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GPAS - Global Pathogen analysis system

GPAS: A global microbe sequence analysis pipeline to support local, national and international public health

Microbes that cause infection (e.g. bacteria, viruses) are made up of a genetic code, which governs how they behave and which medicines can be effectively used to treat infections caused by them. We have built world-leading expertise in optimizing methods that enable us to take microbes from patient samples and process them with sequencers. Sequencers output a representation of a microbe’s genetic code on a computer (known as “sequencing data”) so that we can say what type of microbe is causing an infection, and which drug should be used to treat the infection. This can improve the speed and effectiveness of patient treatment, which is clearly really important to patients and the public.

Sequencing data are however not easy to analyse, and we have undertaken a lot of work to develop a single sequence data pipeline which is flexible, accurate and fast. Analyses of sequencing data can also take up a lot of computing resource, particularly if large numbers of sequences need to be processed across the world.  For example, if you wanted to analyse these data on your computer at home, it might take many months or years. One type of large-scale computing resource known as cloud computing overcomes some of these difficulties, but is very expensive, meaning that it is often not available to healthcare or public health institutions.

As a result of our work (Yang-Turner F et al, 2019, Xu Y et al, 2020), a computer software company has donated unlimited cloud computing resource for a decade to help set up our sequencing data analysis pipeline for use completely free-of-charge.

This service, called the Global Pathogen Analysis System (GPAS), can be used by people in healthcare and public health globally to analyse hundreds of thousands of microbe sequences to work out:

(i) which microbes are causing infections in which countries,

(ii) how microbes spread around the world, and

(iii) whether we need to be using different treatments in different settings to better treat patients’ infections.

GPAS is already supporting the analysis of SARS-CoV-2 sequences in Canada, Chile, Vietnam, Australia, South Africa and Tanzania. It has the capacity to process 70,000-100,000 SARS-CoV-2 sequences/day, enabling us to monitor which variants (e.g. Alpha, Delta) are causing SARS-CoV-2 infection globally. We plan further rollout of GPAS to fight other major global disease-causing microbes, such as tuberculosis. These analyses can be used real-time to support national and international public health efforts.

 Please visit the GPAS website for more information.