Africa's $100-million Pathogen Genomics Initiative
Authors: Munyaradzi Makoni
Journal: The Lancet Microbe (2020)

On Oct 12, 2020, the Africa Centres for Disease Control and Prevention (CDC) secured US$100 million for pathogen genomics research and development through a partnership, the Africa Pathogen Genomics Initiative (PGI), expected to transform disease surveillance on the continent and is now preparing to start running programmes in 2021. Africa PGI is a 4-year collaboration between the Africa CDC Institute of Pathogen Genomics, US CDC, the Bill & Melinda Gates Foundation, software giant Microsoft, genomics sequencing technology company Illumina, and UK-based biotechnology company Oxford Nanopore Technologies. The aim of the initiative is to integrate pathogen genomics and bioinformatics into public health surveillance, outbreak investigations, and improved disease control and prevention in Africa. “Pathogen genomics has revolutionised outbreak detection, outbreak investigation, and monitoring of transmission dynamics of infectious agents and antimicrobial resistance across humans, animals, and the environment”, said Sofonias Kifle Tessema, the head of the genomic sequencing programme at Africa CDC. “Despite the high burden of endemic infectious diseases and many infectious diseases that have emerged or re-emerged in Africa, public health pathogen genomics capacity is limited and we haven’t fully harnessed the benefits of this technology”, he told The Lancet Microbe. After a series of assessments to identify the major gaps in the implementation of public health pathogen genomics in Africa, according to Tessema Africa CDC identified the need for continental coordination to create a collaborative environment and for the expansion and strengthening of laboratory and bioinformatic capacity. Well trained workforce across the spectrum of genomics and bioinformatics, the implementation of high-impact applications, and the integration of pathogen genomics into the existing disease surveillance system are required, he said. Africa PGI is building a pan-African disease surveillance and laboratory network based on pathogen genomic sequencing to identify and inform research and public health responses to COVID-19 as well as other epidemic threats and endemic diseases such as AIDS, tuberculosis, malaria, cholera, and other infectious diseases. “Africa is one continent beaten by many pathogens and pandemics”, Tulio de Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform and principal investigator of the Network for Genomic Surveillance in South Africa, told The Lancet Microbe. The new initiative will help shorten the life span of diseases and complement the work his team is already doing as it builds on holistic approaches based on existing capacity. About 140 disease outbreaks hit Africa annually. John Nkengasong, director of Africa CDC believes strengthening genomic surveillance systems is key for early notification and control of these outbreaks. “Use and integration of advanced technologies such as next-generation sequencing into surveillance and emergency response programmes facilitates public health decision-making for better outcomes, as evidenced in two Ebola virus disease outbreaks and the current COVID-19 pandemic”, Nkengasong said. “It is important for Africa to leverage hubs of excellence to empower and guide public health institutions, to enable them make evidence-based decisions”, said Christian Happi, director of the African Centre of Excellence for Genomics of Infectious Diseases based in Ede, Nigeria, during the launch of Africa PGI. Africa PGI will equip the national public health institutes and train scientists in Africa to fully use next-generation sequencing technologies. An African-owned data library and real-time data-sharing platform will be established to support the laboratory network, in alignment with different African Union member states’ regulations. At the initiative's onset, 72% of Africa's genome sequencing capacity is concentrated in four countries: South Africa has 50 institutions, Kenya 20, Nigeria ten, and Morocco five. According to Africa CDC, about 83% of these are in non-public health institutions. A few African countries have a single, privately owned, genomic sequencing institution. “Overall, the initiative is a unique platform for partnerships to effectively implement and translate pathogen genomics into public health action”, said Tessema. Since its launch, Africa PGI has been recruiting the workforce needed to effectively coordinate its implementation and is currently conducting a series of consultative meetings to inform its planning. The initiative will be implemented in phases. After the ongoing phase 1, during which countries that will participate in the initiative are being identified and plans are being finalised, the implementation will begin in 2021. Tessema explained that currently the training framework and curricula for genomics and bioinformatics, which will focus on national public health institutions, are being developed. According to de Oliveira, several requirements must be adhered to, if the initiative is to deliver the desired results. “Genomics is effective when done quickly and close to the site”, he said, adding, “Even with our limited resources, we have to learn more about sample collection and storage, and data curation, logistics of transporting samples, all done at affordable cost”. An integrated national scale SARS-CoV-2 genomic surveillance networkThe Coronavirus Disease 2019 (COVID-19) Genomics UK Consortium (COG-UK) was launched in March, 2020, with £20 million support from UK Research and Innovation, the UK Department of Health and Social Care, and Wellcome Trust. The goal of this consortium is to sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for up to 230 000 patients, health-care workers, and other essential workers in the UK with COVID-19, which will help to enable the tracking of SARS-CoV-2 transmission, identify viral mutations, and integrate with health data to assess how the viral genome interacts with cofactors and consequences of COVID-19. Full-Text PDF Open Access