Festival of Genomics 2023

Our vision and mission

The Global Pathogen Analysis Service (GPAS) Ltd aims to harness the power of pathogen genomics to tackle infectious diseases. Built by a long-established world-leading pathogen genomics team from Oxford University, supported by Oracle’s cloud computing scale and security, GPAS provides rapid, accessible and standardised genomic analysis for a range of pathogens, starting with SARS-CoV-2.  

Pathogen genomics has the potential to revolutionise microbiology, moving towards a world where clinicians start with sequencing and use software to interpret the results. Combined with other datasets, it opens the door to precision medicine. It will benefit not only humans, but also agriculture, animal health and the food chain.

GPAS aspires to be at the forefront of the metagenomics revolution, leading the innovation of infectious disease diagnostics and control.  

Our foundation: genomic surveillance

Pathogens are organisms that cause disease to their host. They may be viruses, bacteria, fungi or parasites and consist of pieces of genetic code, such as DNA or RNA.    

Genomic sequencing allows the reading of the genetic makeup of DNA. The World Health Organization recommends using genomic sequencing in surveillance, including antimicrobial resistance and foodborne diseases.

Genomic analysis offers a rapid, standardised and more capable method of analysing and comparing genomic sequences.

This information can be used to inform public health and individual clinical decision-making. When done on a global scale, this offers enormous benefits, enabling disease spread and possible mutation to be tracked and mapped in near real-time. To date, there has not been a universal approach to genomic pathogen sequencing or the technology to do this comparative work at pace globally, limiting the benefits. 

The SARS-CoV-2 pandemic demonstrated the limitations of global health monitoring systems and highlighted the inequity of sequencing resources globally. Whilst New Zealand has sequenced 38% of their SARS-CoV-2 samples and shared them with GISAID, over 150 countries have sequenced and shared fewer than 1% of positive samples. 

The benefits of near-to-real-time genomic sequencing are clear:

1. A monitoring system to ensure we remain vigilant to any mutations, such as ‘escape-variants’.
2. An early warning system to identify the spread and mutation of new or existing diseases. 
3. A tool to assist in the development of clinical responses, vaccines and therapeutics. Collecting a large number of SARS-CoV-2 samples facilitated the rapid development of mRNA vaccines, and genomic profiling of pathogens can support clinical understanding of an individual’s disease.      
4. A global genomic sequencing analysis system can potentially reduce the economic impacts of future outbreaks (the SARS-CoV-2 pandemic cost the global economy $ 12.5 trillion to date). 

Given the likelihood of further variants and the ongoing global burden of other pathogens such as tuberculosis (TB) and neglected tropical diseases (NTDs), it is critical to develop our global infrastructure, so that pathogen surveillance and analysis becomes a positive pandemic legacy. 

This requires expanding sequencing capabilities and improving the results’ standardisation, sharing and utility. There also needs to be a shared commitment of governments worldwide to adopt solutions that can monitor and prevent the future spread of disease.  

Our future: metagenomics 

Building the technology, infrastructure and skills to rapidly analyse pathogen genomes in future pandemics or ongoing disease outbreaks will provide a vital tool for infectious disease control. But the ultimate aim of pathogen genomic technologies must be metagenomics.    

Metagenomics is the analysis of genomes in a specimen without prior knowledge of what the sample may contain. The sample can be drawn from a host (sputum, blood, CNS) or the environment (wastewater, soil). In infectious diseases, the challenge is identifying the pathogen causing illness from many other pathogens living within the host or in the environment.   

GPAS is building on its existing technology to overcome this challenge, so that pathogen genomics analysis can be at the forefront of disease detection and treatment.   

The uses of metagenomics are broad:

Our products and services

GPAS makes near real-time pathogen sequencing analysis available to all. Its sustainable and scalable solution to genomic sequencing analysis is already operational in laboratories and institutions globally.   

GPAS’s first use case is SARS-CoV-2, with an accelerated pipeline of pathogens in development to expand our service. A toolset for tuberculosis will be launched in 2023, followed by products to identify and classify foodborne illnesses, influenza, and other pathogens. GPAS is working to develop compliant, certified clinical microbiology diagnostic tools to support individual patient care.   

Benefits of GPAS 

Speed: Many labs worldwide currently wait days or weeks for their sequencing results, with decisions made on out-of-date information. GPAS works in near real-time, delivering a critical early warning system, and bringing swift, clear data to aid effective decision-making. A single sequence can be analysed in around 20 minutes, and GPAS can concurrently assemble and analyse up to 100,000 genomes per day. 

Efficiency: The platform lowers the global barrier to entry. Currently, genomic data can only be assembled by highly trained experts. GPAS automates this assembly service, allowing a wider range of scientists and public health experts to interpret and analyse the data. This allows expert bioinformaticians to concentrate on in-depth analysis of results and enables more laboratories to participate in genomic analysis.

Scale: GPAS allows simultaneous processing, analysis and comparison of thousands of sequences, allowing multiple countries to track variants globally, spot outbreaks, and take appropriate action. Countries wishing to do so can share data and compare across borders at the touch of a button. 

Standardisation: The platform removes variation. Currently, organisations assemble their genomes in different ways (often in response to local resource constraints). GPAS works with a range of sequencing technologies, allowing organisations to share data, compare sequences and precisely track pathogen spread and mutation as scientific understanding evolves.

Security: Each user has full control over the data uploaded to GPAS, with sharing and privacy options available. The platform automatically removes personally identifiable information (PII) before upload, and industry-leading security measures designed by Oracle protect the cloud infrastructure.   

Breadth: GPAS aims to be ‘platform agnostic’, working with a range of sequencing platforms. Currently available for SARS-CoV-2, the platform will rapidly expand to other pathogens such as tuberculosis, foodborne diseases and influenza.  

What GPAS is for

GPAS has a range of uses across human and animal health, agriculture and the food chain. 

Pathogen Surveillance: During the SARS-CoV-2 pandemic, it rapidly became clear that monitoring disease, understanding mutations and tracking spread enabled tailored public health responses. A more widespread approach to pathogen surveillance across known and emerging infections could ensure the world is better prepared for future outbreaks. GPAS has the potential to be part of that universal, coordinated global response to monitoring the evolution of infectious disease pathogens.  

Outbreak Management: Responding quickly to small-scale outbreaks, such as those within a healthcare setting or those caused by a foodborne illness, is essential to prevent further transmission and spread. GPAS can identify whether two cases are related and track the outbreak’s source. The tool can also hold information on past outbreaks and identify any re-emergence of a pathogen. 

Disease Diagnosis: Understanding the exact genomic makeup of a patient’s infection can be beneficial in tailoring a treatment response. This approach can also be antibiotic sparing. By understanding the infection and the most appropriate treatment, clinicians can tailor the antibiotic response and prevent further antibiotic resistance amongst infectious pathogens.  

Whilst initially targeted at human disease, GPAS could be rapidly adapted to support infectious diseases in animals, such as TB in cattle or across the food chain, such as fungal wheat diseases.

Data Security and Storage 

GPAS is built on the principle of sovereign data ownership, with any decision to share results remaining solely with the submitting organisations. The platform does not have access to users’ data and will not publish the data without the consent and involvement of the owner.

However, if organisations wish to share their data with others, such as their national public health agency, neighbouring countries, multilateral organisations or global repositories, the functionality of GPAS makes it easy and quick to do so. By sharing data and utilising GPAS’s proprietary FindNeighbour4 (FN4) functionality, it is possible to compare sequencing results with all other sequencings globally, further supporting the rapid identification of new disease variants. 

Data is stored in a highly secure cloud, where users can share results with existing global repositories. The platform automatically removes any Personal Identifying Information (PII) before any analysis is conducted. No PII is stored or shared.