Ambitious project to develop low-cost genome sequencing for pathogens known and unknown

Wellcome Trust-funded project will build on research that facilitated thousands of diagnostic laboratories to adopt sequencing capacity for COVID-19 during the pandemic and permit the characterisation of future infectious threats

A low-cost genome sequencing technique that was used by thousands of laboratories globally
to spot COVID-19 variants of concern will now be extended to cover all pathogens, known or
unknown, in an ambitious new project launched today.

The ARTIC-2 project brings together an international collaboration led by the University of Birmingham. The team includes researchers from the Democratic Republic of Congo, Ghana and Kenya with expertise in responding to numerous viral threats using genomic surveillance including recent outbreaks of Ebola virus and Mpox in Africa. The ARTIC-2 project will develop the underlying technology for the surveillance of emerging pathogens around the world. ARTIC-2 will work alongside the Africa CDC, Asia Pathogen Genomics Initiative and the WHO International Pathogen Surveillance Network to ensure that processes can then be rolled out worldwide.

Genomic surveillance is a powerful tool in the fight against infectious diseases. By analysing the genetic makeup of pathogens like viruses or bacteria, scientists can track the spread of outbreaks and understand their evolution over time. This information can help public health officials predict future outbreaks, develop targeted treatments, and implement effective control measures. It also aids in tracing the source of an outbreak and understanding how it has been transmitted between different populations. Easy access to genomic sequencing will enable public health laboratories around the world to respond more quickly and effectively to outbreaks of new and emerging viruses as well as better understand the mutations that occur randomly which lead to immune evasion or increased resistance to treatments.

A key element of the ARTIC-2 programme will be the continued development of a low-cost laboratory protocols and equipment that significantly reduce the cost of sequencing. The team are focused on reducing the cost of sequencing to under £10 per sample, reducing costs by focusing on open-source methods and reducing the reliance on expensive proprietary equipment and reagents. Lower costs allow more labs to perform sequencing where it is badly needed such as in low- and middle-income countries (LMIC) and the global south.

The project will also improve the way in which data is shared between researchers through a new initiative called Pathoplexus. Better data sharing can significantly improve outbreak response and public health decision-making as it allows for more accurate monitoring and tracking of disease transmission, enabling early detection and control efforts. The team also aims to rationalise the approach to develop a knowledge engine that will link all aspects of existing processes and tools with new learning to provide a universal and global toolkit for surveillance of pathogenic threats.

Professor Elijah Songok the Ag Director general KEMRI noted “KEMRI is at the forefront of the development and adoption of cutting-edge technologies to improve health. We saw the impact genomic surveillance during the COVID 19 pandemic, and this research provides a much-needed tool in ensuring we are adequately equipped in identification of emerging pathogens and the continued efforts in the fight against infectious diseases”.

Professor Nick Loman, Professor of Microbial Genomics andBioinformatics at the University of Birmingham and lead researcher for ARTIC-2 said: “ARTIC-2 will help to realise the ambition that any laboratory, anywhere in the world could access affordable, high-quality genomic sequencing for their work. During the global pandemic, sequencing was one of the most important tools at our disposal to understand how the coronavirus was changing to help inform development of new treatments and vaccines as well as public health policies. With funding from Wellcome to develop ARTIC-2 we can develop a universal, global toolkit and learning platform that means any endemic virus or pathogen around the world can be sequenced quickly and cheaply.”

Dr. George Githinji, The Head of Bioinformatics at the KEMRI- Wellcome Trust Research Programme in Kenya said “The impact of genomic surveillance has yet to be fully realised in LMIC settings, The Programme has shown how we can potentially use sequencing as a tool to fight disease outbreaks and provide timely interventions. Our work with the Public health Laboratories in Kenya has shown how useful it is to ensure capacity building of public health
teams to ensure that this technology translates to real life solutions for health improvement”.

Dr Placide Mbala Kingebeni, National Institute of Biomedical Research in the Democratic Republic of Congo and co-researcher on the project said:
“The ARTIC-2 initiative represents a major leap forward in our ability to detect and respond to infectious disease threats in real time. By expanding genomic surveillance beyond high- consequence viruses to include endemic and emerging pathogens, we are strengthening our capacity to act swiftly and effectively in the face of new outbreaks. This funding will enable
us to build a more robust and adaptable response system; one that is accessible, cost- effective, and capable of guiding public health action where and when it is needed most.”

Real world testing
To ensure that the programme is easy to adopt anywhere in the world, the ARTIC-2 programme will also develop locally accessible bioinformatics support to help determine best ways to tackle pathogens as part of this project. ARTIC-2 will build on the success of the initial project that developed an integrated field-deployable viral sequencing system which could be rapidly deployed to study outbreaks and epidemics anywhere in the world. The same lab- in-a-suitcase concept will be further developed in ARTIC-2 for a variety of potential uses including surveillance of known endemic pathogens including zoonotic viruses such as Mpox and Marburg.

Natsuko Imai, Research Lead, Epidemics at Wellcome, said:

“Genomic sequencing is crucial for understanding the circulation, spread, and evolution of
pathogens, providing essential insights to protect public health. By making this technology accessible and affordable, researchers in regions affected by diseases such as mpox,mosquito-borne viruses and TB can conduct in-situ sequencing, dramatically enhancing theirability to inform tailored public health strategies. Developing in-country capabilities andexpertise strengthens local health systems, enabling rapid responses to emerging and endemic diseases to protect vulnerable communities, both locally and worldwide.”

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Press contacts: Cynthia Mauncho cmauncho@kemri-wellcome.org
                             Roselyne Namayi rnamayi@kemri-wellcome.org

Institutional Notes to Editor

The Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme was formally established in 1989, is a partnership between KEMRI, Oxford University and the Wellcome Trust. It conducts basic, epidemiological, and clinical research in parallel, with results feeding directly into local and international health policy and aims to expand the country’s capacity to conduct multidisciplinary research that is strong, sustainable and internationally competitive.           www.kemri-wellcome.org

The Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme formally established in 1989, is a partnership between KEMRI, Oxford University and the Wellcome Trust. We conduct high quality, purposeful, and relevant research in molecular biology, epidemiological and clinical research. This research feeds directly into local and international health policy, with a parallel aim of supporting and nurturing the next generation of African researchers                                                 www.kemri-wellcome.org.