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Oxford University uses Oracle Cloud to speed up analysis of Covid-19 variants

The University of Oxford is availing itself of Oracle Cloud Infrastructure in the genomic sequencing and analysis of SARS-CoV-2, in part to identify new Covid-19 variants

Oxford University and Oracle have joined forces to set up a Global Pathogen Analysis System, which they say will improve sequencing to combat Covid-19 variants. It will be free for researchers and non-profits to use worldwide.

The system comprises Oxford’s Scalable Pathogen Pipeline Platform (SP3) running on Oracle Cloud Infrastructure.

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.”

John Bell, regius professor of medicine at the university, added: “The opportunity of applying systematic examination for genetic variants in a range of pathogens will have major benefits for global public health. This programme, with Oracle as a partner, takes us a step closer to this goal.”

SP3 was first used for tuberculosis and has been repurposed for the genomic analysis of SARS-CoV-2, in part to identify new variants.

Now based on the Oracle cloud, it will deliver results of Covid-19 analyses within minutes of submission. The results will be shared with countries around the globe in a secure environment.

There are said to be machine learning capabilities in the system, along with analytic dashboards, and these will show which strains are spreading more quickly than others. They will also show whether genetic features contribute to increased transmissibility and vaccine escape.

Oxford has processed half the world’s SARS-CoV-2 sequences – more than 500,000 in total – but this initiative is said to be built on the work of a broader Wellcome Trust-funded consortium including Public Health Wales, the University of Cardiff and Public Health England.

Read more about computer-enabled Covid-19 analysis

Isabel Oliver, director of the National Infection Service at Public Health England, commented: “This donation is a welcome boost to the ability to share genomic sequencing data with colleagues all across the world. Not only are strong genomic examination and widely available data crucial to our collective efforts to combat the current pandemic, but they will have ongoing benefits to the response to other pathogens in the future.”

Thomas R Connor, professor, School of Bioscience, Cardiff University, said: “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.”

Larry Ellison, chairman and CTO at Oracle, said: “There is a critical need for global cooperation 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.”

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