Findings from the Coronavirus (COVID-19) Infection Survey for England.

COVID-19Plots and analysis relating to the coronavirus pandemic. Includes five sets of plots and associated R code to generate them.1) HeatmapsUpdated every few days - heatmaps of COVID-19 case and death trajectories for Local Authorities (or equivalent) in England, Wales, Scotland, Ireland and Germany.2) All cause mortalityUpdated on Tuesday (for England & Wales), Wednesday (for Scotland) and Friday (for Northern Ireland) - analysis and plots of weekly all-cause deaths in 2020 compared to previous years by country, age, sex and region. Also a set of international comparisons using data from mortality.org3) ExposuresNo longer updated - mapping of potential COVID-19 mortality exposure at local levels (LSOAs) in England based on the age-sex structure of the population and levels of poor health.There is also a Shiny app which creates slightly lower resolution versions of the same plots online, which you can find here: https://victimofmaths.shinyapps.io/covidmapper/, on GitHub https://github.com/VictimOfMaths/COVIDmapper and uploaded to this record4) Index of Multiple Deprivation No longer updated - preliminary analysis of the inequality impacts of COVID-19 based on Local Authority level cases and levels of deprivation. 5) Socioeconomic inequalities. No longer updated (unless ONS release more data) - Analysis of published ONS figures of COVID-19 and other cause mortality in 2020 compared to previous years by deprivation decile.Latest versions of plots and associated analysis can be found on Twitter: https://twitter.com/victimofmathsThis work is described in more detail on the UK Data Service Impact and Innovation Lab blog: https://blog.ukdataservice.ac.uk/visualising-high-risk-areas-for-covid-19-mortality/Adapted from data from the Office for National Statistics licensed under the Open Government Licence v.1.0.http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/

Estimates of differences in coronavirus (COVID-19) mortality risk by self-reported disability status for deaths occurring up to 9 March 2022, using linked data from the Office for National Statistics’ Public Health Data Asset.

Due to changes in the collection and availability of data on COVID-19 this page will no longer be updated. The webpage will no longer be available as of 11 May 2023. On-going, reliable sources of data for COVID-19 are available via the COVID-19 dashboard, Office for National Statistics, and the UKHSA

This page provides a weekly summary of data on deaths related to COVID-19 published by NHS England and the Office for National Statistics. More frequent reporting on COVID-19 deaths is now available here, alongside data on cases, hospitalisations, and vaccinations. This update contains data on deaths related to COVID-19 from:

NHS England COVID-19 Daily Deaths - last updated on 28 June 2022 with data up to and including 27 June 2022.


ONS weekly deaths by Local Authority - last updated on 16 August 2022 with data up to and including 05 August 2022.

Summary notes about each these sources are provided at the end of this document.

Note on interpreting deaths data: statistics from the available sources differ in definition, timing and completeness. It is important to understand these differences when interpreting the data or comparing between sources.

Weekly Key Points

An additional 24 deaths in London hospitals of patients who had tested positive for COVID-19 and an additional 5 where COVID-19 was mentioned on the death certificate were announced in the week ending 27 June 2022. This compares with 40 and 3 for the previous week. A total of 306 deaths in hospitals of patients who had tested positive for COVID-19 and 27 where COVID-19 was mentioned on the death certificate were announced for England as whole. This compares with 301 and 26 for the previous week. The total number of COVID-19 deaths reported in London hospitals of patients who had tested positive for COVID-19 is now 19,102. The total number of deaths in London hospitals where COVID-19 was mentioned on the death certificate is now 1,590. This compares to figures of 119,237 and 8,197 for English hospitals as a whole. Due to the delay between death occurrence and reporting, the estimated number of deaths to this point will be revised upwards over coming days These figures do not include deaths that occurred outside of hospitals. Data from ONS has indicated that the majority (79%) of COVID-19 deaths in London have taken place in hospitals.

Recently announced deaths in Hospitals

21 June 22 June 23 June 24 June 25 June 26 June 27 June London No positive test 0 0 1 4 0 0 0 London Positive test 3 7 2 10 0 0 2 Rest of England No positive test 2 6 4 4 0 0 6 Rest of England Positive test 47 49 41 58 6 0 81

16 May 23 May 30 May 06 June 13 June 20 June 27 June London No positive test 14 3 4 0 4 3 5 London Positive test 45 34 55 20 62 40 24 Rest of England No positive test 41 58 33 23 47 23 22 Rest of England Positive test 456 375 266 218 254 261 282 Deaths by date of occurrence

21 June 22 June 23 June 24 June 25 June 26 June 27 June London 20,683 20,686 20,690 20,691 20,692 20,692 20,692 Rest of England 106,604 106,635 106,679 106,697 106,713 106,733 106,742 Interpreting the data The data published by NHS England are incomplete due to:

delays in the occurrence and subsequent reporting of deaths deaths occurring outside of hospitals not being included

The total deaths reported up to a given point are therefore less than the actual number that have occurred by the same point. Delays in reporting NHS provide the following guidance regarding the delay between occurrence and reporting of deaths: Confirmation of COVID-19 diagnosis, death notification and reporting in central figures can take up to several days and the hospitals providing the data are under significant operational pressure. This means that the totals reported at 5pm on each day may not include all deaths that occurred on that day or on recent prior days. The data published by NHS England for reporting periods from April 1st onward includes both date of occurrence and date of reporting and so it is possible to illustrate the distribution of these reporting delays. This data shows that approximately 10% of COVID-19 deaths occurring in London hospitals are included in the reporting period ending on the same day, and that approximately two-thirds of deaths were reported by two days after the date of occurrence.

Deaths outside of hospitals The data published by NHS England does not include deaths that occur outside of hospitals, i.e. those in homes, hospices, and care homes. ONS have published data for deaths by place of occurrence. This shows that, up to 05 August, 79% of deaths in London recorded as involving COVID-19 occurred in hospitals (this compares with 44% for all causes of death). This would suggest that the NHS England data may underestimate overall deaths from COVID-19 by around 20%.

Comparison of data sources

Note on data sources

NHS England provides numbers of patients who have died in hos

NHS UK - COVID-19 Daily Deaths

This section contains information on deaths of patients who have died in hospitals in England and had tested positive for COVID-19 at time of death. All deaths are recorded against the date of death rather than the date the deaths were announced. Interpretation of the figures should take into account the fact that totals by date of death, particularly for most recent days, are likely to be updated in future releases. For example as deaths are confirmed as testing positive for COVID-19, as more post-mortem tests are processed and data from them are validated. Any changes are made clear in the daily files.

These figures do not include deaths outside hospital, such as those in care homes. This approach makes it possible to compile deaths data on a daily basis using up to date figures.

Dataset Content

These figures will be updated at 2pm each day and include confirmed cases reported at 5pm the previous day. Confirmation of COVID-19 diagnosis, death notification and reporting in central figures can take up to several days and the hospitals providing the data are under significant operational pressure. This means that the totals reported at 5pm on each day may not include all deaths that occurred on that day or on recent prior days.

The original dataset is sourced directly from the NHS source site, this original dataset is then cleaned and converted to a csv format available for inclusion into a Kaggle notebook.

There are 3 files considered within the data :- 1. Fatalities_by_age_uk 2.Fatalities_by_region_uk 3.Fatalities_by_trust_uk

Data runs from March 1st up to the current day. Any discrepancies will be outlined. The first is cumulative for any previous days leading up to of relevance. The following days are not cumulative and represent the updated value for the date under consideration.

A start kernel is provided to demonstrate using the dataset.

Citations

This dataset is sourced from the NHS statistical work areas:- https://www.england.nhs.uk/statistics/statistical-work-areas/

This dataset has been sourced and provided to aid in the following competition:- https://www.kaggle.com/c/covid19-global-forecasting-week-4

This feature service contains COVID-19 data automatically updated from the Public Health England (PHE) API service, daily. Using this API, this service takes the current day request minus two days. Therefore the data will always be two days behind. This is a result of the delay between PHE's specimen date and reporting date.The Polygon Layers, which all contain spatial data, provide information about the latest cumulative figures at three geographies; Local Authority, Regions and Nations. The Tables, which are not spatially aware, provide historical data for each feature. The format of these tables allow you to use the Join tool with the Polygon Layers and create a time enabled layer. This can be used within a dashboard or on the animation tool to view patterns over time.

11th January 2020 Change to vaccination data made available by UK gov - now just cumulative number of vaccines delivered are available for both first and second doses. For the devolved nations the cumulative totals are available for the dates from when given, however for the UK as a whole the total doses given is just on the last date of the index, regardless of when those vaccines were given.

4th January 2020 VACCINATION DATA ADDED - New and Cumulative First Dose Vaccination Data added to UK_National_Total_COVID_Dataset.csv and UK_Devolved_Nations_COVID_Dataset.csv

2nd December 2020:

NEW population, land area and population density data added in file NEW_Official_Population_Data_ONS_mid-2019.csv. This data is scraped from the Office for National Statistics and covers the UK, devolved UK nations, regions and local authorities (boroughs).

20th November 2020:

With European governments struggling with a 'second-wave' of rising cases, hospitalisations and deaths resulting from the SARS-CoV-2 virus (COVID-19), I wanted to make a comparative analysis between the data coming out of major European nations since the start of the pandemic.

I started by creating a Sweden COVID-19 dataset and now I'm looking at my own country, the United Kingdom.

The data comes from https://coronavirus.data.gov.uk/ and I used the Developer's Guide to scrape the data, so it was a fairly simple process. The notebook that scapes the data is public and can be found here. Further information about data collection methodologies and definitions can be found here.

The data includes the overall numbers for the UK as a whole, the numbers for each of the devolved UK nations (Eng, Sco, Wal & NI), English Regions and Upper Tier Local Authorities (UTLA) for all of the UK (what we call Boroughs). I have also included a small table with the populations of the 4 devolved UK nations, used to calculate the death rates per 100,000 population.

As I've said for before - I am not an Epidemiologist, Sociologist or even a Data Scientist. I am actually a Mechanical Engineer! The objective here is to improve my data science skills and maybe provide some useful data to the wider community.

Any questions, comments or suggestions are most welcome! I am open to requests and collaborations! Stay Safe!

Age-standardised mortality rates (ASMRs) for deaths involving COVID-19 by ethnic group, England.

This dataset contains daily data trackers for the COVID-19 pandemic, aggregated by month and starting 18.3.20. The first release of COVID-19 data on this platform was on 1.6.20. Updates have been provided on a quarterly basis throughout 2023/24. No updates are currently scheduled for 2024/25 as case rates remain low. The data is accurate as at 8.00 a.m. on 8.4.24. Some narrative for the data covering the latest period is provided here below: Diagnosed cases / episodes • As at 3.4.24 CYC residents have had a total 75,556 covid episodes since the start of the pandemic, a rate of 37,465 per 100,000 of population (using 2021 Mid-Year Population estimates). The cumulative rate in York is similar to the national (37,305) and regional (37,059) averages. • The latest rate of new Covid cases per 100,000 of population for the period 28.3.24 to 3.4.24 in York was 1.49 (3 cases). The national and regional averages at this date were 1.67 and 2.19 respectively (using data published on Gov.uk on 5.4.24).

Context

Public Health England (PHE) coronavirus cases reported daily. This data shows case numbers as reported to PHE. Cases includes people who have recovered.

Content

DateVal : dd/mm/yyyy CMODateCount : The number of cases reported for the day CumCases: The cumulative number of cases IncreasePercent: The percentage increase in cases from the previous day DeathPercent: The percentage increase/decrease in daily deaths from the previous day CumCases7DayAvg: 7 day moving average of the cumulative number of cases CumDeaths7DayAvg: 7 day moving average of the cumulative number of deaths DailyDeath7DayAvg: 7 day moving average of the daily number of deaths

IncreasePercent and moving 7 day averages are calculated fields added to the original source.

Acknowledgements

https://www.gov.uk/government/publications/covid-19-track-coronavirus-cases https://coronavirus.data.gov.uk/

COVID-19 is a infectious Disease which has infected more than 500 people in UK and many more people world-wide.

Acknowledgements Sincere thanks to Public Health England and Local governments. Source of Data: UK Government and Public Health UK

****Notes on the methodology**** This service shows case numbers as reported to Public Health England (PHE), matched to Administrative Geography Codes from the Office of National Statistics. Cases include people who have recovered.

Events are time-stamped on the date that PHE was informed of the new case or death.

The map shows circles that grow or shrink in line with the number of cases in that geographic area.

Data from Scotland, Wales and Northern Ireland is represented on the charts, total indicators and on the country level map layer.

Contains Ordnance Survey data © Crown copyright and database right 2020. Contains National Statistics data © Crown copyright and database right 2020.

Terms of Use No special restrictions or limitations on using the item’s content have been provided.

Following a trial run and official release on the 24th of September 2020, the NHS COVID-19 app has been downloaded more than 29 million times in England and Wales, as of December 2021. Developed to complement the NHS Test & Trace in England and the Test, Trace and Protect program in Wales, the app is aimed at increasing the speed and accuracy of contact tracing, and includes features such as local area alerts and venue check-in.

NHS COVID-19 app usage Between the beginning of June 2021 and the end of July 2021, the number of COVID-19 cases in the United Kingdom started rising again, reaching the peak of 54,674 on the 21st of July. In the previous week, it was reported that more than 600 thousand users of the NHS COVID-19 app in England and Wales had received a self-isolation alert or “ping,” causing what has been since renamed by the media as a “pingdemic.” The NHS COVID-19 app, which works using Bluetooth technology, registers the devices that the users have been in proximity of, and is programmed to send alerts to all the traced contacts in case the app users test positive for coronavirus. While the app’s tracing measurements are currently being reviewed to decrease the number of alerts sent, two in 10 users have reported switching off the app’s contact tracing function. Moreover, according to a survey of online users in Great Britain, only 22 percent of the online users who have the app are using it correctly, while one in ten reported deleting the app altogether.

Travel health pass and COVID-19 apps In 2021, the rolling out of vaccination plans worldwide prompted health institutions and travel companies to start releasing new apps or updating their current ones to function as health passports. With close to 5,7 million downloads in the first half of 2021, the NHS app was the most downloaded app used to show digital certifications. The CovPass app, which is available to residents in Germany, followed with more than 5.56 million downloads as of the second quarter of 2021. According to a February survey of travelers worldwide, the main concerns over the use of digital health passports related to security risks over personal data being hacked and privacy protection.

Background

This Sqlite database contains data publicly available from GOV.UK and can be found here: https://coronavirus.data.gov.uk/. The data is available via a REST API and come data is available in CSV format. However, it can be difficult to pull all this data together, so this Sqlite database contains a number of tables which includes all the data imported via the API.

How was this data generated?

For more information on how to generate this database, and extract and load the data using the REST API, you can use the additional Jupyter Notebooks which can be found in the following Git Repo: https://github.com/happyadam73/c19-notebooks

Currently this data runs up to 25 February 2022.

NOTE: As of 31st January 2022, publish date based cases include all episodes but historic data has not been updated. It is recommended for historical analysis to use specimen date cases. For more details, see: https://coronavirus.data.gov.uk/details/whats-new/record/beb802ac-1ed2-47ac-b314-69a5c3f712b5

Data Dictionary

The following provides a list of all 9 tables and the columns that can be found in each table.

In early-February, 2020, the first cases of the coronavirus (COVID-19) were reported in the United Kingdom (UK). The number of cases in the UK has since risen to 24,243,393, with 1,062 new cases reported on January 13, 2023. The highest daily figure since the beginning of the pandemic was on January 6, 2022 at 275,646 cases.

COVID deaths in the UK COVID-19 has so far been responsible for 202,157 deaths in the UK as of January 13, 2023, and the UK has one of the highest death toll from COVID-19 in Europe. As of January 13, the incidence of deaths in the UK is 298 per 100,000 population.

Regional breakdown The South East has the highest amount of cases in the country with 3,123,050 confirmed cases as of January 11. London and the North West have 2,912,859 and 2,580,090 cases respectively.

For further information about the coronavirus (COVID-19) pandemic, please visit our dedicated Facts and Figures page.

Context

• Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus SARS-CoV2.
• Person to person transmission occurs via several different modes, mainly when people are in close proximity to one another through respiratory droplets.
• Mitigations by various countries have been put into place to limit the spread of this virus.

Content

• ConfirmedCasesByDateReported.csv
• ConfirmedCasesBySpecimenDate.csv
• Deaths.csv
• PatientNewAdmissions.csv
• PatientsInHospital.csv
• PatientsMVBeds.csv
• PCRTesting.csv
• Vaccinations.csv
• VaccinationsDaily.csv

Acknowledgements and Collection Methodology

Data downloaded from https://coronavirus.data.gov.uk

Version

• Version 11 - 25 - Various Files Updated.
• Version 10 - Added VaccinationsDaily File, data upto and including the 20th Jan 2021.
• Version 9 - Updated Deaths file, data upto and including the 20th Jan 2021.
• Version 8 - Updated ConfirmedCasesByDateReported and ConfirmedCasesBySpecimenDate files, data upto and including the 17th to 19th Jan 2021 respectively.
• Version 7 - Updated PatientNewAdmissions, PatientsInHospital and PatientsMVBeds files, data upto and including the 12th to 15th Jan 2020 depending on file.
• Version 6 - Updated PCR Testing file, data upto and including the 14th Jan 2021.
• Version 4 - Updated Vaccinations file, data upto and including the 3rd Jan 2021.
• Version 3 - Updated to include data unto and including the 28th December 2020. Additionally added data on the progress of Vaccinations.
• Version 2 - Updated to include data unto and including the 3rd November 2020.

The COVID-19 dashboard includes data on city/town COVID-19 activity, confirmed and probable cases of COVID-19, confirmed and probable deaths related to COVID-19, and the demographic characteristics of cases and deaths.