HDR UK - Resources for 🦠 Coronavirus (COVID-19) Research

HDR UK COVID-19 Response Webpage

United Kingdom

NHS

• NHS DIgital ICD-10 Classification Guidelines
  • NHS-D SNOMED-CT COVID-19 Terms
• NHS Digital - Data and Services to support the management of Coronavirus
  • NHS 11 Data and Dashboard Direct Link to dataset
• Health Research Agency - Guidance for sponsors, sites and research
• NHSX Data Platform Blog Post

Professional Record Standards Body

• PRSB COVID-19 Guidance
  • Direct Link to SNOMED-CT COVID-19 terms

ICO

• ICO Guidance on Data protection and Coronavirus

National Institute for Health research

• NIHR Response

UK Research and Innovation

• UKRI call for proposals

󠁧󠁢󠁥󠁮󠁧󠁿 England - Public Health England - Covid-19 Tracker

• ArcGIS Tracker
  • Track Coronavirus (Desktop)
  • Track Coronavirus (Mobile)
• Latest Data Extracts
  • Daily Indicators - Excel XLSX
  • Daily Confirmed Cases - Excel XLSX
  • NHS England Regions Case Table - Excel XLSX
  • Upper Tier Local Authority Cases Table - CSV
  • UK Countries Cases - Shapefile
• Community Repositories
  • Google Sheets - Author: Unknown
  • github.com/emmadoughty/Daily_COVID-19 - Author: Emma Doughty - University of Birmingham
  • github.com/tomwhite/covid-19-uk-data - Author: Tom White
  • COVID-19 Phenomics - Author: Spiros Denaxas
  • King's College London COVID-19 Tracker
  • c19track.com Community & Household Tracker

Northern Ireland - Public Health Agency COVID-19 Information

󠁧󠁢󠁳󠁣󠁴󠁿 Scotland - Scotish Government COVID-19 Information

󠁧󠁢󠁷󠁬󠁳󠁿 Wales - Welsh Government COVID-19 Information

Government Groups

• Scientific Advisory Group for Emergencies
  • SAGE: Coronavirus (COVID-19) response
• Scientific Pandemic Influenza Modelling Group (SPI-M)
  • SPI-M Modelling Summary Report [Last Updated: 16 Nov 2018]
• New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG)
• Independent Scientific Pandemic Influenza Group on Behaviours (SPI-B)

Datasets

• BSTI COVID-19 Imaging Database

Modelling

• LSHTM - Centre for the Mathematical Modelling of Infectious Diseases
  • CMMID COVID-19 UK Control Measures Model
• Estimating the number of infections and the impact of nonpharmaceutical interventions on COVID-19 in 11 European countries
  • COVID-19 Model Source Code

BioBanking

• UKCRC Tissue Directory and Coordination Centre - COVID-19 Response

Training

• LSHTM - COVID-19: Tackling the Novel Coronavirus - Starts 23 March 2020

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🇪🇺 Europe

• European Centre for Disease Prevention and Control
  • Geographic Distribution of COVID-19 Cases Worldwide
• European Medicines Agency
  • Call to pool research resources into large multi-centre, multi-arm clinical trials to generate sound evidence on COVID-19 treatments
• European Virus Archive - Cronoavirus
• European Clinical Trials Register - COVID-19

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Worldwide

🇺🇳 World Health Organisation

• WHO - A coordinated Global Research Roadmap
• COVID-19 Case Definition
• Daily Situation Reports
• Global Database of Scientific Findings
• Eric Brown's WHO curated Dataset for R
• Online Training
• Infection Prevention and Control for Coronavirus

Red Cross

• Red Cross Covid-19 Vulnerability Index This prototype highlights vulnerability for wards in England by combining clinical factors (some of the underlying health conditions) with social factors (a bespoke COVID-19 index of multiple deprivation, along with community needs).
  • Source Code / More info and underlying code/data: britishredcrosssociety/covid-19-vulnerability

United States of America

• NYTimes Coronavirus (Covid-19) Data in the United States
• Rensselaer Polytechnic Institute - IDEA: COVID-19 Data, Resources & Challenges
• JHU CSSE Covid Dataset
  • JHU AWS Marketplace Subscription by Enigma
• Allen Institute for AI: COVID Open Research Dataset (CORD-19) - Publications
• MIDAS Novel Coronavirus Repository
• Scientist.com Clinical Trial Search and Discovery
• Kaggle Corona Virus 2019 Dataset

Spain

• Juanta de Castilla y Leon Coronovirus Tracker

France

• Corsica Coronavirus Tracker

Canada

• COVID-Net

Jordan

• Jordan Corona Virus Tracker

Research Data Alliance

• COVID-19 Working Group

Google COVID-19 Mobility Reports

• United Kingdom

Our World In Data

• Total Confirmed Cases
• Total Deaths
• New Confirmed Cases
• New Deaths
• Full Dataset

Visulaisations

• NextStrain NCOV
• JHU CSSE COVID-19 Tracker
  • Source Code
• Tableu COVID-19 Data Rosource Hub

Technology Providers

• AIMES COVID-19 update
• Interactive Software COVID-19 update
• COVID-19 High Performance Computing Consortium

Community Repositories

• github.com/ieee8023/covid-chestxray-dataset - Author: Joseph Paul Cohen
• Tweet ID dataset associated with Coronavirus

Knowledge Bases

• Golden COVID-19
• Knowledge Graph Hub - COVID-19
• WikiData COVID-19

Nucleotide sequences, SRA sequences, Reference Genome

• GISAID has the most complete sequence data collection of SARS-CoV-2. [Restricted Access]
• NCBI Reference Sequence Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome
• NCBI COVID-19 SRA Raw Sequencing Data
• NCBI Genbank Sequences SARS-CoV-2
• GenBank Sequence Data
• ENA Pathogens COVID-19
• SRP250294 Illumina & Oxford Nanopore data of depleted host seqiences and other contaminating sequences
• CNCB raw data downloads in coronaviridae
  • Wuhan Seafood Market Pneumonia Virus - ftp://download.big.ac.cn/Genome/Viruses/Wuhan_seafood_market_pneumonia_virus/
  • Coronaviridae Genome - ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/genome/
• ZB MED COVID-19 Hub
• Critical Assesment of Structural Prediction (CASP) COVID-19 Proteome
• CSC SARS CoV2 Sequensing Resources

Metadata Standards

• WHO Emergency Use ICD Codes for COVID-19
• SNOMED-CT COVID-19 Terms
• Schema.org > CovidTestingFacility

Clinical Trials

• International Clinical Trials Registry Platform
• ClinicalTrials.gov
• ISRCTN - Covid-19

Drug Development and Test Assays

• FindDX SARS-COV-1 Diagnostic Pipelines

Analysis Software / Workflows / Pipelines

• Viral Assembly Techniques from ONT Reads
• COVID-19 data using Galaxy
• ViReport Analysis of COVID-19 using GISAID
• Artic Network nCOV-2019 Novel Coronavirus Bioinformatics protocol
• nf-core/covid19
• INSaFLU/INSaFLU
• connor-lab/ncov2019-artic-nf - Automates the Artic Network nCoV-19 protocol. Uses Nextflow DSLv2 and {non-}barcoded Nanopore data.
• RamiKrispin/coronavirus
• PyCOVID

Publications

• Pubmed / Medline
• PRE-PRINT Age-dependent effects in the transmission and control of COVID-19 epidemics
• PRE-PRINT No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics - usegalaxy.org, usegalaxy.eu, usegalaxy.org.au, usegalaxy.be and hyphy.org development teams
• Gautret et al. Hydroxychloroquine and azithromycin as a treatment of COVID-19: results of an openlabel non-randomized clinical trial
• PubAnnotation LitCovid

Journals

• New England Journal of Medicine | Coronavirus
• Journal of American Medical Association | Coronavirus
• Lancet | Coronavirus
• Elsevier | Coronavirus
• Nature | Coronavirus

Grant Application / Holder Information

• NIHR Research Funding Guidance
• Wellcome Trust Guidance
• UK Research and Innovation Guidance
• National Institute for Health Research Guidance

Funding Opportinities / Challenges

• DE-COVID rapid response call
• Health research Board Ireland COVID-19 Funding Opportunity
• Mercatus COVID-19 Innovation Prize
• R Consortium March 2020 Call for Proposals
• National Science Foundation (US)
• Kaggle CORD-19 Challenge
• IMI2 Call 21
• Federal Ministry of Education and Research - Germany
• Wellcome Trust - Epidemic Prepardness Covid-19 Funding Call
• Royal Society: RAPID ASSISTANCE IN MODELLING THE PANDEMIC: RAMP
• COVID-19 Global Hackathon