COVID-19 Cases in England

Tracking Infection Risk at a Local Level

By Dan Winchester [source]

About this dataset

This dataset contains the total number of confirmed COVID-19 cases in each English Upper Tier Local Authority over the past eight days. Aggregated from Public Health England data, this dataset provides unprecedented insight into how quickly the virus has been able to spread in local communities throughout England. Despite testing limitations, understanding these localized patterns of infection can help inform important public health decisions by local authorities and healthcare workers alike.

It is essential to bear in mind that this data is likely an underestimation of true infection rates due to limited testing -- it is critical not to underestimate the risk the virus poses on a local scale! Use this dataset at your own discretion with caution and care; consider supplementing it with other health and socio-economic metrics for a holistic picture of regional trends over time.

This dataset features information surrounding GSS codes and names as well as total numbers of recorded COVID-19 cases per English Upper Tier Local Authority on January 5th 2023 (TotalCases_2023-01-05)

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Research Ideas

• Comparing the total cases in each local authority to population density of the region, to identify areas with higher incidence of virus
• Tracking changes in total cases over a period of time to monitor trend shifts and detect possible outbreak hotspots
• Establishing correlations between the spread of COVID-19 and other non-coronavirus related health issues, such as mental health or cardiovascular risk factors

Acknowledgements

If you use this dataset in your research, please credit the original authors. Data Source

License

License: Dataset copyright by authors - You are free to: - Share - copy and redistribute the material in any medium or format for any purpose, even commercially. - Adapt - remix, transform, and build upon the material for any purpose, even commercially. - You must: - Give appropriate credit - Provide a link to the license, and indicate if changes were made. - ShareAlike - You must distribute your contributions under the same license as the original. - Keep intact - all notices that refer to this license, including copyright notices.

Columns

File: utla_by_day.csv | Column name | Description | |:--------------------------|:------------------------------------------------------------------------------------------------------| | GSS_CD | Government Statistical Service code for the local authority. (String) | | GSS_NM | Name of the local authority. (String) | | TotalCases_2023-01-05 | Total number of confirmed COVID-19 cases in the local authority on the 5th of January 2023. (Integer) |

Acknowledgements

If you use this dataset in your research, please credit the original authors. If you use this dataset in your research, please credit Dan Winchester.

Provisional age-standardised mortality rates for deaths due to COVID-19 by sex, local authority and deprivation indices, and numbers of deaths by middle-layer super output area.

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/

Provisional counts of the number of deaths registered in England and Wales, including deaths involving coronavirus (COVID-19), by local authority, health board and place of death in the latest weeks for which data are available. The occurrence tabs in the 2021 edition of this dataset were updated for the last time on 25 October 2022.

A lookup file between 2019 Local Authority Districts to 2020 Covid Infection Survey Geography in the United Kingdom, as at 1 October 2020. (File size - 48KB) Field Names - LAD19CD, LAD19NM, CIS20CD, FIDField Types - Text, Text, Text, NumericField Lengths - 9, 35, 9FID = The FID, or Feature ID is created by the publication process when the names and codes / lookup products are published to the Open Geography portal.

A lookup file between 2018 Local Authority Districts to 2020 Covid Infection Survey Geography in the United Kingdom, as at 1 October 2020. (File size - 48KB) Field Names - LAD18CD, LAD18NM, LAD18NMW, CIS20CD, FIDField Types - Text, Text, Text, Text, NumericField Lengths - 9, 28, 28, 9FID = The FID, or Feature ID is created by the publication process when the names and codes / lookup products are published to the Open Geography portal. REST URL of Feature Access Service – https://services1.arcgis.com/ESMARspQHYMw9BZ9/arcgis/rest/services/LAD18_CIS20_EN_LU_v1_5fbc82fc73e6407facd67a1c5e4cc043/FeatureServer

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 hospitals in England and had tested positive for COVID-19, and from 25 April, the number of patients where COVID-19 is mentioned on the death certificate and no positive COVID-19 test result was received. Figures are updated each day at 2pm with deaths reported up to 5pm the previous day. There is a delay between the occurrence of a death to it being captured in the daily reporting. The data can be presented both as reported deaths by day and death occurrences by day. Reported occurrences for recent days should be considered incomplete as likely to be revised upwards as more data becomes available. The location of a death reflects the location of the hospital in which it occurred. Source: NHS England COVID-19 Daily Deaths The Office for National Statistics publishes deaths for England and Wales by the week in which they were registered. Due to the delay between the occurrence of a death and its registration, many deaths that occur in a given week will appear in the data for a subsequent week. For 2018, ONS estimated that 74% of deaths were registered within seven days. Additional delays in registration can occur over public holidays, with significant changes in numbers being observable over Easter and Christmas. The location of a death reflects the usual residence of the deceased. There are some differences in total numbers reported for different geographical levels. The figures published at the local authority level have been used in this analysis. The data is updated each Tuesday at 9.30am with data for the week ending eleven days prior. For the 2020 series, ONS has included the number of deaths where coronavirus (COVID-19) was mentioned on the death certificate. This data includes deaths for all places of occurrence. The ONS started publishing deaths in care homes notified to the Care Quality Commission on 28th April for local authorities in England by date of notification. This data includes an additional week of data compared to the main ONS publication. Source: Deaths registered weekly in England and Wales, provisional, Death registrations and occurrences by local authority, Deaths in care homes notified to the Care Quality Commission, report

A lookup file between 2020 Local Authority Districts to 2020 Covid Infection Survey Geography in the United Kingdom, as at 1 October 2020. (File size - 48KB) Field Names - LAD20CD, LAD20NM, CIS20CD, FIDField Types - Text, Text, TextField Lengths - 9, 35, 9FID = The FID, or Feature ID is created by the publication process when the names and codes / lookup products are published to the Open Geography portal. REST URL of Feature Access Service – https://services1.arcgis.com/ESMARspQHYMw9BZ9/arcgis/rest/services/LAD20_CIS20_EN_LU_74a7328e2663450184425b3e9012a565/FeatureServer

A lookup file between Local Authority District (2019) to 2020 Covid Infection Survey Geography in Great Britain, as at 1 October 2020. (File size - 64KB) Field Names - LAD19CD, LAD19NM, LAD19NMW, CIS20CD, FIDField Types - Text, Text, Text, Text, NumericField Lengths - 9, 35, 24, 9FID = The FID, or Feature ID is created by the publication process when the names and codes / lookup products are published to the Open Geography portal. REST URL of Feature Access Service – https://services1.arcgis.com/ESMARspQHYMw9BZ9/arcgis/rest/services/LAD19_CIS20_GB_LU_ed5b75bc28e24b5d81b393cba28c48d3/FeatureServer

The Office for Health Improvement and Disparities (OHID) has updated the mortality profile.

The profile brings together a selection of mortality indicators, including from other OHID data tools such as the https://fingertips.phe.org.uk/profile/public-health-outcomes-framework/data">Public Health Outcomes Framework, making it easier to assess outcomes across a range of causes of death.

For the January 2022 update, 2 new indicators have been added to the profile:

• mortality rate for deaths involving COVID-19, all ages
• mortality rate for deaths involving COVID-19, under 75s

COVID-19 was the leading cause of death in England in 2020, but the pandemic had a much greater impact on mortality in some areas than others. These indicators have been included alongside other indicators for leading causes of death in the mortality profile to provide a more complete picture of mortality for local areas in 2020.

If you would like to send us feedback on the tool please contact profilefeedback@phe.gov.uk.

Childhood Vaccination Coverage Statistics- England 2017-18 [NS] The information in this bulletin about immunisation statistics in England comes from Public Health England (PHE). Information on childhood vaccination coverage at ages 1, 2 and 5 years is collected through the Cover of Vaccination Evaluated Rapidly (COVER) data collection for Upper Tier Local Authorities (LAs). Information on children aged 2 and 3 vaccinated against seasonal flu are collected from GPs through PHE's ImmForm system.

The number of deaths registered in England and Wales due to and involving coronavirus (COVID-19). Breakdowns include age, sex, region, local authority, Middle-layer Super Output Area (MSOA), indices of deprivation and place of death. Includes age-specific and age-standardised mortality rates.

Deaths from infectious and parasitic disease . Directly age-Standardised Rates (DSR) per 100,000 population Source: Office for National Statistics (ONS) Publisher: Information Centre (IC) - Clinical and Health Outcomes Knowledge Base Geographies: Local Authority District (LAD), Government Office Region (GOR), National, Strategic Health Authority (SHA) Geographic coverage: England Time coverage: 2005-07, 2007 Type of data: Administrative data

Laboratory confirmed cases of MRSA bacteraemia. Community-onset cases are all those that are not hospital-onset cases. Hospital-onset is determined by patient location, date of admission, date of specimen, and patient category. Hospital onset is only indicative for cases where NHS patient specimens are taken on the third day of admission onwards (e.g., day three when day one equals the day of admission) at an acute trust (including cases with unspecified specimen location) for inpatients, day patients, emergency assessment, or unspecified patient category. Records with a missing admission date (where the specimen location is acute trust or missing and the patient category is inpatient, day patient, emergency assessment, or unspecified) are also included. Other cases may have hospital onset, but not in acute trusts.

Data is available by Sub ICB (Integrated Care Board) location.

Rationale A long-running voluntary surveillance scheme of laboratory-reported cases of Staphylococcus aureus bacteraemia showed increasing incidence of meticillin-resistant S. aureus (MRSA) infections in England, Wales, and Northern Ireland in the 1990s. This generated both media and public interest. In response, the Department of Health (DH) in England introduced a mandatory surveillance scheme for S. aureus bacteraemias in April 2001, which included data on the number of cases that were due to MRSA. In October 2005, the mandatory surveillance scheme for MRSA bacteraemias was enhanced to collect patient-level data. Additionally, all NHS organisations reporting cases of MRSA bacteraemia from 1 April 2013 were required to complete a Post Infection Review (PIR). This process was commenced to support the delivery of zero tolerance on MRSA bacteraemia, as set out by NHS England in the Planning Guidance Everyone counts: Planning for Patients 2013/14. A PIR is undertaken after all MRSA bacteraemias with the purpose of identifying how a case occurred, to identify actions by local healthcare teams which will prevent a reoccurrence, and to identify the organisation best placed to ensure improvements are made (this is known as “assigning” a case to an organisation). From 1 April 2018, the PIR process changed from being applied by all trusts to trusts identified as having high rates of MRSA. For more information, please see MRSA Guidance: Post Infection Review. A low value is indicative of a low rate of MRSA.

Source of numerator UK Health Security Agency (UKHSA), Healthcare Associated Infection Data Capture System (HCAI DCS) Mandatory Surveillance

Source of denominator Office for National Statistics (ONS), Mid-year population estimates

Caveats These data do not provide a basis for decisions on the clinical effectiveness of infection control interventions in individual Trusts: further investigations considering potential confounders would need to be undertaken before this could be done.

Nor do these data provide a basis for comparisons between acute Trust or SICBLs. Rate information, using rate calculations as currently defined, is not appropriate for comparison. The counts of infections have not been adjusted to give a standardised rate considering factors such as organisational demographics or case mix. Rate information is of use for comparison of an individual organisation over time.

‘All reported cases’ refers to all MRSA-positive blood cultures reported by the Trust whose laboratory processes the specimen. It is important to note that this does not necessarily imply that the infection was acquired there.

Confidence intervals for rates are not currently calculated because appropriate methods for comprehensive coverage are being assessed.

Cases that the UKHSA’s HCAI Data Capture System attributes to a commissioning hub (such as the national commissioning hub, 13Q, or one of the regional Health & Justice commissioning hubs) are not featured in sub ICB Location dashboards but they do still contribute to the highest spatial level—the England national total. This means the England case total & rates may be slightly higher than the sum of all sub ICB Location cases & rates.

IMPORTANT NOTE: SICBL calculations for the period between January 2021 and January 2022 have been based on SICBL boundaries. As such some SICBLs may experience higher or lower rates than expected due to this change. Those SICBLs affected are; Bassetlaw, Glossop, East Leicestershire and Rutland, Lincolnshire, Cambridgeshire and Peterborough, Birmingham and Solihull, Black Country and West Birmingham and Oundle.

Initial estimates of prevalence of ongoing symptoms following coronavirus (COVID-19) infection in staff and pupils from the COVID-19 Schools Infection Survey across a sample of schools, within selected local authority areas in England. This Schools Infection Survey is jointly led by the London School of Hygiene & Tropical Medicine, Public Health England and the Office for National Statistics.

Laboratory-confirmed cases of Staphylococcus aureus bacteraemia detected by blood culture confirmed resistant to any of:

Meticillin Oxacillin Cefoxitin Flucloxacillin

Rationale In January 2011 the enhanced patient-level mandatory surveillance scheme was extended to include meticillin susceptible S. aureus (MSSA) bacteraemia due to both the high national total of MSSA bacteraemias, and the observation that the strides in reducing MRSA bacteraemias had not also been seen among MSSA. It was noted that at a more local level, some organisations had reported reductions in MSSA bacteraemias and including MSSA bacteraemia in the enhanced surveillance scheme may provide details on how these reductions had been achieved, in order to replicate them elsewhere.A low value is indicative of a low count of MSSA.

Definition of numerator All cases of MSSA meeting the 'Definition' section above occurring for the past 11 months are summed with the current month to give a rolling 12-month total. For the calculation of rates, the past 11 months are summed with the current month and the denominator is the sum of the bed-days (for trusts) or population (for SICBLs) for the current month and preceding 11 months.

The rate for a month is then calculated by dividing the numerator by the denominator and multiplying by 100,000 to give a manageable value.

Definition of denominator Denominator values are calculated as an annual rolling sum. For any given month, the denominator includes the value for the defined geography in the given month and the 11 preceding months.

Caveats These data do not provide a basis for decisions on the clinical effectiveness of infection control interventions in individual Trusts: further investigations considering potential confounders would need to be undertaken before this could be done. Nor do these data provide a basis for comparisons between acute Trust or SICBLs. Rate information, using rate calculations as currently defined, is not appropriate for comparison. The counts of infections have not been adjusted to give a standardised rate considering factors such as organisational demographics or case mix. Rate information is of use for comparison of an individual organisation over time. ‘All reported cases’ refers to all MSSA-positive blood cultures reported by the Trust whose laboratory processes the specimen. It is important to note that this does not necessarily imply that the infection was acquired there. Cases that the UKHSA's HCAI Data Capture System attributes to a commissioning hub (such as the national commissioning hub, 13Q, or one of the regional Health & Justice commissioning hubs) are not featured in sub ICB Location dashboards but they do still contribute to the highest spatial level—the England national total. This means the England case total may be slightly higher than the sum of all sub ICB Location cases.