development for the course of this disease - and while it's good news that there's no sign it's more severe, in terms of hospitalisation and death a more transmissible but equally serious illness will have a bigger impact than a more lethal but equally transmissible disease.

Adam Kucharski did a great thread explaining this but gave the example of a virus with R of 1.1 and IFR of 0.8% with 10,000 infections. Given that you'd expect 129 deaths a month. If you increase the fatality rate by 50% you'd expect 193 deaths per month. If you increase the transmission rate by 50% then you'd expect 978 deaths per month.

[Tamas]

All i know is the level of activity I see around me is way higher than during the spring lockdown so I think we could easily squeeze out some further improvement of the situation if he had the willingness to do so.