Oxford and Oracle team up to expedite COVID-19 variant identification

Oxford University and Oracle have created a Global Pathogen Analysis System (GPAS) to help governments and medical communities identify and act on these variants faster.

The system 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 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, said Derrick Crook, Professor of Microbiology in the Nuffield Department of Medicine at the University of Oxford.

The GPAS will help to establish a global common standard for assembling and analysing this new virus, as well as other microbial threats to public health, added Crook. This adds a new dimension in our ability to process pathogen data, he said.

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. The SP3 system will now deliver comprehensive and standardised results of COVID-19 analyses within minutes of submission on an international scale. The results will be shared with countries around the globe in a secure environment.

“There is a critical need for global cooperation on genomic sequencing and examination of COVID-19 and other pathogens,” said Oracle Chairman and CTO Larry Ellison. “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 next step will be to extend this service to all pathogens while simultaneously collaborating with scientists from research establishments, public health agencies and private companies to ensure this work can inform decision-making on pandemic response strategies worldwide.

The platform will be free for researchers and non-profits to use worldwide.

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