Africa Pathogen Genomics Initiative Launches with $100M Investment from Illumina, Oxford Nanopore, Gates Foundation, Microsoft, and CDC

Recently,Jointly by the Africa Centres for Disease Control and Prevention and the African Union CommissionInitiated aPathogen Genome Project(Pathogen Genomics Initiative, PGI), which aims to enhance pathogen disease surveillance and public health collaboration by fully leveraging critical genomic sequencing technologies through a cross-continental integrated laboratory network equipped with tools, training, and data infrastructure. Currently, this four-year sequencing project hasSecured up to $100 million in funding, with contributions from multiple organizations including the Bill & Melinda Gates Foundation, Microsoft, Illumina, Oxford Nanopore Technologies, and the U.S. Centers for Disease Control and Prevention (CDC).

At the webinar launching the Africa Pathogen Genomics Initiative, John Nkengasong, Director of the Africa Centres for Disease Control and Prevention (Africa CDC), stated, “A journey of a thousand miles begins with a single step. Today, we gather to warmly celebrate this crucial first step, marking a significant turning point in our application of genomics to infectious disease prevention and control.” Nkengasong explained that the initiative will be anchored by the Africa CDC’s Institute for Pathogen Genomics. Established in 2019, the Institute aims to integrate pathogen genomics and bioinformatics into public health surveillance and outbreak investigations to strengthen disease prevention and control.

Amira Mohammed, Commissioner for Social Affairs of the African Union, pointed out that the COVID-19 pandemic has made us aware of the necessity and importance of strengthening Africa’s disease surveillance systems and epidemic preparedness.“Although the epidemic is a crisis, we are seizing this opportunity to build health systems in our member states.”

According to reports, the PGI project will begin by expanding next-generation sequencing (NGS) capabilities at more than 20 existing public health institutions across Africa, establishing an African-owned database and a real-time data-sharing platform to build a laboratory network in compliance with the regulations of African Union member states. Additionally, training initiatives will be launched, including the establishment of an NGS Academy, to foster international cooperation in infectious disease genomics.

Regarding the launch of this program,Bill & Melinda Gates FoundationDavid Blazes, Expert in Epidemiology and SurveillanceThey described the $45 million provided to this nonprofit organization as a “catalytic investment.” This funding will enable the Africa Centres for Disease Control and Prevention and its laboratories to establish next-generation sequencing (NGS) capabilities and demonstrate the significant value of NGS in the prevention and control of pathogenic bacteria.“We discussed the potential of NGS technology, with the aim of establishing a national public health laboratory system capable of rapidly utilizing NGS to address infectious diseases, and promoting the adoption of this technology across all regions of Africa.”Perhaps the only solace of the COVID-19 pandemic is that it has genuinely sparked public interest in public health and the technologies available for controlling disease outbreaks.”

IlluminaPhil Febbo, Senior Vice President and Chief Medical Officer, stated, “The company’s $20 million investment will be used to provide NGS platforms, reagents, and training support. We will collaborate with the Africa Centres for Disease Control and Prevention to define testing menus, expected throughput, and optimization of other technologies, and to help emerging laboratories across Africa acquire the necessary tools and equipment.”

Febbo pointed out that Illumina aims to ensure that the cost of the program does not become a limiting factor. “For many years, Illumina has been committed to reducing sequencing costs. As the program matures, we are confident that its sustainable development will be maintained through the continued reduction of sequencing costs.”

Oxford Nanopore CEO Gordon SangheraIt stated that 150 MinION devices have been deployed in Africa, supporting customized training programs, and that it will collaborate with local enterprises to achieve local production and manufacturing of reagents.“We hope to contribute to addressing the current COVID-19 pandemic. In the long term, we aim to continuously cultivate a new generation of scientists and innovators, enabling them to access comprehensive DNA information more conveniently, without financial constraints.”

Mark Ihimoyan, Director of Business Development for Microsoft Middle East and AfricaIndicates that the company will provide access to the Microsoft Azure cloud ecosystem to support the sharing of pathogen genomic data.Furthermore, Microsoft will provide technical resources to support the design and construction of the program’s data architecture, as well as the integration of bioinformatics packages on Azure, thereby helping to establish an African pathogen genomic data repository and providing training for the NGS Academy.

Greg Armstrong, Director of the Advanced Molecular Detection Program at the U.S. Centers for Disease Control and PreventionIt emphasizes the importance of establishing robust collaboration between laboratories and public health institutions. Armstrong stated,The U.S. Centers for Disease Control and Prevention will provide technical expertise to Africa PGI and is expected to offer financial assistance in the near future, aiming to bring NGS technology to more low- and middle-income countries.

In recent years, various regions across Africa have leveraged next-generation sequencing (NGS)-based pathogen surveillance and public health approaches to help respond to outbreaks of infectious diseases caused by pathogens such as Ebola virus, Lassa fever virus, yellow fever virus, malaria parasites, and *Listeria*. Although this technology holds significant potential in Africa, more than 80% of the capacity resides outside public health institutions. Challenges include the absence of relevant policies and guidelines, limited genomic and bioinformatics capabilities, a shortage of technical personnel, and constrained ability to utilize pathogen genomic information for public health decision-making. To address these issues, the PGI initiative aims to assemble teams of outstanding researchers and laboratory scientists in Africa to employ NGS for identifying novel pathogens, monitoring epidemic prevention and control efforts, and building Africa-owned databases and real-time data-sharing platforms, ultimately improving the health outcomes of people across the African continent.

References:

1. PGI Official Website: https://africacdc.org/download/africa-pathogen-genomics-initiative-factsheet/

2. Africa Pathogen Genomics Initiative Launches With $100M Investment

https://www.genomeweb.com/sequencing/africa-pathogen-genomics-initiative-launches-100m-investment#.X4kzup2wOM8