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.

Notably, the West African Centre for Cell Biology of Infectious Pathogens (WACCBIP) at the University of Ghana will lead the project’s Training, Engagement, and Outreach work package (WP5). Drawing on its experience in conducting genomic surveillance and genomic studies during the COVID-19 pandemic in Ghana and across the West African subregion, WACCBIP will deliver innovative, scenario-based training products that cover laboratory techniques, bioinformatics, and data interpretation. The Centre will also play a key role in WP4, supporting project implementation, testing, and validation of the sequencing platform in West and Central Africa, through its network of spoke laboratories established during the pandemic.

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 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 and lead to immune evasion or increased resistance to treatments.

A key element of the ARTIC-2 programme will be the continued development of low-cost laboratory protocols and equipment that significantly reduce the cost of sequencing. The team is focused on reducing the cost of sequencing to under £10 per sample, focusing on open-source methods and reducing reliance on expensive proprietary equipment and reagents. Lower costs will allow more laboratories to perform sequencing where it is most needed, such as in low- and middle-income countries (LMICs) 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, enabling more accurate monitoring and early detection of disease transmission. The team also aims to develop a knowledge engine that links existing tools with new learning to provide a universal, global toolkit for the surveillance of pathogenic threats.

Professor Nick Loman, Professor of Microbial Genomics and Bioinformatics 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 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 such as Mpox and Marburg.

WACCBIP’s role in testing and validating these toolkits in Ghana and across its regional network will provide essential insights into their functionality and readiness for real-world deployment. The Centre's contribution to refining workflows and evaluating system performance in operational settings will be crucial for ensuring the success of the programme across West and Central Africa.

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 their ability to inform tailored public health strategies. Developing in-country capabilities and expertise strengthens local health systems, enabling rapid responses to emerging and endemic diseases to protect vulnerable communities, both locally and worldwide."