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Africa Pathogen Genomics Initiative aims to achieve continent-wide disease surveillance

19 October 2020
Appeared in BioNews 1068

$100 million has been invested into the launch of Africa Pathogen Genomics Initiative (Africa PGI) through the Africa Centres for Disease Control (Africa CDC) and the African Union Commission.

The objective of Africa PGI is to increase the use of genomics in public health, with the aim to identify and challenge epidemic disease threats such as COVID-19. Furthermore, the initiative also aims to survey endemic diseases such as cholera, ebola, HIV and AIDS, Lassa fever, malaria and tuberculosis.  

'Africa is experiencing high burden and frequent outbreaks of diseases and these continue to be magnified as the continent moves towards greater integration,' said Dr John Nkengasong, the director of Africa CDC. 'The Africa PGI will help member states build their capacities to operate strong surveillance and laboratory networks supported by advanced technologies to reduce the burden of disease and respond to outbreaks quickly and effectively.'

Genome sequencing can be used to understand, monitor and react to emerging pathogens by defining them and tracking their changes over time. Africa PGI will involve investment towards training and provision of materials and technology to implement and expand next generation sequencing (NGS) to public institutions. NGS technology, developed over ten years ago, allows parallel sequencing of large numbers of DNA segments in a single reaction – and, once set up, is both faster and cheaper than classic genome sequencing technologies.

'Despite the potential that this technology has for the continent, more than 80 percent of the capacity exists in non-public health institutions,' Dr Nkengasong said. 'Strengthening genomic surveillance systems is key for early notification and control of disease outbreaks.'

Genomic sequencing is currently playing a major part in the surveillance of the global COVID-19 pandemic and subsequent response (see BioNews 1047). Africa PGI will increase the accessibility of NGS and ultimately will help Africa track the evolution of SARS-CoV-2, the virus that causes COVID-19, in order to improve understanding of the disease and help build tools and polices required to control the pandemic in Africa.

Further than COVID-19, genomic sequencing can also help to identify the resurgence of endemic diseases quickly before they spread. Disease transmission can be monitored, leading to informed decisions and targeted, precise responses in rendering the disease under control. It is vital that scientists in Africa are invested with the tools needed to combat endemic and epidemic diseases to more effectively protect people across the continent.

'Over the last five years, I have seen first-hand how pathogen genomics has helped uncover disease outbreaks and guided real-time outbreak responses more and more in West and Central African countries,' said Professor Christian Happi, director of the African Centre of Excellence for Genomics of Infectious Diseases. 'Scaling up and integrating genomics capacity into existing but often-siloed diagnostics platforms, and connecting them to form a pan-African network, will provide exciting opportunities to take public health surveillance to the next level.'

The contributors include biotechnology companies Illumina and Oxford Nanopore and software giant Microsoft, as well as the Bill and Melinda Gates Foundation and the United States Centres for Disease Control and Prevention.

Africa Pathogen Genomics Initiative launches with $100M investment
Genome Web |  12 October 2020
US$100 million Africa Pathogen Genomics Initiative to boost disease surveillance and emergency response capacity in Africa
Africa CDC |  12 October 2020
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