Oxford University partners with Oracle to ID COVID-19 variants

Graphic art depicting the coranavirus.

Oxford University has selected Oracle to help speed up the identification of COVID-19 variants.

A specialist platform developed on Oracle Cloud Infrastructure will help with global genomic sequencing and examination, thereby mitigating the impact of potentially dangerous strains.

The emergence of more infectious variants of the COVID-19 virus is threatening to slow the global recovery and potentially thwart current vaccine immunity, according to Oxford University. To help governments identify and act on these variants faster, the university and Oracle have created a Global Pathogen Analysis System (GPAS) combining Oxford’s Scalable Pathogen Pipeline Platform (SP3) with the power of 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.

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 analyzing 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.”

First used for tuberculosis, SP3 has been repurposed to unify, standardise, analyse, and compare sequence data of SARS-CoV-2, yielding annotated genomic sequences and identifying new variants and those of concern. SP3’s processing capability has been enhanced with extensive new development work from Oracle, enabling high performance and security plus 7 by 24 worldwide availability of the SP3 system in the Oracle Cloud. The SP3 system will now deliver comprehensive and standardized results of COVID-19 analyses within minutes of submission on an international scale. The results are expected to be shared with countries around the globe in a secure environment.

Sir John Bell, Regius Professor of Medicine at the University of Oxford, said: “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.”

Coupled with the machine learning capabilities in the Oracle Cloud, collaborating scientists, researchers and governments worldwide can process, analyse, visualise and act on a wide collection of COVID-19 pathogen data for the first time. 

This includes identifying variants of interest and their potential impact on vaccine and treatment effectiveness. For example, analytics dashboards in the system will show which specific strains are spreading more quickly than others and whether genetic features contribute to increased transmissibility and vaccine escape. Already, Oxford has processed half of the world’s SARS-CoV-2 sequences, more than 500,000 in total.

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