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 📈 📉 📊 👍

There was one research paper that reported that there was twice as much innate immunity ( T cells etc) in the population as antibodies. If 20% have Ab, then 40% could have T-cell immunity, which would really ramp up the level of resistance in the herd.

Obviously this would depend on the specific population. In the Mumbai slums more than 50% had antibodies.

www.sciencefocus.com/news/covid-19-public-immunity-significantly-higher-than-tests-suggest/

Interesting piece in The Spectator re testing regime and false positives here

It looks like countries / regions that were hit hard before are often being hit hard again - e.g. Iran, some European cities -
because the same factors remain,
unless specific SD & hygeine measures were taken to reduce a repeat, e.g. Italy

It doesn't indicate at all that "lockdown doesn't work",
because places that were hit hard had a lockdown ^because of high cases and / or deaths, but too late

As discussed before, "herd immunity" without a vaccine generally leads to an "overshoot of 20-25%" compared to the number required for herd immunity with a vaccine

Hence why some serology studies have found very high levels of antibodies (70%) in some hard hit areas of high population density
It doesn't follow that herd immunity needs to be > 70% for a vaccination program

However, there will be a minority of the population that are immune

• at least to the particular strain they caught before - which would tend to reduce numbers of deaths the 2nd and then 3rd time round

[quote cathyandclare]There was one research paper that reported that there was twice as much innate immunity ( T cells etc) in the population as antibodies. If 20% have Ab, then 40% could have T-cell immunity, which would really ramp up the level of resistance in the herd.

Obviously this would depend on the specific population. In the Mumbai slums more than 50% had antibodies.

www.sciencefocus.com/news/covid-19-public-immunity-significantly-higher-than-tests-suggest/[/quote]
....
We've discussed before that this is still theory that has to be quantified and proven
and
T cells reduce the severity of symptoms, but people can still be infectious
e.g.

"Immunity" and T cells
here is a scientist specialising in vaccines & the immune system:

https://threadreaderapp.com/thread/1293344524731691008.html

Shane Crotty@profshanecrotty

1/ There are various tweets misinterpreting COVID-19 “pre-existing immunity” and making dangerous claims about herd immunity.

Since many of those claims refer to our scientific papers,
we will reiterate the facts.

2/ Our 1st scientific paper showed that ~50% of unexposed people have T cells that recognized SARS-CoV-2 already doi.org/10.1016/j.cell….

The most obvious conclusion was these were memory T cells from previous common cold coronavirus infections,
but that was not directly shown.

3/ Our 2nd paper, very recently published,
showed that these were memory T cells from previous common cold coronavirus infections
https://science.sciencemag.org/content/early/2020/08/04/science.abd3871

Five other labs have also published related findings
doi.org/10.1038/s41577…

4/ These observations about pre-existing T cell immunity (also call "crossreactive immune memory",
which avoids the word "immunity" that sometimes gets misinterpreted as “protective immunity”
[sorry, immunology is complicated] )
are important because...

5/ ...these memory cells MAY impact people’s responses to SARS-CoV-2 infection,
or COVID-19 vaccines.

6/ Therefore, we have pointed out that these coronavirus crossreactive immune memory T cells are important,
to pay attention to in human COVID-19 studies this year.

7/ We SPECULATE that it is conceivable that these T cells may potentially reduce COVID-19 disease severity,
based on things we know about flu and T cells.

8/ These are only speculations (no data)
and because of their potential importance it is key for scientists to test these ideas, as quickly as possible.

While scientists are racing as fast as possible,
sophisticated research like this usually takes a lot of time and resources.

9/ We, and other labs, are working hard on these unanswered questions.

10/ Additionally, even if our most optimistic speculations about crossreactive T cell memory were found to be correct,
it would mean that just as many people would get infected with SARS-CoV-2, but fewer would become severely ill and die from COVID-19.

11/ T cells generally don’t completely prevent infections, they limit disease
(make it shorter and/or less serious).

Thus, wearing a mask is much more effective than hoping you and the people around you have pre-existing T cell memory.
Wearing a mask stops infections.

I think the report uses the healthcare workers as an example of clear "transmission vectors". If this group has got a higher percentage of pre-existing immunity, it should reduce rate of transmission within the broader population:

Some groups will more central to transmission than others, for example health care workers and those mixing more in the community.

I do not think we can count on true herd immunity - the real question is whether prior levels of infection can be a swing factor in slowing down the spread:

However, at present it could be the difference between the reproduction number being at or slightly above 1. The benefit of current levels of immunity will be maximised if policies are maintained that keep the transmission rates so R is around 1.

@wintertravel1980 Also, here are the minutes of another SAGE meeting spent on discussing pre-existing immunity.

You have missed something in that report too. It doesn't say they know nothing, this is what is says:
"15. Current levels of immunity in the population are unlikely to mitigate the impact of a significant winter resurgence."

I'd still like to know why anyone thinks that herd immunity would result in the current facts of infections increasing in boroughs in similar proportions to round 1, logically I can't make sense of that viewpoint.

It seems to me that if an area has a higher level of natural immunity that must have some impact on spread? Not enough to say that other mitigation factors aren't necessary but reducing the susceptible population by 20% seems likely to have some impact, even if only marginal.

SAGE seem to be saying in that report that they can't untangle "herd immunity" from other factors in terms of impact and so can't say that it will reduce spread rather than it isn't possible?

That's not so say we should be aiming for herd immunity by natural infection, more that it might be a factor in the apparent slower spread in certain areas. Obviously I suspect that if numbers get beyond a certain point the minor assistance it might provide will be overridden by sheer volume.

I'm in the SE, still very low cases in my LA. 6.5/100,000 over last 7 days according to CM. We regularly get days with zero positive tests, no schools affected locally that I'm aware of. We live quite near the man who was the first confirmed case of community spread (ie hadn't returned from China, Italy etc) so I suspect we had quite high levels in March although I still don't know of a single person who has tested positive for COVID.

@ fringon, publique sante explain the increase in deaths - 76 have been added retrospectively. The deaths are certainly increasing though. The rate of positivety has been stable for a week or so which gives me some glimmer of hope.
www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/coronavirus-chiffres-cles-et-evolution-de-la-covid-19-en-france-et-dans-le-monde

Fwiw i do think we have a problem of unrealistic expectations of who medicine can save and medical intervention often being used in situations where its not in the best interests of a patient.

But thats a wider debate and not really one to be having in the context of a pandemic where the debate can be used to further a pro-eugenics agenda.

[quote MRex]**@wintertravel1980* Also, here are the minutes of another SAGE meeting spent on discussing pre-existing immunity.*

You have missed something in that report too. It doesn't say they know nothing, this is what is says:
"15. Current levels of immunity in the population are unlikely to mitigate the impact of a significant winter resurgence."

I'd still like to know why anyone thinks that herd immunity would result in the current facts of infections increasing in boroughs in similar proportions to round 1, logically I can't make sense of that viewpoint.[/quote]
....
A 2nd wave as bad as the first would be among the pessimistic scenarios, where a lot would have to go wrong first,
although still less than SAGE's "reasonable worst case" of 80k deaths

The reason it remains at all possible is the "overshoot" we've discussed before,
e.g. using an analysis by Adam Kucharski (Mathematician/epidemiologist at LSHTM, WellcomeTrust)

the % of people infected, in the absence of a vaccine, can reach 20-25% higher than the % required for herd immunity with a vaccine

Sorry wrong thread. My phone keeps jumping to the wrong thread when i click.

I'd still like to know why anyone thinks that herd immunity would result in the current facts of infections increasing in boroughs in similar proportions to round 1, logically I can't make sense of that viewpoint.

I do not think we are in the "herd immunity" territory, i.e. the level of pre-existing immunity in London or elsewhere on its own will not be sufficient to keep under R under 1 without any other measures. This is relatively uncontroversial and this is why I did not highlight the paragraphs relating to this hypothesis.

However I believe the existing level of pre-existing immunity may be a meaningful factor to slow down the spread and can act as a swing factor if R is close to 1. SAGE minutes seem to suggest this particular suggestion is quite plausible.

The infections dropped on those boroughs though @BigChocFrenzy, now they've grown again. So overshoot doesn't apply.

Why "herd immunity" by just letting it rip costs far more lives
https://threadreaderapp.com/thread/1305436391707467776.html

Adam Kucharski @AdamJKucharski
(Mathematician/epidemiologist at LSHTM, WellcomeTrust)
.......
A thread on the problem of 'overshoot' ... 1/
....a misunderstanding about two related, but different metrics:

the % of people infected during an epidemic,
and the point at which immunity leads to a decline in transmission 2/

In an uncontrolled epidemic, 'herd immunity' is reached at the peak (because R

Got it @wintertravel1980, that makes sense. So you think R rate is just slightly suppressed in some areas where it would otherwise be worse and comparisons between boroughs is irrelevant. But this only works for low R, which might rise again. Plausible. I don't know how it can be verifiable even in the next year or so, but that's another matter.

@MRex

The infections dropped on those boroughs though *@BigChocFrenzy*, now they've grown again. So overshoot doesn't apply.

... Overshoot includes the total of infections & deaths over all the waves

So 2nd & 3rd waves would usually have fewer infections & deaths

• although SAGE's "reasonable worst case" of 80k deaths shows this is not a hard & fast rule if a number of unfortunate factors come together

2nd & 3rd waves would usually have fewer infections & deaths because of some immunity form previous waves, I mean

However, we can see regions & countries where 2nd - or 3rd - wave look as bad as the first, e.g. Iran, because too far below the % of effective herd immunity required without a vaccine.

I certainly wouldn't expect to see regions that have 70% antibodies having much of a 2nd wave

@Sunshinegirl82

It seems to me that if an area has a higher level of natural immunity that must have some impact on spread? Not enough to say that other mitigation factors aren't necessary but reducing the susceptible population by 20% seems likely to have some impact, even if only marginal.

SAGE seem to be saying in that report that they can't untangle "herd immunity" from other factors in terms of impact and so can't say that it will reduce spread rather than it isn't possible?

That's not so say we should be aiming for herd immunity by natural infection, more that it might be a factor in the apparent slower spread in certain areas. Obviously I suspect that if numbers get beyond a certain point the minor assistance it might provide will be overridden by sheer volume.

I'm in the SE, still very low cases in my LA. 6.5/100,000 over last 7 days according to CM. We regularly get days with zero positive tests, no schools affected locally that I'm aware of. We live quite near the man who was the first confirmed case of community spread (ie hadn't returned from China, Italy etc) so I suspect we had quite high levels in March although I still don't know of a single person who has tested positive for COVID.

I suspect we are neighbours Sunshinegirl82. Although my town has 12.5/100,000 over last 7 days. I live between London and Brighton in a commuter town. There are often zero positives on CM, the only thing that concerns me is that I know of 5 people who tested positive in my town in the last week and their stats dont appear in CM, 2 of them are teachers. I wonder if they will appear in next weeks stats instead.

Thanks Humphries good to read

@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.

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.

Given high antibodies can we say that NYC is through the woods? Or is this lack of long term immunity still an issue?

@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!

@MarshaBradyo

Given high antibodies can we say that NYC is through the woods? Or is this lack of long term immunity still an issue?

... I'd be astonished - and very dismayed - if that NYC borough with 70% antibodies had more than a handful of new cases

However, other boroughs might have much lower levels

Hence why NYC still has so many SD measures - looks more than the UK