Oxford University and Oracle have created a Global Pathogen Analysis System (GPAS), combining Oxford’s Pathogen Pipeline Platform (SP3) with the Oracle Cloud Infrastructure (OCI), according to a news release from Oracle.
This initiative builds on the work of a Wellcome Trust-funded consortium including Public Health Wales, the University of Cardiff, and Public Health England.
First used for tuberculosis, SP3 has been repurposed to unify, standardize, analyze, 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 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 will be shared with countries around the globe in a secure environment.
Coupled with machine learning capabilities in the Oracle Cloud, collaborating scientists, researchers, and governments worldwide can process, analyze, visualize, and act on a wide collection of COVID-19 pathogen data. 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 the world’s SARS-CoV-2 sequences, more than 500,000 in total.
