Why We Need a Transformative Approach to Data Analysis and Genomic Surveillance for Outbreak Preparedness

Pandemic Management Health

Why We Need a Transformative Approach to Data Analysis and Genomic Surveillance for Outbreak Preparedness

Commentary
Posted on: 15th November 2022
Andrew McInerney
Chief Executive Officer, Global Pathogen Analysis Service

As new variants of SARS-CoV-2 continue to emerge, epidemiologists around the globe warn that future outbreaks of this and new diseases are inevitable. Since 1900, there have been four global influenza pandemics; Ebola viruses have moved from animals to humans about 25 times in the past 50 years, and seven novel coronaviruses have emerged. 

In response, the World Health Organization (WHO) has advocated strengthening global collaboration in genomic surveillance to detect, monitor and respond to threats. In May 2021, it launched the Hub for Pandemic and Epidemic Intelligence in Berlin and, in March 2022, released a ten-year genomic-surveillance strategy. This strategy emphasises the importance of creating an effective and equitable global genomic-surveillance system.

Shared knowledge is crucial in developing an adequate understanding of pathogens and designing an efficient and scalable approach to respond to pathogenic threats. However, until now, countries have mainly worked in silos. Epidemiologists need reliable and timely data to learn about and respond to emerging diseases. The scale and pace of the response required by the latest pandemic hammered home how fragmentation in current health-care systems continues to limit public-health officials’ ability to respond effectively to global-health threats.

A transformative solution is needed. The destruction caused by SARS-CoV-2 has given the world the unique impetus to remodel existing global-health systems, with a focus on working collectively to address future health challenges. New technologies to expedite genomic analysis underpinned by cloud computing offer a groundbreaking economic, low-input, fast and accurate solution that can help to revolutionise global health security.

Since March 2020, we have witnessed a rapid expansion in the availability of next-generation sequencing capacity, as well as data-storage systems, software and tools required to systematically analyse and share large numbers of pathogen genomic sequences. 

A globally integrated system to share this information has the potential to change how the world responds to pandemics. Genomic analysis of pathogens and improved global surveillance must become a positive legacy of the Covid-19 pandemic. Unidentified or unanticipated pathogens will still be difficult to monitor, and no country can do this alone, so an integrated, technology-enabled approach with transparent data sharing is essential. 

What Are the Challenges? 

For a global system to become a reality, several challenges must be overcome.  

First, the expertise needed to assemble and analyse variants. Skilled bioinformaticians are scarce and attempting to develop and retain a standing workforce of the necessary size across all countries is unrealistic. Technologies like GPAS (Global Pathogen Analysis Service), coupled with genome sequencing, help to radically reduce the demands placed on bioinformaticians by providing consistent and easy-to-interpret analysis of genomic-sequence data to aid pathogen surveillance – all at a low cost.

Second, we need to equitably increase the availability of sequencing platforms on a global scale. To sequence a pathogen, scientists need machines to extract and read its DNA. Progress has been made in this field, particularly with the advancement of sequencing technologies like Illumina and Oxford Nanopore, which are becoming more accessible, faster and lower-cost; but there is still more to do. GPAS has been built to be agnostic to whichever sequencing technology is used, enabling instant comparability of data sets. But we must also reduce the gap in genome-sequencing analysis between high-income and low- and middle-income countries (LMICs). For example, more than 70 per cent of genomic-sequencing capacity in Africa is concentrated in just five countries. By December 2021, more than 80 per cent of all SARS-CoV-2 genomes uploaded to the Global Initiative on Sharing Avian Influenza Data (GISAID) database came from Europe and North America. Reducing this gap will strengthen the global-health-security system and avoid the risk that future pathogenic threats will emerge and spread before we are ready to respond – wreaking further health and economic havoc on the world. It’s in our collective interest to increase surveillance capacity in LMICs.

Finally, we need to consider the issue of data interoperability. Establishing standardised analytical processes allows for valid comparisons across internationally sourced samples.

A new, integrated and transformative approach has the potential to become a catalyst for countries, organisations and scientists across the world to reshape our system and make it equitable for all. 

Offering a Solution to Genome Analysis

The GPAS is a transformative service that delivers a global solution to standardise how genomic-sequence data from any sequencing methodology is processed and analysed. This innovative tool allows easy interpretation and consistent analysis and will help to inform policy development and decision-making during future health-care crises.

GPAS Ltd – working with the world-class pathogen genomics team at the University of Oxford and the cloud-computing scale and security of Oracle – is now expanding beyond its initial focus on Covid-19 to include genomic analysis of multiple pathogens, available to organisations and laboratory scientists around the world. 

In August, GPAS Chief Scientific Officer Professor Derrick Crook presented his pilot study at the International Conference on Emerging Infectious Diseases in Atlanta. He highlighted GPAS’s efficacy in taking raw outputs from genomic-sequencing machines (a chaotic group of short snippets of genetic reads), rapidly reassembling them into full genomes and doing so in multiple countries concurrently. GPAS also compares the full genome to a standard reference, notes each genetic mutation, and analyses them in the context of all other global samples in the system – facilitating global genomic epidemiology and real-time surveillance. Once processed, users can hold their data or store their sequences in any repository, including GISAID or the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI).

The GPAS service is simple, stable, scalable and fast, and can change the paradigm of pathogen surveillance and diagnosis as well as support approaches to the management of infectious diseases. 

Looking forward, the international community has a choice. We can decide to overlook what we learned during the pandemic about pathogen mutation, or we can use the knowledge and infrastructure we built to give us a unique understanding of other infectious diseases. The latter will require focus, time and resources to establish, but has the potential to create a global pathogen-surveillance system that follows principles of fair distribution of technology, globally adopted standards and governance, and a robust ethical framework. 

We must collectively build pathways to a future where pathogen genomics is integrated into the public-health decision-making process, employed to inform vaccine and treatment development and improve the health of millions of people who fall ill with an infectious disease every year.

TBI supports GPAS through The Tomorrow Partnership, our work with political leaders and governments to find tech and digital solutions to their biggest challenges.

 

 

 

 

 

 

 

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