Oracle and Oxford University are partnering to bring Oxford’s Scalable Pathogen Pipeline Platform (SP3) to the global community to more quickly identify COVID-19 variants in what it calls the Global Pathogen Analysis System. COVID-19 variants have emerged as a serious threat to inoculation and public health initiatives in many regions of the world. Mutations don’t generally weaken a virus, but do have the potential to make it stronger or easy to spread.
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Identifying COVID-19 variants is a pressing issue for the medical research community, but prior to GPAS, Oxford professor of microbiology Derrick Crook said in an Oracle press release, there has been no common standard for identifying, annotating and sharing knowledge of variants.
Oxford’s SP3, originally used to analyze tuberculosis sequences, was envisioned as a way to create a single web-based platform to collect, process, and analyze pathogen genetic sequences. Most labs have traditionally had custom, in-house software for the process.
SP3 fetches data from public repositories of genome data and uses container technology like Docker to build workflows capable of examining new genome sequences against known pathogens to identify variants. While available as a cloud-hosted platform, it was (and is) traditionally designed to be deployed in private environments; its head node only needs to be an Ubuntu machine running 18.04 or higher, and can be installed with a simple bash command.
GPAS, on the other hand, is SP3 running on Oracle Cloud Infrastructure and designed to be accessed by researchers and non-profits around the world. It’s main workflow on COVID-19 variants will “analyze, and compare sequence data of SARS-CoV-2, yielding annotated genomic sequences and identifying new variants and those of concern,” Oracle said.
In addition to establishing a generally-accessible SP3 instance in GPAS, Oracle also made modifications to the software that it said increases performance capability via machine learning and enhances security.
GPAS can identify variants that may be spreading more rapidly or show resistance to vaccines and other treatments, and it displays that data on an analytics dashboard alongside other information, like whether certain genetic features are contributing to increased transmissibility.
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The platform is free for researchers and non-profits worldwide, and Oracle has hopes that it can eventually be expanded to all pathogens to “inform decision-making on pandemic response strategies worldwide.”
“The opportunity of applying systematic examination for genetic variants in a range of pathogens will have major benefits for global public health. This program, with Oracle as a partner, takes us a step closer to this goal,” said John Bell, Regius professor of medicine at the University of Oxford.