Daily stats, numbers, data thread 28 Dec

[PatriciaHolm]

UK govt pressers Slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
R estimates UK & English regions www.gov.uk/guidance/the-r-number-in-the-uk
Imperial UK weekly LAs, cases / 100k, table, map, hotspots imperialcollegelondon.github.io/covid19local/#table
School statistics Attendance explore-education-[statistics.service.gov.uk/find-statistics/attendance-in-education-and-early-years-settings-during-the-coronavirus-covid-19-outbreak]]
NHS England Hospital activity www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/
NHs England Daily deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
Cases Tracker England Local Government lginform.local.gov.uk/reports/view/lga-research/covid-19-case-tracker
ONS MSAO Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
CovidMessenger live update by council district in England www.covidmessenger.com/
Scot gov Daily data www.gov.scot/publications/coronavirus-covid-19-daily-data-for-scotland/
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t www.travellingtabby.com/scotland-coronavirus-tracker/
PH Wales LAs, tests, ONS deaths [[public.tableau.com/profile/public.health.wales.health.protection#!/vizhome/RapidCOVID-19virology-Public/Headlinesummary
NI Dashboard app.powerbi.com/view?r=eyJrIjoiZGYxNjYzNmUtOTlmZS00ODAxLWE1YTEtMjA0NjZhMzlmN2JmIiwidCI6IjljOWEzMGRlLWQ4ZDctNGFhNC05NjAwLTRiZTc2MjVmZjZjNSIsImMiOjh9]]
ICNRC Intensive Care National Audit & Research reports www.icnarc.org/Our-Audit/Audits/Cmp/Reports
NHS t&t England & UK testing Weekly stats www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
PHE Surveillance reports & LA Local Watchlist Maps by LSOA www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
ONS England infection surveillance report each Friday www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/previousReleases
Datasets for ONS surveillance reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsurveydata/2020
ONS Roundup deaths, infections & economic reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19roundup/2020-03-26
Zoe Uk data covid.joinzoe.com/data#interactive-map
ECDC rolling 14-day incidence EEA & UK read https_www.ecdc.europa.eu/?url=https%3A%2F%2Fwww.ecdc.europa.eu%2Fen%2Fcases-2019-ncov-eueea
Worldometer UK page www.worldometers.info/coronavirus/country/uk/
Our World in Data GB test positivity etc, DIY country graphs ourworldindata.org/coronavirus/country/united-kingdom?country=~GBR
FT DIY graphs compare deaths, cases, raw / million pop ig.ft.com/coronavirus-chart/?areas=gbr&areas=fra&areas=esp&areas=ita&areas=deu&areas=swe&areasRegional=usny&areasRegional=usnj&byDate=1&cumulative=1&logScale=1&per100K=1&values=deaths
Alama Personal COVID risk assessment alama.org.uk/covid-19-medical-risk-assessment/
Local Mobility Reports for countries www.google.com/covid19/mobility/
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery www.centreforcities.org/data/high-streets-recovery-tracker/

⏭ Our STUDIES Corner ⏮www.mumsnet.com/Talk/coronavirus/3869571-Studies-corner?msgid=99913434

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

@RosesforMama - A group get the vaccine and a similarly structured control group get something else (e.g. saline / meningitis vaccine); who receives which dose is kept hidden during the trial and they count infections until an agreed point. Then they stop the trial and see how many are vaccinated versus the control group; depending on the number of infections they adjust the tolerance so e.g. 110 infections but only 10 in the vaccinated group is a great result, but the tolerance is still fairly wide because 150 is a small number; 55 in each group would indicate no effect from the vaccine. I don't know the rules behind creating the exact percentages and tolerances.

[quote TheSunIsStillShining]@Em777
Afaik these trials were not set up to deliberately infect people and see how they respond. They were given the vaccine and then let out into gen pop to live their lives as before and let's see what happens. In very basic terms :)

I've heard many scientists voicing opinions that there should be a phase 4 where they actively recruit for people to be infected, but haven't seen more about it than wishing for it. I'm not convinced it would pass an ethical panel though.[/quote]
Thank you. 🙂 Yes, I’ve read about the so-called challenge trials.

I was just wondering how we interpret the 90% figure from Pfizer — does it mean that 9 out of 10 vaccinated people that encounter the virus will not develop symptoms? I presume so, and the confidence intervals they provide are because they can’t be sure of that without the study size being much, much higher. As it is there will be surely be some random chance involved re: how many people from each arm actually had exposure.

@witchend Yes it relates to the vector they used which they started using for SARS1 I think didn’t they. They’d already been working on the vaccine for that. The point being I believe they’ve used a vector which many probably show some immunity to. The criticism was the small number of people they tested and then applied globally, which apparently wasn’t v sensible.

@Witchend

That article you've linked to says it was published online July 13th 2012.

That is quite a long time ago in scientific terms.

Was that to me? It's simply the maths behind the definition of vaccine efficiency rate. That maths doesn't change.

Where did the data thread go?

@lunar1

Where did the data thread go?

😂😂😂😂

Here’s some data for you.
One poster has posted approximately 100 times since 5pm this evening.

[quote Oaktree55]@witchend Yes it relates to the vector they used which they started using for SARS1 I think didn’t they. They’d already been working on the vaccine for that. The point being I believe they’ve used a vector which many probably show some immunity to. The criticism was the small number of people they tested and then applied globally, which apparently wasn’t v sensible.[/quote]
The vector for the Oxford vaccine is a chimpanzee virus which, in theory, no human will have immunity to.

www.research.ox.ac.uk/Article/2020-07-19-the-oxford-covid-19-vaccine

Details here

@JamesAnderson there is a degree of immunity in some to the chimpanzee vector.

I've lurked, read and enjoyed these data threads since the beginning. When the schools discussion began, I thought why don't posters just ignore the the few who were derailing?
I'm thinking the same now. Why are people responding to this poster?

@JamesAnderson it’s in the paper I linked.

Do you have details for this?

@JamesAnderson I linked the paper.

I missed whether this was discussed, but the govt dashboard is now showing number of vaccinations on the healthcare tab (not by region, yet, though)
coronavirus.data.gov.uk/details/healthcare

There's also this, in beta digital.nhs.uk/dashboards/coronavirus-in-your-area

[quote Oaktree55]@JamesAnderson it’s in the paper I linked.[/quote]
The viral vector used in the current Oxford vaccine isn't referenced in the paper you linked.
I would assume they've researched this in the last 8 years and learnt from it

@RosesforMama

Hi everyone. Can someone explain vaccine efficacy stats to me?

For example, say a vaccine is tested and found to be 90 percent effective. What does that mean? Does it mean that if you expose 100 people to "certain" infection, 90 of them will not get ill at all, and 10 will be equally as I'll as if they had not been vaccinated?

Or does it mean that for every person in an exposure situation there is a 90 percent chance they won't catch it, and if they do it will be mild?

Or does it mean that they are 90 percent less likely to be seriously ill from a covid infection?

Or something else?

Take two same size groups. Give one the vaccine and one the placebo. Sit back and watch.

In the placebo group, 50 get covid. In the vaccine group, 5 get covid.

You'd expect 50 cases in the vaccine group - it's the same size as the placebo group, after all. So the vaccine prevented 45 out of 50 probable cases.

45 is 90% of 50. The vaccine is 90% effective.

For the Oxford trial, in the standard dose/standard dose cohort there were 98 cases, of which 71 were in the control group. Thus 27 (98-71) were in the vaccine group. You'd expect 71 cases in the vaccine group, too. The vaccine prevented 44 of them. 44/71 = 62%.

(Slight fudging needed for the Oxford figure because the groups weren't quite the same size.)

Shout if that's confusing - it's late, I'm tired, I might be writing gibberish.

@JamesAnderson no I believe it’s the same vector and opinion is that might be why the U.K. cohort showed better efficacy compared to Brazil.

The vector being referenced in the paper you linked to is ChAdY25

The vector used in the Oxford trial is ChAdOx1

I would think the different names mean they're different vectors

[quote Oaktree55]@JamesAnderson no I believe it’s the same vector and opinion is that might be why the U.K. cohort showed better efficacy compared to Brazil.[/quote]
The vector in the HIV vaccine article was Ad5 and, indeed, some trial participants were immune to it at the start of the trial. It's those seropositive individuals who showed increased risk of contracting HIV. www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32156-5/fulltext

Oxford is based on a chimp derived vector, ChAdOx1. This is not the same as Ad5 and I am not aware of any evidence of pre-existing human immunity, although if you link to the evidence I will gladly read it.

THe chinese have been working on an Ad5 based covid vaccine. There is a discussion of this vaccine compared with the Oxford vaccine at www.sciencemediacentre.org/expert-reaction-to-two-vaccine-candidate-studies-a-phase-1-2-trial-of-the-university-of-oxfords-chadox1-vaccine-candidate-and-a-phase-2-trial-of-chinas-ad5-vectored-covid-19-vaccin/, the main take home for this discussion is to illustrate that these are two different vectors.

[quote Quarantino]I missed whether this was discussed, but the govt dashboard is now showing number of vaccinations on the healthcare tab (not by region, yet, though)
coronavirus.data.gov.uk/details/healthcare

There's also this, in beta digital.nhs.uk/dashboards/coronavirus-in-your-area[/quote]
Thank you for the links Quarantino. The beta digital NHS dashboard is interesting. I always wondered how many people lived in my ward. Seems we do like to ring 111 quite a lot too.

A quote from the last article I linked to: "The Beijing approach is based on the backbone of a conventional human, common-cold virus to which some people have pre-existing antibodies and they therefore make a lower response in some people to the vaccine because people have pre-existing antibodies to their vector, so may clear it before it has a chance to work properly. The Oxford approach overcomes this by deriving a chimp adenovirus platform to which humans have not made prior antibodies."

[quote Oaktree55]The Oxford trial is littered with errors here’s one

100 people in the UK (0% seroprevalence, NCT00890760, NCT00890019) & 57 people from Gambia (9% seroprevalence, NCT01373879).

this is literally all the ChAdOx1 paper uses to justify "low pre-existing seroprevalence [NT50 > 200]".

www.ncbi.nlm.nih.gov/pmc/articles/PMC3396660/#s3g[/quote]
@Motorina here's the article linked to. It mentions other "Chad" vectors but not the
ChAdOx1 vector

I'd like to see more breakdown of how the numbers work, so if 1m people get something 90% effective, how many m need something 62% (or possibly more) effective to be equal? My back of an envelope calculation is that 1m to 90% is 900000, but 2m to 62% is 1240000 people protected. If you can get double the number of people vaccinated asap by using community halls and any old building, not one that is within x radius of a - 80 storage hub, you will prevent more infection.
There is no perfect answer from where we are now, but if the majority of the population have something 62% effective, it will be enough to buy us time.
Are there any indications that having one vaccine will effect the usefulness of another, or is it just that we don't know until the study is done and there is no problem with having an interim and then a final (or yearly booster) vaccine?

@jamesanderson - thank you. That rather proves the point that the vector of concern (the one that gave increased HIV susceptibility) is different from the one Oxford are using.

If I'm understanding right (a maybe!) that article lists a number of human derived adenovirus vectors, of which HAd5 (the HIV article one) is one. It says that human derived vectors - the ones starting with 'H' - haven't lived up to expectations for vaccines, because lots of people are already resistant to them. But chimp-derived - starting 'Ch' - look like they'll be better because immunity to them in humans is low.

Have I understood that right?

In any event, the article makes it clear that the two aren't the same thing. So the suggestion from @Oaktree55 that they are is incorrect.

Which is cool. I admit freely this is not my area of professional expertise. I'm probably making mistakes all over the place, and I know I don't have the knowledge to adequately critique the Oxford research. I can't blame anyone else for also making errors in understanding in what is pretty dense stuff! That's why I'm happy to leave it to the MHRA. But it illustrates to me that Oaktree55 is also not understanding things fully, which gives some context to their critiques and helps me assess how much weight I can give their comments.