Data, Stats, Daily Numbers started 14th November 2021

[boys3]

Welcome to the DATA thread.

Our preference is for actual, data driven and analytical contributions.
Please try to keep discussion focused on these

Our links below probably need a refresh ready for the festive season,. so all reasonable suggestions welcome.

UK govt press conferences slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
PHE Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201
PHE Vaccine efficacy www.gov.uk/government/publications/phe-monitoring-of-the-effectiveness-of-covid-19-vaccination
SAGE : Minutes and Models www.gov.uk/government/collections/scientific-evidence-supporting-the-government-response-to-coronavirus-covid-19
Data Dashboard coronavirus.data.gov.uk/ includes R estimates
PHE Weekly Flu & Covid Surveiilance Reports 2021-22 Season www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2021-to-2022-season
Dashboard Vaccine Map to MSOA level coronavirus.data.gov.uk/details/interactive-map/vaccinations
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Sanger Genome Maps & Data covid19.sanger.ac.uk/lineages/raw
UCL Virus Watch ucl-virus-watch.net/
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
Sewage www.gov.uk/government/publications/wastewater-testing-coverage-data-for-19-may-2021-emhp-programme/wastewater-testing-coverage-data-for-the-environmental-monitoring-for-health-protection-emhp-programme.
Sewage reports www.gov.uk/government/publications/monitoring-of-sars-cov-2-rna-in-england-wastewater-monthly-statistics-june-2021
Global vaccination data ourworldindata.org/covid-vaccinations
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 imperialcollegelondon.github.io/covid19local/#map
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 MSOA Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/

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, cases, tests, deaths Dashboard public.tableau.com/profile/public.health.wales.health.protection#!/vizhome/RapidCOVID-19virology-Public/Headlinesummary
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 (from last summer) 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 (European Centre for Disease Control rolling 14-day incidence EEA & UK www.ecdc.europa.eu/en/cases-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=eur&areas=usa&areas=bra&areas=gbr&areas=cze&areas=hun&areasRegional=usny&areasRegional=usnj&areasRegional=usaz&areasRegional=usca&areasRegional=usnd&areasRegional=ussd&cumulative=0&logScale=0&per100K=1&startDate=2020-09-01&values=deaths

PHE local health data fingertips.phe.org.uk/profile/health-profiles
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/

Thanks Fred.

I've just skimmed a couple of articles. Sharing for info. I wish I'd caught the name of the SA medic/scientist/public health official on the news.

www.reuters.com/world/africa/safrica-festival-halted-after-36-test-positive-covid-site-2021-12-01/

www.nature.com/articles/d41586-021-03614-z

www.google.co.uk/amp/s/amp.theguardian.com/global-development/2021/dec/02/omicron-may-cause-more-covid-reinfections-say-south-african-experts

@PrincessNutNuts - she commented in depth in the NY article someone linked above.

Coetzee was one ?

[quote MRex]@PrincessNutNuts - she commented in depth in the NY article someone linked above.[/quote]
Thank you. What did she say?

I've read the New Yorker piece because I follow Tulio Oliveira.

The

"That herd immunity from previous infections will protect us. Herd immunity from vaccination will probably protect us. But herd immunity from letting the virus circulate and infect everyone? That variant may be the last nail in that coffin."

part hit me like a truck.

I don't understand where my map comment went, how did it get lost? Urgh.
Summary version - I haven't had time to look in enough detail, but most of London and Surrey are little school surges that die off. Earlsfield through Clapham South and down into Tooting is different and growing fast, they need surge testing. In my opinion. Caveat that not much time etc.

I'm also annoyed the team took away my date scrolling by phone, it drastically reduces the time I can spend flicking at maps (while on conference calls etc)

@Piggywaspushed

Coetzee was one ?

Yeah, it wasn't Angelique Coetzee. I remembered her name because so much of what she was saying seemed at odds with well... science.

We already know what a lot of those mutations generally do - so to play omicron down seemed at odds with reality to be honest.

SA whole population data re reinfections, not encouraging

twitter.com/miamalan/status/1466460836143239179?s=21

Looks like omicron can reinfect 3.5 as many people as previous variants.

Useful Twitter thread on the new data coming out of SA about Omicron evading immunity from past infection. twitter.com/kallmemeg/status/1466470718674284553?t=2vScAWWKCTu-dM7Gmtb43w&s=19

Seems to say that transmitability to people without past infection is about the same as Delta (so Ro about the same?) But it's about 3 times as infectious to people with past infection (doesn't split by strain - SA would be a mix of beta and Delta mainly) Doesn't seem to say to what extent it evades immunity from vaccines I presume the numbers aren't quite in on that yet.

Looks like omicron can reinfect 3.5 as many people as previous variants

Isn't that subtly different, as if we're talking original to alpha/delta re-infection then as well as the variant difference, we also have a longer period, ie if we're looking at original to omicron then it's over a year later of waning immunity. It's alpha and then delta to omicron that's interesting.

As to different immunities providing protection - it's all about protection against serious illness, like most respiratory infections surely, we've not got any long term immunity to any of them, but we are mostly well protected from serious illness?

Oh and 3.5 times more re-infection, is still very little re-infection in those stats 35,000 out of 2.8 million is the re-infection in the tweet.

actual depends on prevalence etc. as we don't know detection rates etc. but it would be what 150,000 re-infections in the larger UK dataset, so an extra weeks worth of data?

Yes that data is just about protection from (symptomatic?) infection. The consensus on Twitter seems to be that data on protection against severe disease will take longer to collect, mainly because in a fast growing epidemic you'd need to know a very precise lag between cases and hospitalisations (which isn't known), or track outcomes for individual cases, which again takes longer. It's logical though that past infection with a different strain might help you fight off a new strain a bit faster than if you'd not caught anything before.

@sirfredfredgeorge

Oh and 3.5 times more re-infection, is still very little re-infection in those stats 35,000 out of 2.8 million is the re-infection in the tweet.

actual depends on prevalence etc. as we don't know detection rates etc. but it would be what 150,000 re-infections in the larger UK dataset, so an extra weeks worth of data?

Yes that's true - the number of definite reinfection cases in the UK is still pretty low (around 1% of cases I think) so trebbling it wouldn't matter much. But the number of UK cases in vaccinated people is large, so if it turned out to be also three times as infectious to vaccinated people we'd have more problems

3 times what though - it says it seems to cause reinfections at a 3 fold increase on previous variants but what level of reinfection did preivous variants have

SA scientists assumed protection from prior infections was as high as 80% (page 3):

www.medrxiv.org/content/10.1101/2021.11.11.21266068v2.full.pdf

Do we know the answer about sequencing and how long it takes? When they said that this variant shows up on pcr tests quickly does that mean any labs can see it or only particular labs.

My area in the last 3 weeks had a Streep rise then a fast drop now the beginnings of a rise again.

South Africa has 24%fully vaccinated which is vastly different

They can see the S drop-out, but that could also be a particular Delta strain, so genome testing is needed and that's a longer process, fewer labs, more limited capacity due to machine usage. If that Delta strain disappeared they they would track it by S drop-out.

mrex can you elaborate on your comment regarding Clapham South and tooting? There was a definite secondary school surge in mid Oct and there’s been a surge in the last week amongst parents attending Xmas events. (No cases of new variant that I’ve heard of). DD’s year at PHS have had a significant number of cases over last 2 weeks but seems to be on the wane.

I appreciate it’s anecdotal as opposed to hard data but many kids describing tummy ache or upset as first symptom before a positive LFT.

Yes that has indeed been the case since Alpha. Totally overlooked as a symptom. Not just kids. Gastroenteritis was my main symptom.

You all know I love a graph.

From @Rid1tweets

@Stircrazyschoolmum

I appreciate it’s anecdotal as opposed to hard data but many kids describing tummy ache or upset as first symptom before a positive LFT.

Yes, have heard this recently.

@PrincessNutNuts that graph is sobering. I hope the key difference will be levels of vaccination? (Although that doesn’t stop our youngest population being at risk)

One very good thing about the pandemic has been that children are generally unlikely to get very ill with covid, with only a very few exceptions.

I would like to know more about the data on infections in children from South Africa, though, as the reports don't entirely match each other,