Pathogen analysis system to identify COVID-19 variants

The emergence of more infectious variants of SARS-CoV-2 is threatening to slow the global recovery and potentially thwart current vaccine immunity. To help governments and medical communities identify and act on these variants faster, the University of Oxford 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).

SP³ came out of engagement, design and testing activities that have been running over the past several years through collaboration between researchers at Cardiff University, the University of Oxford, Public Health England and the European Bioinformatics Institute, along with other stakeholders from public health in the UK. First used for tuberculosis, the platform 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 now been enhanced with extensive new development work from Oracle, enabling high performance and security plus 24/7 worldwide availability of the SP³ system in the Oracle Cloud. The system will now deliver comprehensive and standardised results of COVID-19 analyses within minutes of submission, with the results shared around the world in a secure environment.

Coupled with the extensive 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. 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.

“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 the 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 use by researchers and non-profits.

“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,” said Professor Derrick Crook from the University of Oxford.

“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.”

Image credit: ©stock.adobe.com/au/MiaStendal

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