Data, Stats and Daily Numbers started 18th January 2022

[boys3]

Welcome to another instalment of the DATA thread.

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

UK govt press conferences slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
UKHSA Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefing
UKHSA Vaccine efficacy www.gov.uk/guidance/monitoring-reports-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
UKHSA 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/

@Firefliess

90 days does seem quite long to class something as a reinfection, especially with Omicron hitting soon after a big Delta wave. But within 30 days seems unlikely for a genuine reinfection, and quite likely to be the same infection.

The dashboard update to include reinfections will go by the 90 day interval too. Agreed, with Omicron this seems too long! I wonder how many people still test positive from a first infection towards the end of that time.

oops, sorry, chart doesn't go with that comment but is:

case rates by age group (see increase in rates in 5-9 and 10-19, plus likely parents' age groups) from UKHSA's Twitter today.

keeping an eye on BA2 growth. Has anyone come across info on whether LFTs still detect it? I tried looking for info from Denmark but couldn't find it, I'm guessing yes. I know PCR can (but without S gene dropout so was being referred to as "Stealth" Omicron earlier on).

Tim Spector and Dr John Campbell have done videos on it today and yesterday.

Yes, LFT's still detect it, it's really not very different.

Reinfection info is going to be crucial for how the situation is managed going forward. Surely, if reinfections are common, rates remain high, and people get covid every 90 days or so it could be a nightmare for the symptomatic people being ill forever more on a 90 day cycle. Any evidence of people getting it worse 2nd time or does everybody get it the same or milder?

Incredible increases again in primary aged children reported by UKHSA today.

Left hand graph - last week
Right hand graph - from the same report this week

Note that the scale has changed and the bars have been widened, presumably because otherwise they look ridiculously tall. Colour palette has changed too this week making it much harder to read.

Incredible increases again in primary aged children reported by UKHSA today

Still half the peak in the 20-29 year olds, so quite a bit more to come unless we think detection rates will be massively lower in the age group (I'd simplistically expect higher as parents choose to test and schools encourage)

I think that comparisons between ONS rates and reported cases by age group suggests that cases in young children are underreported, but not a huge impact by other age groups. Maybe a bit more routine testing of secondary aged kids, but a lot of workplace and voluntary testing too currently, and kids still a bit more likely to have symptoms you easily miss/be truly asymptomatic.

Hospitalisations look quite between the waves. Take note the two graphs have different scales. Obviously vaccines have been very effective in most age groups. However child admissions have risen, however this looks more stark as other age groups have gone down. Women between 20 and 39 have also gone up. This seems strange when this second group are vaccinated, maybe to do with pregnancy?

@containsnuts

Reinfection info is going to be crucial for how the situation is managed going forward. Surely, if reinfections are common, rates remain high, and people get covid every 90 days or so it could be a nightmare for the symptomatic people being ill forever more on a 90 day cycle. Any evidence of people getting it worse 2nd time or does everybody get it the same or milder?

Where do you get 90 days as being the average re-infection period? That seems extremely short to me.

This seems strange when this second group are vaccinated, maybe to do with pregnancy?

The second one is biased much more by "with covid", because the number of people infected is so much higher and vaccination is little to no protection against infection, the proportion of the cases which are not primarily covid increases which means the age breakdown begins to reflect the hospital demand much more, rather than the covid hospital demand.

Hence you get an increase in younger age groups and pregnant women.

The problem is we don't know how much of it is with etc.

Definitely new infections as tested neg a few times in between

If they test negative 4 times in between they will be included as a re-infection. it is not simply 90 days.

Of course, if you didn't bother registering the tests in between...

Still half the peak in the 20-29 year olds, so quite a bit more to come

It is much more than half way to the 20-29 peak but we have no idea whether it will pan out the same. Primary children aren't vaccinated.

Good to hear absences have decreased for HCP

The hospitalisation rate difference for women of childbearing age is quite stark isn't it? As previously mentioned this will be in part incidental admissions for labour who happen to have covid. But it's likely also to be in part unvaccinated pregnant women who are higher risk of being hospitalised due to covid.

BA.2 update
From the technical briefing today:
www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings

"SGTP is now a reasonable proxy for BA.2 (accounting for 80% of
sequenced SGTP cases with an increasing trend). The proportion of SGTP cases is now
increasing. As of the 24 January 2022, the overall proportion of SGTP cases in England is 4.4%
compared to 2.2% on the 17 January. There is geographical variation with the highest
proportion in London (9.5%) and the lowest in the North-East region (0.9%).

Growth rate
BA.2 has an increased growth rate compared to BA.1 in all regions of England where there are
sufficient cases present to make an assessment. Whilst growth rates can be overestimates
early in the emergence of a variant, the apparent growth advantage is currently substantial.

Secondary attack rates
Analysis from routine contact tracing data indicated higher secondary attack rates amongst
contacts of BA.2 cases in households (13.4%; 95% CI: 10.7%-16.8%) than those for contacts of
other Omicron cases (10.3%; 95% CI: 10.1%-10.4%) in the period 27 December 2021 to 11
January 2022. These secondary attack rates are not adjusted for vaccination status and reflect
overall growth advantage rather than transmissibility.

Vaccine effectiveness
A preliminary assessment did not find evidence of a difference in vaccine effectiveness against
symptomatic disease for BA.2 compared to BA.1. However, numbers included in this study are
relatively small and it will be iterated. The University of Oxford has reported preliminary
unpublished pseudovirus neutralisation data. In this study, BA.1 and BA.2 pseudoviruses did
not differ substantially in neutralisation by sera from vaccinated individuals"

New risk assessment:
assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1051013/26-january-2022-risk-assessment-for-VUI-22JAN-01_BA.2.pdf

containsnuts
"Reinfection info is going to be crucial for how the situation is managed going forward. Surely, if reinfections are common, rates remain high, and people get covid every 90 days or so it could be a nightmare for the symptomatic people being ill forever more on a 90 day cycle. Any evidence of people getting it worse 2nd time or does everybody get it the same or milder?"

treeflowercat
"Where do you get 90 days as being the average re-infection period? That seems extremely short to me".

No, not average just POSSIBLE from around 90 days.

Here are some great graphs on the global BA.2 situation:

mobile.twitter.com/Mike_Honey_/status/1487040411256307716

Reinfection being possible in the space of 6 weeks has been described since April - June 2020 (with different strains)

And more thoughts on BA.2.

twitter.com/trvrb/status/1487105396879679488

.

A household secondary attack rate of 13% ?

Erm, that's still pretty small?

Erm, that's still pretty small?

I guess boosters and acquired immunity are driving the number down, but still…

FWIW, I was always surprised by low household SARs reported in PHE technical briefings. The highest for Delta was around 15-16%, if I remember correctly. There must be some methodology nuances I do not fully understand.

The household attack rate has always been lower than most people imagine it to be. A lot of people are fatalistic about catching it off anyone in their family has it, but the evidence has always shown that to be far from certain and much more likely that you'll escape it. I assume this is down to the K factor thing when a small number of people are super infectious and infect dozens, whilst most people infect noone at all.

I think they only count it as household transmission if the second person tests positive within a certain time period of the first person - I'm not how that might be affected by different strains having different incubation periods.