Oxford University has partnered with global technology corporation Oracle, to create a Global Pathogen Analysis System (GPAS) that enables scientists and decision-makers to quickly identify COVID-19 variants.

GPAS combines Oxford University’s Scalable Pathogen Pipeline Platform (SP³) with Oracle Cloud Infrastructure (OCI). SP³, which was originally used to sequence tuberculosis, has been repurposed to unify, analyse and compare different SARS-CoV-2 sequence data, producing annotated genomic sequences and identifying new variants of COVID-19.

An in-built analytics dashboard simplifies this process by highlighting which strains of the virus are spreading most quickly and which genetic features contribute to increased transmissibility and vaccine resistance.

With the OCI-increased processing and machine learning capabilities, scientists, researchers and governments across the world can use the data to inform their responses and mitigate the impact of potentially dangerous variants.

WHY IT MATTERS

Vaccine rollouts are underway across the world. Britain, for example, has administered almost 57 million doses, contributing to eased lockdown restrictions in England, Wales and parts of Scotland. However, the consequences of virus mutations are uncertain.

With incidences of the more-transmissible Indian variant increasing, there is growing concern that restrictions may tighten again. Other mutations, such as the Kent, South African and Brazilian variants, can prove resistant to current vaccines.

The earlier scientists and governments are aware of the individual characteristics of variants, the faster they can formulate appropriate responses, which could potentially save lives.

THE LARGER PICTURE

The news of the Oxford-Oracle GPAS comes shortly after WHO and Germany announced the launch of the “WHO Hub”, an epidemic and pandemic intelligence hub that will use data and analytics to predict and prevent the risks of future pandemics and epidemics worldwide.

A new online data platform, Global.health, was also launched in February to support epidemiological study and modelling.

In January, UK health secretary Matt Hancock announced the launch of the New Variant Assessment Platform, a scheme that enables scientists across the globe access to the UK’s genomics labs to sequence the full genetic code of COVID-19.

ON THE RECORD

Derrick Cook, 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.”

He continued: “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.”

Larry Ellison, Oracle Chairman and CTO, 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.”