Data, Stats & Daily Numbers started 9th Feb

[NoGoodPunsLeft]

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 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 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

@Firefliess - it was this that particularly raised my eyebrows: "Novavax announcedspectacular resultsfor its phase 3 trial, while preliminary data suggest the AstraZeneca vaccine isineffectiveagainst the South African variant."
Those aren't similar trials.

More real world confirmation from Israel, that the Pfizer/BioNTech vaccine is highly effective - over 90% after two doses.

Study finds 94% drop in symptomatic Covid cases with Pfizer vaccine
via The Irish Times
www.irishtimes.com/news/world/middle-east/study-finds-94-drop-in-symptomatic-covid-cases-with-pfizer-vaccine-1.4484846

[quote MRex]@Firefliess - it was this that particularly raised my eyebrows: "Novavax announcedspectacular resultsfor its phase 3 trial, while preliminary data suggest the AstraZeneca vaccine isineffectiveagainst the South African variant."
Those aren't similar trials.[/quote]
No, I do agree that you shouldn't be comparing how one vaccine does against the SA strain with how another did in trials against different strains to make precise comparisons. - but to be fair I don't think she's factored in anything about the SA strain in her chart - she's just looked at the effecacy rates according to the phase 3 trials.

The point she's making is that if a third of your population can still catch and transmit post-vaccination, and you don't vaccinate children, you won't stop the disease spreading exponentially unless you maintain social distancing indefinitely. I do think this is something we need to be taking about. We will need to get a vaccine licenced for children soon, and may well need to give boosters of one of the more effective vaccines to those who've had the Oxford one initially.

I do find the assertion that you can’t compare the results of clinical trials bizarre. I attach the graphs from the Pfizer/BioNtech and Ox/AZ vaccines showing symptomatic infections post-vaccine. Pfizer is from day 1 of the first dose, AZ only provided the results from 3 weeks after dose 2.

It is clear which one has performed better.

I’d be happy to have any, but I suspect that those who have had AZ will get a booster in the autumn.

@Eyewhisker

I do find the assertion that you can’t compare the results of clinical trials bizarre. I attach the graphs from the Pfizer/BioNtech and Ox/AZ vaccines showing symptomatic infections post-vaccine. Pfizer is from day 1 of the first dose, AZ only provided the results from 3 weeks after dose 2.

It is clear which one has performed better.

I’d be happy to have any, but I suspect that those who have had AZ will get a booster in the autumn.

See my comments above about why you shouldn't do this

The other thing worth pointing out with Zoe Hyde's analysis is that she's not factored in any natural immunity. She's talking about the Australian context so this is fair enough. But in the UK context the vulnerable population will be about 25-30% lower, because those people have immunity from having caught Covid, so that will help us a bit.

Chinese - both the trials used similar methods - symptomatic infection.
If anything, only having results from under 55s, we would expect higher raw efficacy numbers from AZ.

The medical authorities do compare as they use these measures to decide whether to approve or not.

@Eyewhisker

Chinese - both the trials used similar methods - symptomatic infection. If anything, only having results from under 55s, we would expect higher raw efficacy numbers from AZ.

The medical authorities do compare as they use these measures to decide whether to approve or not.

The MHRA will approve a drug or vaccine based on its trial results and whether it is safe and efficacious. They don't make any recommendations as to which drug or vaccine should be used for a condition in preference to any other - or whether the drug in question is cost-effective and should be used by the NHS. They just say that it can be used.

Judgements about preferential usage are down to HTA bodies such as NICE or, for vaccines, the JCVI. I don't believe the JCVI has made any judgements as to which covid vaccines should be used in preference to any others.

.

To be clear, I'm not making any comment on the efficacy of any covid vaccines, just pointing out that you can't naively compare trials, which I think is important to remember on a data thread.

Scientific committees do compare different vaccines or drugs. If a new one is invented that's less effective than one already available it won't normally be licensed for use. The reason we've licenced less-effective vaccines for Covid is because there's a global shortage - the alternative to not licencing the Oxford one isn't that everyone would have Pfizer instead, it would mean many people have none at all for a year or more. And the Oxford vaccine is clearly good enough to be well worth taking. But scientific committees advising governments do compare the results of different phase 3 trials and use them to advise using one product rather than another.

@ceeveebee

Thanks *@boys3*, very interesting graphs and shows how different the trends have been across the country

Was part of the north west table chopped off, as I couldn’t see Cumbria or Lancashire (other than Blackburn)? Was particularly interested in Cumbria as they apparently had the Kent variant before Christmas?

@ceeveebee Lancs & Cumbria combined graph plus data

Whilst it’s true that scientists do of course compare data trials, it isn’t in the blunt way Dr Hyde has. Having said that she can arguably only construct comparison on the data she has available - would have been good to see a note of caution though.

Also very few drugs are licensed in a vacuum from the real world - of price, ease of availability etc. So less effective but cheaper drugs are indeed licensed for use.

Going back a bit @MRex I did look at the GISAID link thank you. Agree with your assessment. Though I don’t understand how to interpret the data entirely. Sometimes the number of samples attributed to a country appear to be less than the number of cases mentioned in the media, and I’m also not clear how the proportions are determined especially for countries with more limited sequencing. I’m sure the answers are in there - I just need to read up.

One question I have about boosters is, how do you boost a vector vaccine when you have immunity to the vector? Presumably with a different vector or a different type of vaccine altogether. Any good discussion of this anywhere?

@ATieLikeRichardGere - GISAID relies on actual uploads, so if their figures are lower then that could be cases not loaded, or cases that have not yet been sequenced but have been identified as a phylogenetic cluster (that's how the UK were identifying Kent quickly and confirming later, using the 69-70 spike deletion making the PCR test negative on the S-gene target only). If it's higher on GISAID then the media figure must be wrong.
I haven't found anything to suggest typical timeframes they are operating under, proportion of sequences submitted to GISAID rather than INSDC / not at all, and I've no idea how different countries are confirming their variant percentages. I think it's especially problematic with countries who genome test very few cases, as well as managing the information when cases might be travellers rather than community transmission. If you find anything explaining more please post it.

@ATieLikeRichardGere - the viral vector may explain why the Oxford second dose effectiveness improves over a longer period; this article suggests it more specifically than I've seen elsewhere:
www.vaccitech.co.uk/technology/.
It looks like it all depends how quickly the viral vector immunity degrades; adenoviruses don't create much of an immune response, so after a period of time people would theoretically be susceptible again. Very Strong Caveat - I learned everything I know about viral vectors from this article, so I have no way of knowing any flaws with the article contents: www.nature.com/articles/3302037#:~:text=Finally%2C%20adenoviral%20vectors%20deleted%20of,induce%20markedly%20reduced%20immune%20responses.&text=Animals%20administered%20the%20PEGylated%20vectors,resulting%20in%20prolonged%20transgene%20expression.

Interesting tweet from RP131 - 86% of the population is now at rates at or below what was previously classified as “tier 2”
twitter.com/rp131/status/1361014559058911232?s=21

That's very interesting @ceeveebee.

The goalposts have definitely shifted significantly, with leaks suggesting the loosening will be still be stricter than the tier restrictions.

If schools are opening, it make sense to watch and wait for a time. If not it would seem to be sensible to open areas that don't appear to have driven infections like not essential retail for example.

9,765/230

Anecdotally a close family member - medic in a surge area has told me they they are seeing cases of infection several weeks after the jab. Large cluster in a nursing home. But the number of cases presenting overall in hospital is much lower. Apparently they are sworn to secrecy regarding the surge data, as it's not out yet.

[quote ceeveebee]Interesting tweet from RP131 - 86% of the population is now at rates at or below what was previously classified as “tier 2”
twitter.com/rp131/status/1361014559058911232?s=21[/quote]
Isn’t this just based on positive cases per 100,000?

This is compounded by the fact that generally we are testing more than ever (bar the last two days for some reason). So 100 per 100,000 now is actually better than it sounds due to increased testing.

Like many I suspected we might see reported cases falling below 10,000 tomorrow, the fact it is today another positive step, one that @MRex correctly called ? So tomorrow which picks up primarily the weekend spec date cases likely to be lower again.

So in England Mondays have been the peak day of the week for a while.

Monday 25 Jan. 27188

Monday 1 Feb. 20168

Monday 8 Feb 13880

Monday 15 Feb - likely to be back into four figures, or very close as this week plays out.

Again wishing to steer clear of Harper-Baker syndrome:

England’s 7 day case average, using a four day reporting lag, has now just dipped below 12,000

At the same level therefore as 7th October (12278) or if we want to maintain a tenuous grasp on reality the 12105 on 2nd December

A week prior to 7 Oct the figure was 7405

Mid September 2666

Start September 1169

Start August 722

Although testing had scaled up in those earlier dates it was some way off current levels. That said if Boris can hold his nerve alongside the vaccination roll out then after what has been some bleak months the future starts to look a lot more positive.

I am really surprised by the speed of drop in positive cases. I am wondering if it is the impact of vaccine or seasonality but there should be other factors at play on top of ongoing restrictions.

France said they were ready to open up most of the economy if the case count dropped under 5,000 (which roughly translates into the 7 day rate of 50/100,000). We are not at this level (yet) but we are getting closer and closer.

Did I call it @boys3? Woohoo me (I would have thought I'd go for Tuesday). I remember I predicted a bad strain coming out of Africa back in November/ December and was disturbed that one came to pass so quickly.

5,000 is still awfully high for daily cases IMO. Personally I hope more like under 3,000 cases with schools, under 1,000 for restaurants.

I am really surprised by the speed of drop in positive cases. I am wondering if it is the impact of vaccine or seasonality but there should be other factors at play on top of ongoing restrictions

I suspect it's more that the people who still have to (or choose to) go out during lockdown had a very high chance of having already had it with the added transmissibility in Nov/Dec, so there's substantial immunity in groups that do the most mixing. That wasn't the case in previous lockdowns so would be a big difference that makes rates fall faster.

I would be interested in stats showing the differences in care home/hospital outbreaks, as a steep fall in those would point to vaccine impacts as they would not be behaving differently - although obviously the staff moving between them would still have a higher chance of having had it.