Daily numbers, graphs, analysis thread 19

[BigChocFrenzy]

Daily numbers, graphs, analysis thread 19

Welcome to thread 19 of the daily updates

Resource links:

Welcome to thread 18 of the daily updates

Resource links:

Uk dashboard deaths, cases, hospitals, tests - 4 nations, English regions & LAs
Imperial UK weekly LAs, cases / 100k, table, map, hotspots
Modelling real number of infections February to date
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
R estimates UK & English regions
PHE Surveillance report infections & watchlists each Thursday
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 test positivity etc, DIY graphs
FT DIY graphs compare deaths, cases, raw / million pop
Covidly.com world summary & graphs
Alama Personal COVID risk assessment

⏭ Our STUDIES Corner ⏮

We welcome factual, data driven, and civil discussions from all contributors 📈 📉 📊 👍

@cathyandclare

Herd immunity isn't all or nothing. I don't think anyone is suggesting let the virus rip and hope for the best. Rather that greater levels of protection within a population will reduce transmission, and drop the R.

As suggested in this BMJ paper:
Protective levels of immunity, not measurable through serology alone but instead the result of a combination of pre-existing and newly formed immune responses, could now exist in the population, preventing an epidemic rise in new infections.

... The key word is "could" Also, reduction from the peak when R was 2.5 - 3.0 could still leave an R>1

Hence presumably SAGE's "reasonable worst case" of a worse 2nd peak,
for which any responsible govt would have to make contingency plans

My personal opinion fwiw is that the 2nd wave / ripple in the UK will be much lower than the 1st wave ...

mostly because of the extra knowledge gained bringing more effective & targeted SD meaasures
and because the time gained has been used to build up mass testing, track & trace systems

• not as good as we hoped, but miles better than what was there in March The higher immunity levels would help too, but we don't know how much

There are many possible future scenarios, as it all depends on so many variables & factors

[quote Sunshinegirl82]@MarshaBradyo

I would have thought that, if a vaccine is available fairly quickly then NYC might have a decent chance of being ok. If natural immunity wanes before the vaccine can replace it then I imagine they might start to have issues again. I'd be hopeful though![/quote]
...
Trump has revised back the date for vaccine rollout to April,
not expected to be anything for this winter

imo, nowhere near enough justification - atm - for that 2-week October lockdown being floated

@BigChocFrenzy

I'd still hope that would be soon enough for the vast majority who were infected to still have some residual immunity. Obviously we don't know for definite but a year of immunity doesn't seem completely outside the realms of possibility.

[quote Sunshinegirl82]@BigChocFrenzy

I'd still hope that would be soon enough for the vast majority who were infected to still have some residual immunity. Obviously we don't know for definite but a year of immunity doesn't seem completely outside the realms of possibility.[/quote]
....
Yes those who actually had COVID should have full or partial immunity, even if not to all strains.
This will reduce R to some extent
The question is whether it can reduce it to < 1 which depends on what R would be atm without this

Currently R ~ 1.6 for the UK,
but will this reduce soon because of the combination of SD and some % immunity ?
Or further increase

Looking at France & Spain, which serology studies indicate have similar % with antibopdies to the UK,
we can see there is a 2nd wave of deaths starting.
The hope is that this will not rise much above yesterday's ~150 deaths for France

Controversial idea:
I wonder even if the current short 2nd wave now could also reduce the winter infections & deaths,
providing it doesn't spin out of control
An additional few % with very recent antibodies would further reduce the % that can be infected

It's still a matter of flattening the curve

not just so that the NHS can cope,
but all the testing, track & trace systems too
which stop the infections curve rising too rapidly

I'm also hoping that the various other cold type viruses that are now doing the rounds (which was entirely to be expected when you take large groups of DC who haven't really socialised for months and put them back together) will stabilise at a lower level than we seem to have at the moment.

These viruses will be in part driving the demand for testing due to causing coughs and temps. If that stabilises and the new lab gets up and running in the next two weeks I'm hopeful we can get back on top of testing before Winter really kicks in.

Obviously two weeks is a long time and cases can rise substantially in that time but if we can keep things at a manageable level I can see that it's possible for things not to spiral too much further.

Good, researched, article on why airborne transmission is the thing to try and limit:

elemental.medium.com/the-most-likely-way-youll-get-infected-with-covid-19-30430384e5a5

Off to email my MP about mask wearing in schools.

We now have guidance issued by school. Covid symptoms=get a test. No guidance on what to do if you can't get a test coughs and colds can go in if there's been a negative test. That's fine if you can get a test!

@Bercows

We now have guidance issued by school. Covid symptoms=get a test. No guidance on what to do if you can't get a test coughs and colds can go in if there's been a negative test. That's fine if you can get a test!

At least it says Covid symptoms. My friends granddaughter has a cold, no Covid symptoms and her school won't let her back without a negative test

Ridiculous

It will be interesting to see how France get on now they've reduced the isolation period to 7 days, I wonder if they'll see improved compliance.

If successful a 7 day isolation period in schools would certainly help in situations where testing is limited.

I appreciate it only works for those with symptoms, not those who come into contact with a positive case.

I agree France's 7-day rule will be interesting to watch. I would expect compliance to go up sharply for 1 week rather than 2, but it may just not be long enough.

We don't actually know what R would be with no mitigations, which is surprising; this article suggests it could be 4.7-6.6 not 2.2-2.7, and it's only lockdown suppression that kept it lower. The article isn't peer reviewed, so treat with caution but: www.medrxiv.org/content/10.1101/2020.02.07.20021154v1.

Interestingly, epiforecasts seems to think R is still low in most places: epiforecasts.io/covid/posts/global/

[quote Sunshinegirl82]@Jenasaurus

I'm in Hampshire between London and Southampton. I think CM runs 6 days behind in order to have complete data so I'm sure those cases will appear.

We have had the odd day of 3 or 4 infections which skews things for a bit but then have dropped back to 1/2. Everyone I know (including my family) was poorly in February/March. Whether they had Covid or something else we will probably never know but given that we 100% know it was spreading in the community locally back then it seems possible.[/quote]
I'm hangs between S ton and Portsmouth. We have the same sort of pattern.

Hants was hit quite hard at beginning and certainly is thought to have some of the easiest cases. Also hit very hard late feb/March with illness a lot of us now suspect to be COVID since newer symptoms released. Mainly loss of taste and smell and the feeling of an elephant sat on your chest!

Things are going up and down but I'm taking it as a hopeful good sign T and T is keeping on top of it rather than the possibility it's lack of testing combined with not having recording correctly. Cases are maybe higher due to this but it's the fluctuations that lead me to think it's not constantly on the rise (yet!)

A 2nd wave as bad as the first would be among the pessimistic scenarios

The fact that so many seem to think "fuck it, I'm not doing lockdown again" (Cummings Effect) I think the 2nd wave will be at least as bad as the first.
The Govt have no idea what to do - they have very poor leadership. There aren't enough Police or Army to enforce local, let alone national lockdowns. Another national lockdown is unaffordable, as the country is already well into it's overdraft anyway. Brexit is still affecting everything (from 1st Jan). There have been so many years of austerity that the Local Authorities are not in a position to leap into action and deal with any of this without a massive injection of funds.
We're screwed.

From a Twitter thread by an intensive care doctor:

"Second wave or slow burn? We talk about a second wave but the most likely experience will be a steady flow of patients with COVID-19 over the winter months. We think (hope) we will avoid the very high peaks of demand which put services most at risk."

mobile.twitter.com/rupert_pearse/status/1307242471789912065

(Worth reading the whole thread though for context).

[quote MRex]I agree France's 7-day rule will be interesting to watch. I would expect compliance to go up sharply for 1 week rather than 2, but it may just not be long enough.

We don't actually know what R would be with no mitigations, which is surprising; this article suggests it could be 4.7-6.6 not 2.2-2.7, and it's only lockdown suppression that kept it lower. The article isn't peer reviewed, so treat with caution but: www.medrxiv.org/content/10.1101/2020.02.07.20021154v1.

Interestingly, epiforecasts seems to think R is still low in most places: epiforecasts.io/covid/posts/global/[/quote]
...
A paper was published by most of the same authors on the CDC J. Emerging Infectious Diseases a while ago,

suggesting R0 = 5.7 (95% CI 3.8–8.9)

High Contagiousness and Rapid Spread of Severe Acute Respiratory Syndrome Coronavirus 2

wwwnc.cdc.gov/eid/article/26/7/20-0282_article

I read the whole thread @CoffeeandCroissant and it does sound encouraging, however it seems somewhat at odds with the NHSers thread which has been going for a few days on here.

I think the NHS era thread reflects plans or a reasonable 'Worst Case' scenario which is sensible planning, but it hopefully won't be as bad as that ( which is what the twitter thread is saying).

Some more info on the Bolton's spike:

www.bbc.co.uk/news/uk-england-manchester-54205353

Testing of arrivals (e.g. on day 1 and day 8) might not be as effective as the 100% quarantine but it is definitely better than loose quarantine not followed by a significant number of people.

Interesting that they've identified a Bolton superspreader. Actually I think that's the kind of publicity that might encourage compliance.
I know anecdotally of groups of young people who were away on holiday together and out in the pub the first night home instead of quarantining.

Scottish numbers looking grim. 350 cases, 3 deaths, 5.3% of newly tested people positive now.

A chart showing rising/ falling/ static areas across the UK:

twitter.com/RP131/status/1307283312805896193

@MRex, interestingly on the London boroughs, most of the ones that you mention (Harrow, Hackney, Tower Hamlets, Lambeth) have seen a fall in cases over the last week:
coviddatashare.s3-eu-west-1.amazonaws.com/Week_20200918.png

They have definitely seen more cases this time around again than the more affluent outer boroughs (different occupations and different housing situations leading to greater exposure, different ethnic mix and different health situations maybe explaining some of the differences both times around?)

I suppose I find it somewhat reassuring that cases don't appear to be growing consistently ie if it were out of control anywhere near the way it was in March there would be no fall, however small, week on week. Admittedly difficulties accessing tests may mean these numbers aren't that accurate.

I think lack of testing and focusing of testing on hotspots makes it impossible to draw anything from declines unfortunately. We have a decline, we are middling area, it worries me if anything as how can they whack the moles?!

I know that Dido Harding seemed to agree that London’s testing availability had been cut by 20% the last two weeks ( well she agreed it had been cut and didn’t really dispute the 20%) - I wonder if that has any impact on its numbers ( although even with that cut I think that just brought it into line re access to tests as the rest of the country with similar levels) ?

London's hospital admissions have been flat over past 4 days. It is too early to say whether it is a meaningful trend but I would say other areas need more testing capacity than London does.

FWIW, all the London based "worried well" I know in real life are still managing to get tests. Someone has just tested his whole family (5 people!) for no good reason. I really wanted to tell him what I think about it but didn't have the courage.