Africa Joins Global Effort to Monitor Emerging Pathogens via Genomics

A revolutionary low-cost genome sequencing technology, which played a crucial role in tracking COVID-19 variants globally during the pandemic, is set to be expanded to detect all pathogens under an ambitious new Wellcome Trust-funded project.

The ARTIC-2 project, led by the University of Birmingham and funded by the Wellcome Trust, aims to enhance global capacity for genomic surveillance, particularly in low- and middle-income countries (LMIC) and the Global South. The project brings together leading scientists from the Kenya Medical Research Institute (KEMRI) – Kenya, Ghana, and the Democratic Republic of Congo, alongside international partners including the Africa CDC, the Asia Pathogen Genomics Initiative, and the WHO’s International Pathogen Surveillance Network.

Genomic surveillance involves analysing the DNA or RNA of pathogens like viruses or bacteria to trace their spread, track mutations, and inform public health responses. In addition, this tool is instrumental in aids in the source of an outbreak and understanding how it has been transmitted between different populations. It is against this background that, the ARTIC-2 initiative seeks to make this powerful tool more accessible by refining low-cost sequencing technologies and protocols, targeting a cost of less than £10 per sample. 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.

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

Significantly, the project will advance the continued development of open-source methods and low cost laboratory equipment that reduce dependence on expensive patented technologies. The goal is to democratise access to sequencing, enabling more laboratories to conduct essential disease surveillance.

The project will also improve the way data is shared between researchers through a new initiative called Pathoplexus. The platform will also support real-time sharing of genomic data and insights, significantly improving 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.

Head of Bioinformatics at the KEMRI-Wellcome Trust Research Programme, Dr. George Githinji noted, “The impact of genomic surveillance has yet to be fully realised in LMIC settings. Our work in Kenya has shown the value of building capacity in public health teams to ensure this technology translates into real-life health solutions.”

Using Pathoplexus, the ARTIC-2 team also plans to create a global knowledge engine by integrating existing tools, protocols, and new learnings into a universal surveillance toolkit for use worldwide.

“This initiative represents a major leap forward in our ability to detect and respond to disease threats in real time,” said Dr. Placide Mbala Kingebeni from the Democratic Republic of Congo’s National Institute of Biomedical Research. “It will enable us to build a more robust, cost-effective, and adaptable response system capable of guiding public health actions where and when they are needed most.”

 According to lead Prof. Nick Loman researcher University of Birmingham, “ARTIC-2 will help make affordable, high-quality genomic sequencing accessible to any laboratory, anywhere in the world. With Wellcome’s support, we can establish a universal toolkit that empowers countries to monitor and respond to endemic and emerging pathogens effectively.”

The ARTIC-2 project marks a significant step towards global health equity by ensuring that cutting-edge scientific tools are available to all in the shared fight against infectious diseases.