A new partnership between Oxford University and Oracle will see the speed identification of COVID-19 variants and will help further understanding of infectious diseases.
To help governments and medical communities identify and act on COVID-19 variants faster, Oxford University and Oracle have created a Global Pathogen Analysis System (GPAS) that combines Oxford’s Scalable Pathogen Pipeline Platform (SP3) with the Oracle Cloud Infrastructure (OCI). This initiative builds on the work of a Wellcome Trust-funded consortium including Public Health Wales, the University of Cardiff, and Public Health England.
The partnership will enable global genomic sequencing and examination through the platform to help mitigate the impact of potentially dangerous COVID-19 variants. Already, Oxford has processed half the world’s SARS-CoV-2 sequences – totalling more than 500,000.
Advancing understanding
SP3 was first used for tuberculosis and will now be repurposed to unify, standardise, analyse, and compare sequence data of SARS-CoV-2, yielding annotated genomic sequences and identifying new variants – including variants of concern. For this, its processing capability has been enhanced with extensive new development work from Oracle, enabling high performance and security, and worldwide availability of the SP3 system in the Oracle Cloud.
The system will now help to deliver comprehensive and standardised results of COVID-19 analyses within minutes of submission on an international scale, which will be securely shared with countries around the globe.
Derrick Crook, Professor of Microbiology in the Nuffield Department of Medicine at the University of Oxford, said: “This powerful new tool will enable public health scientists in research establishments, public health agencies, healthcare services, and diagnostic companies around the world to help further understanding of infectious diseases, starting with the coronavirus.
“The Global Pathogen Analysis System will help to establish a global common standard for assembling and analysing this new virus, as well as other microbial threats to public health. This adds a new dimension in our ability to process pathogen data. We are excited to partner with Oracle to further our research using this cutting-edge technology platform.”
“The opportunity of applying systematic examination for genetic variants in a range of pathogens will have major benefits for global public health. This program, with Oracle as a partner, takes us a step closer to this goal,” added Sir John Bell, Regius Professor of Medicine at the University of Oxford.
Utilising machine learning
Utilising the extensive machine learning capabilities in the Oracle Cloud, scientists, researchers, and governments can process, analyse, visualise, and act on a wide collection of COVID-19 pathogen data for the first time – including identifying variants and their potential impact on vaccines and treatments.
Oracle Chairman and CTO, Larry Ellison, said: “There is a critical need for global co-operation on genomic sequencing and examination of COVID-19 and other pathogens. The enhanced SP3 system will establish a global standard for pathogen data gathering and analysis, thus enabling medical researchers to better understand the COVID-19 virus and other microbial threats to public health.”
“The SP3 platform has come out of engagement, design, and testing activities that have been running over the past several years through close collaboration between researchers at Cardiff University and the University of Oxford, Public Health England, and the European Bioinformatics Institute, along with other stakeholders from public health in the UK. This new Global Pathogen Analysis System will enable collaborating scientists to analyse a pool of worldwide data in new ways, providing better intelligence on virus variants of concern and their potential for spread,” said Professor Thomas R Connor, School of Bioscience at Cardiff University.
The service will be to all pathogens while also collaborating with scientists from research establishments, public health agencies, and private companies to inform decision making on pandemic response strategies worldwide.
The platform will be free for researchers and non-profits to use.
