Daily numbers, graphs, analysis thread 22

[BigChocFrenzy]

Welcome to thread 22 of the daily updates

Resource links:

Uk dashboard deaths, cases, hospitals, tests - 4 nations, English regions & LAs
R estimates UK & English regions
Imperial UK weekly LAs, cases / 100k, table, map, hotspots
School statistics Attendance
Modelling real number of UK infections February to date
NHS England Hospital activity
NHs England Daily deaths
MSAO Map of English cases
Cases Tracker England Local Government
ONS MSAO Map English deaths
CovidMessenger live update by council district in England
Scot gov Daily data
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t
PH Wales LAs, tests, ONS deaths
NI Dashboard
Zoe Uk data
UK govt pressers Slides & data
ICNRC Intensive Care National Audit & Research reports
NHS t&t England & UK testing Weekly stats
PHE Surveillance reports & LA Local Watchlist Maps by LSOA
ONS England infection surveillance report each Friday
Datasets for ONS surveillance reports
ONS Roundup deaths, infections & economic reports
ECDC rolling 14-day incidence EEA & UK
Worldometer UK page
Our World in Data GB test positivity etc, DIY country graphs
FT DIY graphs compare deaths, cases, raw / million pop
Alama Personal COVID risk assessment
Local Mobility Reports for countries
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery

⏭ Our STUDIES Corner ⏮

We welcome factual, data driven and analytical contributions
Please try to keep discussion focused on these
📈 📉 📊 👍

@TheSunIsStillShining - no sorry, I like to look things up in general but I don't think it is psychologically helpful for you to be looking up more on personal risk factors than you already have. You could drive yourself crazy looking at these things. You can't influence every risk factor, but people are not evenly affected and you simply can't know for certain a real life outcome; some overweight older diabetics have been fine and other younger people with no comorbidities have not been. There can be luck involved: do you catch low viral load / a milder strain / have had the right other coronacirus (cold) recently. There are things you can influence: daily vitamins including liquid vitamin D3, keep well rested, wear a mask, wash your hands, avoid crowded indoor places, keep on top of any medication or diet, contact a GP if you're concerned about your heart / lung function in general. If you get unwell - use an oximeter to check your oxygen, and call 999 if you need help. One of the most effective tricks to staying healthy is actually a positive attitude; keep calm and smiling until there is a reason not to. Instead of research - watch a few comedies, or read "Habits of a Happy Brain".

@Mrex Thanks, it's actually not me driving myself up a wall. I know my risks, I know what mitigations I use and I know what I'm willing to put up with. I am perfectly fine going shopping in a mask for example...
We were talking about exit strategy as a family and came to some criterias. One of them was knowledge about longer term effects.
For example. my son can wear a mask in school all day, but if no one else does it'll diminish his effort. Or if they order him to take it off. Or if they don't let him come home for lunch and has to take it off there. If we know that even if he gets it he has no bigger chance of long term complication than say chickenpox, then that is an acceptable risk.
Things along these lines.
So we're not totally doomsday/apocalypse mentality, but more on a let's wait and see what the science says. Especially that we are a family of introverts, so it is not really a pain in the arse :)

[quote whatsnext2]@Regulus most virus become endemic at some point, for example Influenza A is what became of Spanish flu. Just a question of how long it takes and at what costs. Most mutations by Covid so far are neutral or deleterious to the virus.

www.sciencedirect.com/science/article/pii/S1567134820301829[/quote]
But that was from a time with less global travel, less population, we've been vaccinating for influenza A since the 1940's. I've yet to read aby scientific proof that herd immunity would be achieved, and certainly not in a time frame that would be acceptable.

TheSun There is insufficient data to calculate risk of Long Covid for someone

Spiegelhalter's table, attached, gives the risks of hospitalisation, ICU, death - at each age if you catch COVID

https://medium.com/wintoncentre/how-much-normal-risk-does-covid-represent-4539118e1196

So use Alama to calculate your "Covid age," for your sex with any health conditions, then look up this age in this table

For your son, if he has only a theoretical hereditary risk of something and currently has no signs of it, then just take his unamended age
Or has his doctor said he is at increased risk of Covid ?

If he is aged 0-9, he has only 0.1 % chance of hospitalisation, 0.005% of ICU and 0.002% chance of death
If 10-19, only 0.3% chance hospitalisation, 0.015% of ICU and 0.006% of death

In fact, since the table is from May, improved treatment and new meds have improved chances for those seriously ill by 20-30%

Then take mrex's excellent pragmatic advice and get on with life

Todays numbers for Liverpool.

postitivity rate still going up...

Coronavirus cases by area
Report published 8th October 2020
Cases data from week 29th September - 5th October 2020

Data extracted covering testing up to 5th October 2020 show that the total number of confirmed cases for the last 7 days is 2881, an increase of 949 cases on the previous week. The latest weekly rate of Covid-19 in Liverpool is 578.5 per 100,000 population and the latest positivity testing rate* is 24.8%.

There has been a rapid and worrying increase in cases in Liverpool since the 1 September, when there were 94 cases per week, to the current level of 2881 cases per week.

I just posted this on the NE thread but thought it might also be of interest on the data thread.

The latest positive cases have been published from the two Universities in Newcastle.

619 positive cases among students for Northumbria Uni (not sure of exact number previous week but reported in media as 770)
1003 positive cases for students at Newcastle University (up from 94 previous 7 days)

Not surprising, but quite shocking.

I'm assuming other universtities may also publicly publish positive test numbers too but I don't think this is centralized anywhere as far as I know.

@TheSunIsStillShining - The only reasonable study on long covid with a paper seems to be based on hospitalised cases in Italy. The type of issues faced by those who've been on ventilators / CPAP will include physical and PTSD issues, as well as time needed for recovery for organs that have been damaged, physio, occupational therapy etc. It doesn't cover those who may have "recovered" at home, but have a long tail of viral symptoms, post-viral fatigue and other ME-type symptoms. Quite frankly it can't, there isn't tracking of a large enough cohort, nor enough time passed to confirm if this has caused short or long-term issues. I think some people may also be unrealistic, they have a severe case and then aren't 100% better in 3 months - but why would they expect to be in such a short time? It's actually normal for the body to need a surprisingly lengthy recovery time after getting hammered by a virus.

The recent REACT survey by Imperial found ~ 6% of the population with antibodies,
with highest being ~13 % in London and lowest 3% in the SW

www.imperial.ac.uk/news/201893/largest-study-home-coronavirus-antibody-testing/

This is down ~5% from the highest % measured, so imo it seems likely that ~11% in the UK could have immunity for about a year

We have posted recent research on T Cells & immunity, with the authors warning that T cells would not stop people catching Covid and infecting others;
T cells would probably reduce the severity of symptoms in those who have them

Some densely populated parts of the world have 40-70% antibodies
So there are still many more people in the Uk and the rest of Europe who could become infected
We can see infections rising again in Sweden, who average ~8% antibodies, higher in Stockholm

Herd immunity by vaccination protects the very small minority, ~3% iirc, who medically cannot be vaccinated

All vaccinations to date have varying degrees of effectiveness, but once a comprehensive vaccination program has been completed

• and it will probably have to annual at least for a few years -

I would expect that life would "get back to normal," because vaccination is all that can reasonably be done to protect the vulnerable

Fauci and others say the first vaccination may only be 50% effective, but this should still be enough to keep down Covid to a very low level, without continuing SD

positivity testing rate is 24.8%.*

Is this the percentage the WHO says should be below 3%?

TheSun We had upthread a table showing that for children and until at least age 20, flu causes a higher risk of death than Covid

Covid only really starts to pull ahead after age 30 and becomes several times more dangerous in middle age and beyond

@Regulus

positivity testing rate is 24.8%.*

Is this the percentage the WHO says should be below 3%?

.... um yes !

< 3% and if it reaches 5% then take more measures

Regulus - yes, the WHO consider anything above 5% to be a problem. Liverpool at 24.8% is a long way above a level where we have a problem.

This is down ~5% from the highest % measured, so imo it seems likely that ~11% in the UK could have immunity for about a year

I don't think we have any such evidence from that survey on what it says for longer term immunity, the assay they're using is only 72% effective when there's lots of antibodies from a recent infection, we've got no evidence at all on how effective it is on lower levels of antibodies.

If the 5% of Londoners who had antibodies three months ago but now don't were actually susceptible today, I cannot see how we would not have many more cases of repeat infection than we do.

I added on the missing 5% to reach that 11%
In London it would then be 18%

So I already assumed those no longer with detectable antibodies have immunity

Measures and actions matter
e.g. Spain and Italy had similar % antibodies in serology studies, ~5%, but very different results in this 2nd wave

e.g. Iran should have high levels after their high cases and deaths, with a very young population who should be mostly with very mild symptoms or asymptomatic
However, they are in their 3rd wave, with hundreds of daily deathsm because they are not managing the epidemic well

@MRex "Can we discuss the evidence on them so far please, might they be a game changer?"

I don't think there is much evidence beyond what is reported in your links. I don't think there has even been a pre-print yet, just press releases. The Regeneron cocktail has I think been given to less than 300 patients so far.

Perhaps the best we can say is they have potential and look promising, but until we have further data from the trials it's really too early to say more than that?

I think there might be a logistical issue in manufacturing doses in bulk, at least in the short term and there were some concerns about infusion reactions from the single antibody dose, as mentioned in the Statnews article.

The article also says Visits to the hospital or ER were made by 5.8% of patients in the placebo group, but just 0.9% of those who received the antibody combination. That difference, however, was just barely statistically significant.

Lilly don't yet have EUA from the FDA and talk about mid 2021 for full FDA approval, so early days.

Quite a few details on both in this article, including this bit about using hamster 🐹 ovary cells:

The monoclonal antibodies from the two companies are clones of potent SARS-CoV-2 antibodies that can “neutralize” the virus in test tube studies. Researchers plucked the genes for these antibodies from humans who recovered from COVID-19 or from mice artificially infected with the virus. The companies then put the genes in Chinese hamster ovary cells to bulk manufacture the antibodies, which were given to the COVID-19 patients as infusions.
www.sciencemag.org/news/2020/09/provocative-results-boost-hopes-antibody-treatment-covid-19

Danny Altmann, professor of immunology at Imperial college in London, guesses that those who recover from Covid-19 will have perhaps 90% protection for a “fair while”. But how long is that? “I would bet my house on you being safe for possibly a year but not much longer,” he said. “The problem is that whenever an immunologist says anything about Covid immunity to a journalist, it’s right for about two weeks and then it’s completely wrong.”
www.theguardian.com/world/2020/oct/06/flurry-of-coronavirus-reinfections-leaves-scientists-puzzled

Thanks @CoffeeandCroissant, fascinating stuff. Don't tell Haffertee! Poor hamsters. I was imagining something a bit more synthetic rather than hamster ovaries. I wonder how much antibody one hamster's ovaries can create, it doesn't sound hugely scalable.

There's a study from researchers in the COVID-19 'hot spot' in the Tyrolean region of Austria. They looked at patients who were hospitalised at the University Clinic of Internal Medicine in Innsbruck, the St Vinzenz Hospital in Zams or the cardio-pulmonary rehabilitation centre in Münster, Austria. They evaluated them at 6 and 12 weeks after their discharge from hospital, and plan to do so again at 24 weeks.

The study shows that although they had considerable heart and lung impairment 6 weeks after discharge, by 12 weeks there was improvement.

There's a similar study on that paper from Grenoble. Both are advocating rehabilition sooner rather than later after coming off a ventilator.

This is a photo from the zoom call with MPs today about the restrictions from next week (it’s on BBC, looks like someone took a photo of the slideshow).

They should publish this data and let us understand it properly in my opinion. But interesting observation (aside from the hospitality stuff) - supermarket shopping appears to be riskier than hospital visiting or working now, which is good news for the hospitals having got in hospital transmission more under control

I read in the Guardian that Belgium has a positivity rate of one in seven (14%) for the entire country but it was just a quote in passing on their liveblog so I don’t know where to check it. Worrying if true.

Belgium isn’t a big country and is relatively densely populated but it’s not tiny - eleven and a half million is a serious population, and it’s less densely populated than England.

I thought Belgium was the most densely populated country in Europe?

But interesting observation (aside from the hospitality stuff) - supermarket shopping appears to be riskier than hospital visiting or working now, which is good news for the hospitals having got in hospital transmission more under control

This is not what that slide says - it's not about risk (4% of the incidents were in a hospital, but it doesn't provide the relative numbers of people attending a hospital vs a pub, supermarket etc.) It's also (presumably) the ARI data we've had on previous weeks, although the complete disappearance of educational settings suggest it's limited further? Households have certainly not dropped to being one of the least relevant.

Looks like 50% missing for the Educational, Prison and care home (living in) outbreaks, which is a bit lower than recent previous weeks - it's in e.g. assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/923668/Weekly_COVID19_Surveillance_Report_week_40.pdf

The main thing is the ARI data is only based on the identified large spreading events, which is not the majority of transmission, and the low number of ARI events shows the poor backwards tracing done on cases.

17, 540 cases today