Oxford University to help speed up identification of Covid variants globally

University and infrastructure firm Oracle unite to improve genomic sequencing

People line up outside a mobile vaccination centre, amid the outbreak of the coronavirus disease (COVID-19) in Bolton, Britain, May 16, 2021. REUTERS/Phil Noble
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The University of Oxford is attempting to speed up the identification of Covid variants worldwide by offering its technology on a specialist platform.

The platform, developed by Oracle Cloud Infrastructure, will be free for researchers and non-profit organisations.

The emergence of more infectious strains of Covid-19 threatens to slow the global recovery and potentially thwart current vaccine immunity.

In the UK, the high transmission of the Indian variant has raised concerns over the easing of lockdown and sparked a renewed surge in the vaccination programme. Health Secretary Matt Hancock warned it could "spread like wildfire among the unvaccinated groups".

Antibodies produced in response to some vaccines were slightly less effective against the Indian variant, early research suggested.

The earliest samples of the B.1.617 variant were found in India in October and Indian authorities said in March it was spreading fast in the western state of Maharashtra.

On Wednesday, the World Health Organisation said the B.1.617 variant had been detected in 44 countries and classified it as of "global concern", citing evidence that it is more transmissible.

Now, Oxford and Oracle have created a Global Pathogen Analysis System combining Oxford's Scalable Pathogen Pipeline Platform (SP3) with cloud computing infrastructure.

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.

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.

"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 Derrick Crook, professor of microbiology at 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."

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 opportunity of applying systematic examination for genetic variants in a range of pathogens will have major benefits for global public health. This programme takes us a step closer to this goal," said Sir John Bell, Regius professor of medicine at the University of Oxford.

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 effects 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 co-operation on genomic sequencing and examination of Covid-19 and other pathogens," Oracle chairman Larry Ellison said. "The enhanced system will establish a global standard for pathogen data gathering and analysis."

Dr Isabel Oliver, director of the National Infection Service at Public Health England, said the data would help collective efforts to combat the pandemic, and benefit the response to future pathogens. "This could potentially have a far-reaching positive impact on international public health and global health security,” she said.