Pure data thread #1: Daily numbers, graphs, focused analyses

[BigChocFrenzy]

This is pure data, NOT for the "worried about Corona"

We welcome calm factual, data-driven contributions
Please try to keep discussion focused on these and avoid emotional venting or politics
📈 📉 📊 👍

Resource links

UK:
Uk dashboard R, deaths, cases, hospitals, tests - by postcode, 4 nations, English regions, LAs
Interactive 7-day rolling cases map click on map or by postcode
UK govt pressers Slides & data
SAGE Table Interventions with impacts and R
Imperial UK weekly tables & extrapolations LAs, cases / 100k, table, map, hotspots
School statistics Attendance - Tuesdays
ICNRC Intensive Care National Audit & Research reports
UK testing and NHS England track & trace - Thursdays
ONS Roundup deaths, infections & economic reports
ONS England, Wales & NI Infection surveillance report - Fridays
ONS Datasets for surveillance reports
Our World in Data UK test positivity
R estimates & daily growth UK & English regions - Fridays
Modelling real number of UK infections February in first wave

England:
NHS England Hospital activity
NHS England Daily deaths
PHE COVID Clinical Risk Factors Non-respiratory by region, area, district etc
Cases Tracker England Local Government
PHE surveillance reports Covid, flu, respiratory diseases - Thursdays
CovidMessenger live update by council district in England

Scotland, Wales, NI:
Scot gov Daily data
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t
PH Wales LAs, tests, ONS deaths
NI Dashboard

COVID-19 Risk Factors
Alama Personal COVID risk assessment
PHE Clinical RFs - summary & social vulnerability indicators
PHE Clinical RFs - respiratory disease
PHE Clinical RFs - non-respiratory - CVD,T1, T2, obesity, flu jab coverage
PHE Non-Clinical RFs - deprivation, demography, economic inactivity, ethnicity
PHE Non-Clinical RFs - Vulnerable Groups (1): care / nursing home, MH, visual disabilities
PHE Non-Clinical RFs - homeless, children in care, ESL

Miscell:
Zoe Uk data
ECDC rolling 14-day incidence EEA & UK
Worldometer UK page
FT DIY graphs compare deaths, cases, raw / million pop
Local Mobility Reports for countries
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery
NHS Triage Dashboard Pathways - triages of symptoms
NHS Triage Dashboard Progression - # people pillar 1&2, # triages

⏭ Our STUDIES Corner ⏮

I was fully vaccinated for MMR as a child, had a booster at uni due to a mumps outbreak. And then still tested negative for rubella immunity when pg with my first at 24.

I've had chicken pox twice and whooping cough twice. Apparently I have a crappy immune response...

Abraid2 two of my kids got mumps even though they had the two jabs, they had it very mildly so perhaps the jab helped them if not totally protecting them. I remember mumps as being horrendously painful so I was happy to think it probably protected them from that.

I was surprised they'd caught it and my doctor said it wasn't 100% effective, less than 80% I think but it is a few years ago so I might not have the percentage right. He said if you then add in the children who don't get the jab you just don't have enough for herd immunity. I don't know where you would get evidence of this but obviously as he is my doctor I assumed he was telling me the truth.

@boys3 I love your spreadsheets . Would you be able to add a column to the right of the current week's positivity rates that gives the direction of travel? Just the diff between current & prev week, maybe with a gradient colouring to indicate lower by more than 2%, relatively unchanged, or higher by more than 2% would be super helpful for immediately spotting which regions are doing well or not.

@ancientgran if that doctor is correct about herd immunity then it is very worrying with respect to coronavirus as I believe we will be lucky if we are able to vaccinate the 50% most vulnerable.

[quote ChristmasCantComeSoonEnough]@Abraid2 yes I was saying it gives immunity to a large percentage if given twice not to all. I don’t think any vaccine guarantees immunity which is a common misconception.[/quote]
I think the problem with this generation of students is that they were due to be vaccinated during the MMR scandal. Lots were not vaccinated and so herd immunity has been affected. DD ( fully vaccinated) also had a miserable time with mumps in March this year.

I see I agree with you doctor Ancientgran

ChristmasCantComeSoonEnough, I hadn't thought of that but I will try to be positive and think the vaccine might be more effective than the mumps one and that my youngest two (who caught mumps) were probably in a cohort that was very much influenced by the vaccination causes autism so vaccination rates were low. Well I'm crossing my fingers. Actually thinking about teenagers there was probably alot of kissing going on as well so maybe an effective vaccine, reasonable number having it and social distancing will save us all? I live in hope.

@ancientgran

Abraid2 two of my kids got mumps even though they had the two jabs, they had it very mildly so perhaps the jab helped them if not totally protecting them. I remember mumps as being horrendously painful so I was happy to think it probably protected them from that.

I was surprised they'd caught it and my doctor said it wasn't 100% effective, less than 80% I think but it is a few years ago so I might not have the percentage right. He said if you then add in the children who don't get the jab you just don't have enough for herd immunity. I don't know where you would get evidence of this but obviously as he is my doctor I assumed he was telling me the truth.

This is what I heard too.

Interesting, didn't know about this project.

"10 per cent of all positive tests in UK go on to have their genome sequenced."
mobile.twitter.com/whippletom/status/1320690142202527744

www.thetimes.co.uk/article/a-track-and-trace-success-story-as-teams-reveal-virus-s-dna-fingerprint-zm8sb5b6q (paywall)

Bit more information here (from July)
www.bbc.co.uk/news/uk-wales-53579785

Mumps has always had a lower immunity percentage than measles and rubella; measles is the most deadly.

CDC figures:
"One dose of MMR vaccine is 93% effective against measles, 78% effective against mumps, and 97% effective against rubella.
Two doses of MMR vaccine are 97% effective against measles and 88% effective against mumps."
www.cdc.gov/vaccines/vpd/mmr/public/index.html#:~:text=One%20dose%20of%20MMR%20vaccine%20is%2093%25%20effective%20against%20measles,(weakened)%20live%20virus%20vaccine.

@Quarantino was mentioning about issues if the virus is running rampant when we vaccinate. I can think of a few:

1. A big win for the conspiracy theorists, who will say the vaccine caused illness. (And hard to monitor real life metrics.)
2. Vaccines commonly take a few weeks to take effect; you can say that 1000 times as you vaccinate, but how many will go straight to a club and then on to Grandpa's because they've been jabbed?
3. Not everyone can be vaccinated; common that some of the most vulnerable can't be vaccinated, if enough people still have the virus they remain unsafe.
4. You build herd immunity with a vaccine creating an effective firewall; if there is lots of virus about then people will catch it anyway leading to massive overshoot, because you can't vaccinate everyone and have it take effect in time (hmmm, this might be the main point from what you read?)

I think we might need to adjust our thinking a bit about what we are expecting the vaccine to achieve. The vaccine will not eradicate covid in the same way that the MMR has not eradicated Mumps. Certainly not without a sustained global effort that is likely to take several years.

What we can be hopeful that it will do is shrink the pool of susceptible individuals significantly enough that we can all live as normal AND keep infections rates and deaths from covid at the sorts of low levels you would expect to see from any other infectious disease. To my mind that is the aim of the vaccine.

In addition you continue to improve treatments for those that do contract it and use tactics such as large scale testing for big events, travel etc and possibly ring vaccination if you identify a positive case.

www.theguardian.com/society/2020/feb/14/young-people-england-mmr-vaccine-mumps
Interesting piece from earlier this year - I assume that PHE would have done a push for year 13s to catchup over the summer if they hadn’t had other things on their mind.
Mumps is the least effective segment of the MMR. Even if absolutely everybody has the vaccine its herd immunity is on the brink, so even the smallest group of unvaccinated students will push it over the edge to produce small outbreaks.

@CoffeeandCroissant - the maps here are fascinating if you're interested in the genomics: www.gisaid.org/.

The NHS had become a leader in this in normal times: www.england.nhs.uk/genomics/. This is the 100,000 genomes project page, which seem to have led UK covid-19 efforts: www.genomicsengland.co.uk/.

Some Oxford vaccine info from the Guardian (as the FT article mentioned earlier is paywalled).

The Covid-19 vaccine being developed by the University of Oxford produces a similar immune response in both older and younger adults, and adverse responses were lower among the elderly, British drugmaker AstraZeneca Plc said on Monday.

A vaccine that works is seen as a game-changer in the battle against the novel coronavirus, which has killed more than 1.15 million people, hammered the global economy and shuttered normal life across the world.

“It is encouraging to see immunogenicity responses were similar between older and younger adults and that reactogenicity was lower in older adults, where the Covid-19 disease severity is higher,” an AstraZeneca spokesman told Reuters.

“The results further build the body of evidence for the safety and immunogenicity of AZD1222,” the spokesman said, referring to the technical name of the vaccine.

The news that older people get an immune response from the vaccine is positive because the immune system weakens with age and older people are those most at risk of dying from the virus.

The Financial Times reported earlier that the vaccine, being developed by Oxford and AstraZeneca, triggers protective antibodies and T-cells in older age groups – among those most at risk from the virus.
The Oxford/AstraZeneca vaccine is expected to be one of the first from big pharma to secure regulatory approval, along with Pfizer and BioNTech’s candidate.

If it works, a vaccine would allow the world to return to some measure of normality after the tumult of the pandemic.

Immunogenicity blood tests carried out on a subset of older participants echo data released in July which showed the vaccine generated “robust immune responses” in a group of healthy adults aged between 18 and 55, the Financial Times reported.

I'm watching the Wales latest. He said they had 56 in critical care. He said they had up to 292 if necessary.

Only 56? I know it's not good. But 56 is very few?

If anyone is interested in how those 10% of positive tests have the viral genome sequenced, check out this preprint from the fabulous Sam Nicholls & Nick Loman at the COVID-19 Genomics UK (COG-UK) Consortium using the MRC Climb infrastructure: www.biorxiv.org/content/10.1101/2020.10.06.328328v1

COG-UK launched 23 March, MRC Climb committed to providing the compute infrastructure on 27 March. Sam literally spun up the first instance of MAJORA in under two weeks of crazy intensive work. By 10 April he had 3000 viral genomes from sites across the UK going through the pipeline automatically. It's running all the time now, continually pumping new viral sequences into repositories like GISAID and fuelling major research projects.

@MRex Genomics England has been sequencing whole genomes of COVID patients in association with the GenOMICC consortium. COG-UK is sequencing viral genomes. I'm a minor (and one of many) investigator in ISARIC-4C which has heavy collaborator & data overlap with GenOMICC, and have done some of the analysis of the WGS GenOMICC samples.

@MRex Thanks, will have a good look at those websites later, they look very interesting at first glance. If anyone else is interested covid.genomicc.org/ gives a direct link to the GenOMICC Covid-19 study info/ introduction.

If anyone is interested in what those whole genomes have told us, well, not much yet! We've used them only to confirm the results from the cheaper array-based genotyping that was done on the same patients. See www.medrxiv.org/content/10.1101/2020.09.24.20200048v2

The problems come if they still stay for so long in ICU (median 8 days) and the growth factor.
Wales had 41 on 23rd, 32 on 16th but it was that level for a while after jumping from the teens a month ago, but now it's 25% growth in the course of each week.
People get admitted on a rolling but growing basis; 56 stay for 8 days, next week that number is 70, then 88, then 110, then 138, 173, 216... Then in second week of December ICU has run out of beds when 270 need treating and no sign of an end. That assumes staying with lots of lockdown measures keeping growth at today's low base and flu hasn't started yet.
(8 days median stay source: bmcmedicine.biomedcentral.com/articles/10.1186/s12916-020-01726-3)

Ah fascinating @TheMShip, so you you can tell us about what's being looked at, please be assured you have a very interested audience if you feel like telling us more!
I have a question you or someone else in the group might be able to help on; the gene IFNAR2, the one that seems to be responsible for making covid patients so ill - does that normally make people more vulnerable (it's an immune deficiency after all), or is the covid reaction much stronger?

MRex I had genetic tests last year due to a family history. The Consultant I saw is one of the people running the 100,000 genomes project, not sure if that means I am included in that.

Sadly @MRex I'm a bioinformatician, not a molecular biologist, and I don't have the background to answer questions about specific genes. We write and run analysis pipelines to process sequencing data from raw files (basically long lists of strings composed of A/C/G/T and associated quality scores for each DNA/RNA 'letter') to usable information, and identifying samples of poor quality which shouldn't be used for further analyses.

In the case of the whole genome sequencing data, I was identifying places where the patient genomes were different from the reference human genome. A subset of commonly variant genomic positions had already been genotyped on arrays, which is cheap and fast. Because humans inherit their genomic variation in blocks from their parents, we can impute (that means take a highly informed guess) the genotypes of common variant positions between the sites that were actually genotyped. The WGS was used to confirm the genotypes at both the experimentally determined and imputed genotypes. The statistical geneticists in the consortium then compared patient genotypes to those of people in the UK Biobank, that is, the general population, to see if there was anything different - the IFNAR2 gene was one of a few strong and statistically significant hits.

The advantage of WGS beyond that is to identify rare variation that can't be imputed but might have large effects on how an individual with that variation reacts to SARS-Cov2 infection. That analysis is yet to be done, but it's again work for statistical geneticists.

On another arm of ISARIC-4C, my team is involved in the analysis of RNA sequencing for measuring the expression of genes in patients with COVID-19 at different points in their ICU stay for the purposes of a time series analysis. Many of the same patients also have genotyping data and data from several other experiment types, and one my team is helping to ensure that all these data types can be integrated (lots of headaches with mapping identifiers!) so other researchers can see how they interact.

Anyway, it's been extremely busy for us since March, and seems set to continue. Some arms of the project are now wrapping up but others will continue data gathering throughout subsequent waves of the pandemic.

That sounds really fascinating and very helpful @TheMShip, thank you for sharing that. It would be a delightful connection if you had processed @ancientgran's DNA at some stage in the past.

@ancientgran - you aren't one in a million then, but a tenth as special

@ancientgran

MRex I had genetic tests last year due to a family history. The Consultant I saw is one of the people running the 100,000 genomes project, not sure if that means I am included in that.

If you were offered whole genome sequencing, then yes, you would be included. That's super cool! I hope you got results that were explanatory.