Pathogen genomics initiative to boost disease control in Africa

The virtual launch this month of the Africa Pathogen Genomics Initiative (Africa PGI) marked a ground-breaking initiative to tackle infectious disease in Africa. Led by the African Union Commission through the Africa Centres for Disease Control and Prevention (Africa CDC), the four-year partnership will expand access to next generation genomic sequencing tools and expertise and aims to strengthen laboratory networks and public health surveillance, including disease prevention and control, across Africa. Partners in this US$100 million public-private-non profit initiative include the Bill and Melinda Gates Foundation, US CDC, Microsoft, Illumina, and Oxford Nanopore Technologies.

Beyond COVID

Genomic sequencing is currently playing a major part in the surveillance of the pandemic and subsequent response, and during the launch there was acknowledgment that having SARS-CoV-2 sequences from Africa, and on global databases, is ensuring that any vaccines being developed will also be suitable for use on the African continent. The current pandemic provides additional incentive for this initiative, and further demonstrates the need for more extensive pathogen genomics capacity in Africa.

In addition to COVID-19, Africa has around 140 disease outbreaks annually as well as combating ongoing disease burden caused by malaria, HIV, cholera and tuberculosis; West Africa has to cope with viral haemorrhagic fevers such as Lassa Fever, which is endemic and causes yearly outbreaks. Monitored by the WHO, outbreaks in Africa are reported in a weekly WHO health emergencies bulletin.

The importance of pathogen genome sequencing to managing these threats was highlighted by the speakers, from the impact on healthcare and emergency responses during the recent Ebola outbreaks, the management of a listeria outbreak in South Africa, and antimicrobial resistance tracking – a particular challenge with malaria and tuberculosis. It is critical to empower scientists with the tools they need to stay one step ahead of these pathogens.

Where to start?

To establish this ambitious and timely initiative, five cross-cutting strategic priorities have been identified: enabling mechanisms, policies, and guidelines; pathogen genomics and bioinformatics network; capacity building; data systems; and genetic epidemiology. An integrated and holistic approach with phased implementation will be used.

The aim is to build a functional continent-wide pathogen genomics network of laboratories, bioinformatics capabilities, data systems and expert personnel, which will require strengthening the current infrastructure and workforce development. It is envisioned that this is an investment that will act as a catalyst, having an impact beyond pathogen sequencing in human disease, for example use of sequencing in agriculture.

The importance of  how the data generated will be stored and archived has also been considered. This is where Microsoft and its Azure cloud platform will play an important role in the initiative – they will provide support for the technical infrastructure as well as help design data architecture and systems, which will be used to store and manage sequence and associated data as well as bioinformatics pipelines. This will support the sharing of sequencing and associated data, as well as support the training of data scientists.

As one speaker succinctly commented, ‘Machines work but we have got to keep them running’: access to the technicians who maintain and service highly sensitive equipment is essential and highlights a need to train Africa-based experts and technicians. Speakers also noted the need to ensure supply of sequencing reagents and to have access to lower priced reagents; the PGI will be coordinating ways to overcome these and other issues.

Bright future

This initiative cannot be delivered by one partner alone and its success is being centred on commitment, collaboration and coordination of efforts. Equally important is the need to empower public health officials and ministers so they understand how they can leverage genomics to make evidence based policy.

Despite the challenges there is huge potential to improve health across the continent and the Africa PGI could very well demonstrate to the rest of the world how pathogen genomics can best be used for public health. While ambitious, the PGI has put in place many of the building blocks to enable it to become a leader in the field of pathogen genomics. As Dr John Nkengasong, Director of the Africa CDC, said at the close of the event ‘This is the beginning of a long journey. This is the first step.’ It will be exciting to see how the Africa PGI develops over the coming months and years.