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Deeply-phenotyped hospital COVID patients: severity, acuity, therapies, outcomes

Dataset
Version: 1.0.0
Hospital COVID patients (6th Jan 2020 onwards). Granular severity, ethnicity, co-morbidity. Serial physiology, blood biomarkers, images, treatments, ITU, outcome, pre/post admission healthcare use. Deeply phenotyped, longitudinal. Waves 1/ 2

Summary

Citation:
Deeply-phenotyped hospital COVID patients: severity, acuity, therapies, outcomes

Documentation

Description:
PIONEER: Deeply-phenotyped hospital COVID patients: severity, acuity, therapies, outcomes Dataset number 4.0 Coronavirus disease 2019 (COVID-19) was identified in January 2020. Currently, there have been more than 6 million cases& more than 1.5 million deaths worldwide. Some individuals experience severe manifestations of infection, including viral pneumonia, adult respiratory distress syndrome (ARDS)& death. There is a pressing need for tools to stratify patients, to identify those at greatest risk. Acuity scores are composite scores which help identify patients who are more unwell to support & prioritise clinical care. There are no validated acuity scores for COVID-19 & it is unclear whether standard tools are accurate enough to provide this support. This secondary care COVID dataset contains granular demographic, morbidity, serial acuity and outcome data to inform risk prediction tools in COVID-19. PIONEER geography The West Midlands (WM) has a population of 5.9 million & includes a diverse ethnic & socio-economic mix. There is a higher than average percentage of minority ethnic groups. WM has a large number of elderly residents but is the youngest population in the UK. Each day >100,000 people are treated in hospital, see their GP or are cared for by the NHS. The West Midlands was one of the hardest hit regions for COVID admissions in both wave 1 & 2. EHR. University Hospitals Birmingham NHS Foundation Trust (UHB) is one of the largest NHS Trusts in England, providing direct acute services & specialist care across four hospital sites, with 2.2 million patient episodes per year, 2750 beds & 100 ITU beds. UHB runs a fully electronic healthcare record (EHR) (PICS; Birmingham Systems), a shared primary & secondary care record (Your Care Connected) & a patient portal “My Health”. UHB has cared for >5000 COVID admissions to date. Scope: All COVID swab confirmed hospitalised patients to UHB from January – May 2020. The dataset includes highly granular patient demographics & co-morbidities taken from ICD-10 & SNOMED-CT codes but also primary care records& clinic letters. Serial, structured data pertaining to care process (timings, staff grades, specialty review, wards), presenting complaint, acuity, all physiology readings (pulse, blood pressure, respiratory rate, oxygen saturations), all blood results, microbiology, all prescribed & administered treatments (fluids, antibiotics, inotropes, vasopressors, organ support), all outcomes. Linked images available (radiographs, CT, MRI, ultrasound). Available supplementary data: Health data preceding & following admission event. Matched “non-COVID” controls; ambulance, 111, 999 data, synthetic data. Available supplementary support: Analytics, Model build, validation & refinement; A.I.; Data partner support for ETL (extract, transform & load) process, Clinical expertise, Patient & end-user access, Purchaser access, Regulatory requirements, Data-driven trials, “fast screen” services.
Is Part Of:
NOT APPLICABLE

Coverage

Spatial:
United Kingdom, England, West Midlands
Typical Age Range:
0-100
Follow Up:
OTHER
Physical Sample Availability:
NOT AVAILABLE
Pathway:
Data focuses on in-patient stay in hospital during the acute episode but can be supplemented on request to include previous and subsequent hospital contacts (including outpatient appointments) and ambulance, 111, 999 data. A matched non-COVID control population can be generated upon request.

Provenance

Origin

Purposes:
CARE
Sources:
EPR
Collection Situations:
  • ACCIDENT AND EMERGENCY
  • IN-PATIENTS

Temporal

Accrual Periodicity:
QUARTERLY
Distribution Release Date:
2020-10-20
Start Date:
2018-01-01
End Date:
2020-11-03
Time Lag:
LESS 1 WEEK

Accessibility

Access

Access Service:
Trusted Research Environments (TRE) are built using Microsoft Azure services and hosted in the UK to provide research teams a safe, secure and agile environment which allows users to quickly analyse, interpret and form an enriched view of primary care information through a range of integrated datasets. Health data collated from multiple sources is ingested into a secure data lake which will then allow subsets of data to be made available to research teams on approval of a data request. Once approved a customer specific TRE is made available with a standard set of leading analytical tools from Microsoft including Azure Databricks, Azure Machine Learning, Azure SQL and Azure Synapse (for large-scale data warehouses). Specific tools can be provided at an additional cost over the standard platform data access charge and the PIONEER team will work with you to determine your exact needs. Access to the TRE is managed using the latest virtual desktop technology to provide a safe and secure end-user experience. By utilising leading edge design PIONEER are able to create TREs rapidly to enable us to service any customer requirement.
Access Request Cost:
www.pioneerdatahub.co.uk/data/data-services-costs/
Delivery Lead Time:
1-2 MONTHS
Jurisdictions:
GB
Data Controller:
University Hospitals Birmingham NHS Foundation Trust
Data Processor:
NOT APPLICABLE

Usage

Data Use Limitations:
RESEARCH USE ONLY
Data Use Requirements:
PROJECT SPECIFIC RESTRICTIONS
Resource Creators:
  • This publication uses data from PIONEER
  • an ethically approved database and analytical environment (East Midlands Derby Research Ethics 20/EM/0158)
Is Referenced By:
Sapey, E., Gallier, S., Mainey, C., Nightingale, P., McNulty, D., Crothers, H., Evison, F., Reeves, K., Pagano, D., Denniston, A. K., Nirantharakumar, K., Diggle, P., Ball, S., & All clinicians and students at University Hospitals Birmingham NHS Foundation Trust (2020). Ethnicity and risk of death in patients hospitalised for COVID-19 infection in the UK: an observational cohort study in an urban catchment area. BMJ open respiratory research, 7(1), e000644. https://doi.org/10.1136/bmjresp-2020-000644

Format and Standards

Vocabulary Encoding Schemes:
SNOMED CT
Conforms To:
LOCAL
Languages:
en
Formats:
SQL

Observations

Statistical Population
Population Description
Population Size
Measured Property
Observation Date
Events
Currently 5943 covid positive patients
5943
Count
2020-11-03