Public Health Wales NHS Trust: Government against COVID-19 ^{Funding Support}

Entity: Public Health Wales NHS Trust

Category: Funding support

Description: Public Health Wales NHS Trust (PHW) is the national public health authority for Wales. PHW works to protect and improve health and well-being and reduce health inequalities for the people of Wales. PHW is leading the national response to COVID-19 in Wales. PHW operates diagnostic laboratories across Wales and has been providing SARS-COV-2 testing in Wales. In addition, PHW epidemiology teams have been providing support across Wales to track cases and support management of the outbreak. Sequencing of Welsh samples is being undertaken by the Pathogen Genomics Unit (PenGU). PenGU was formally launched in 2018, and provides an accredited sequencing environment for a range of clinical pathogen genomics services for the whole of Wales. The Pathogen Genomics team in Public Health Wales will be contributing to COG-UK by sequencing and analysing Welsh SARS-COV-2 cases. Data that is being generated is being fed back in real time to clinical colleagues across the NHS in Wales as well as feeding into outbreak management and planning within the Welsh NHS and Welsh Government. In addition to sequencing samples, the team are providing bioinformatics support to build production-ready pipelines for processing samples, supporting the development of systems on CLIMB for consortium use and leading efforts to enable metadata sharing across the UK.

1. Project: 'COVID-19 Genomics UK (COG-UK) Consortium'
Public Health Wales NHS Trust is Parner of the 'COVID-19 Genomics UK (COG-UK) Consortium' as reasearcher of Public Health Scotland

'COVID-19 Genomics UK (COG-UK) Consortium' is a collaboration between the NHS, Public Health England and other UK public health agencies, the Wellcome Sanger Institute, University of Cambridge and other academic institutions.

2. Project: COVID-19 Genomics UK (COG-UK) Consortium
Research Group: Cardiovascular Epidemiology Unit
Project Description: The COVID-19 Genomics UK (COG-UK) Consortium aims to increase the current capacity for SARS-CoV-2 genetic sequencing in the UK. This sequencing data will be used to understand the epidemiology and spread of the virus, and to monitor and evaluate interventions for COVID-19. SARS-CoV-2 genomic data will be integrated with NHS electronic health records and other existing genomic data to generate insights into susceptibility to COVID-19. From within the DPHPC, Professor John Danesh is a member of the COG-UK Steering Group, Dr Ewan Harrison will serve as the Scientific Project Manager and Dr Michael Chapman will lead the health informatics component.

Contributors:
Dr Sally Corden, Pathogen Genomics Unit lead
Dr Thomas Connor, Consultant Bioinformatician/Bioinformatics lead for Pathogen Genomics
Dr Catherine Moore, Consultant Clinical Scientist, Wales Specialist Virology Centre
Dr Simon Cottrell, Principle Epidemiologist, Communicable and Vaccine Preventable Diseases
Joanne Watkins, Laboratory Senior, Pathogen Genomics Unit
Dr Matt Bull, Senior Bioinformaticain, PHW Pathogen Bioinformatics
Dr Sara Rey, Bioinformatician, PHW Pathogen Bioinformatics
PHW Pathogen Genomics laboratory and Bioinformatics teams

+ Beneficiaries
. Cardiovascular Epidemiology Unit
. COVID-19 Genomics UK (COG-UK) Consortium

3. Programme Title: Call for COVID-19 rapid response data science taskforce (DECOVID)
Summary: Most of what we currently know of COVID-19 comes from data about its outbreak in China and Italy, but there may be differences in presentation and course within the multi-ethnic communities of the UK which have not been described thus far. Within the UK, high level mapping is being captured by Public Health England, but there is a lack of in-depth and granular data capture. This in-depth data is needed to inform prognostic prediction tools, enable effective clinical care or model the ongoing and likely future impact of COVID-19.

DECOVID is an emerging research collaboration between The Alan Turing Institute, NHS Trusts, HDR UK and other academic partners. This collaboration aims to use near real-time health data as the Covid-19 pandemic unfolds to allow researchers and clinicians to identify factors and generate insights that can lead to more effective clinical treatment strategies. DECOVID will be affiliated to PIONEER - the Health Data Research Hub for Acute Care. This is a rapid response call for teams of researchers as well as individual researchers to join collaboration in addressing these urgent questions. Teams will rapidly trial tested, robust and reproducible data science and machine learning methods on this new national data resource of COVID 19 data, to create a near real-time, human-in-the-loop analytics platform and information console to support acute care management and clinical decision making. DECOVID has been structured to be nationally scalable.