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Africa Pathogen Genomics Initiative Launches With $100M Investment

NEW YORK – The Africa Centres for Disease Control and Prevention and the African Union Commission has launched an initiative to expand genomics-based public health pathogen surveillance. The four-year public-private partnership was officially launched on Monday with $100 million in support pledged by partners that include the Bill and Melinda Gates Foundation, Microsoft, Illumina, Oxford Nanopore Technologies, and the US Centers for Disease Control and Prevention.

"A journey of 1,000 miles begins with a first step; today we are here to celebrate that first step, an important turning point in our ability to apply genomics in fighting infectious diseases," said John Nkengasong, director of the Addis Ababa, Ethiopia-based Africa CDC, in a webinar to launch the African Pathogen Genomics Initiative (PGI).

Amira Mohammed Elfadil, commissioner of social affairs at the African Union, officially launched the initiative. She noted that the COVID-19 pandemic has underscored the need to strengthen disease surveillance systems and epidemic preparedness in Africa. While the pandemic is a crisis, she said, "We are taking it as an opportunity to build our health systems in our member states."

The initiative is part of an overarching drive to enhance health and economic prosperity on the continent through a program called the Africa Health Strategy 2016 – 2030.

It will be anchored in the Africa CDC's Institute for Pathogen Genomics (IPG), Nkengasong said. The institute was established in 2019 "to integrate pathogen genomics and bioinformatics into public health surveillance, outbreak investigation, and improved disease control and prevention," he said.

During the webinar, speakers from across the continent of Africa spoke about how next-generation sequencing-based pathogen surveillance and public health approaches have already been used in recent years to help squash infectious disease outbreaks of pathogens like Ebola, Lassa fever, yellow fever, malaria, and listeria. 

However, "Despite the potential that this technology has for the continent, more than 80 percent of the capacity exists in non-public health institutions," Nkengasong said. "Additional challenges include lack of continental policies and guidance, limited genomes and bioinformatics capacity, inadequate technical workforce, and limited translation of public health decision-making using pathogen genomic information."

The PGI will initially begin by expanding next-generation sequencing capacities in more than 20 extant public health institutes spread across the continent.

The Initiative will include establishment of an African-owned data library and real-time data-sharing platform to support the laboratory network in alignment with African Union member state regulations. It will also incorporate training programs, including establishing an NGS Academy that will foster international collaborations in infectious disease genomics.

Nkengasong commented that the launch of the PGI is a "pivotal moment" for strengthening health systems and responding to pandemics and endemic diseases in Africa.

"We are now convinced that disease threats do not just create a social harm, but are also a serious economic and security threat for our continent," Nkengasong said. "We should not only be thinking about pandemics and outbreaks, [but also] how we can use this technology to address issues related to tuberculosis, malaria, and neglected tropical diseases," he said.

David Blazes, a specialist in epidemiology and surveillance at the Bill & Melinda Gates Foundation, said the non-profit's contribution of $45 million is a "catalytic investment." The funding will empower the Africa CDC and the lab network "to establish and demonstrate the value of next-gen sequencing of pathogens," he said.

Blazes said that the initiative had initially been proposed a few years ago by Nkengasong. "We discussed with Dr. John the potential of democratizing the use of next-gen sequencing, bringing this technology to all parts of Africa by creating a network of national public health labs that are capable of rapidly using [NGS] to address infectious diseases," Blazes said. "Perhaps one of the only silver linings of the COVID-19 pandemic is that it really accelerated interest in public health and in technologies that can be used to control outbreaks."

Phil Febbo, Illumina's senior vice president and chief medical officer, said the San Diego, California-based firm's $20 million investment will include providing next-generation sequencing platforms, reagents, and training support. "We will partner with the Africa CDC to determine the testing scope, expected throughput, and other requirements to optimize performance and help these emerging labs across Africa have the tools they need," Febbo said.

Gordon Sanghera, CEO of Oxford Nanopore, did not disclose the specific contribution of the firm to the initiative, but said that it will utilize the 150 MinIon instruments already deployed in Africa and support tailored training programs. "We look forward to having an initial impact in the current COVID pandemic, but in the longer term, in a sustainable way, to be able to generate a new generation of scientists and innovators for whom access to DNA information will be broad, easy, and affordable," Sanghera said.

The price point and decentralized potential of the MinIon will also drive sustainability, but in addition the Oxford, UK-based firm will "work with local partners regionally to generate and make the reagents locally," Sanghera said.

Febbo noted that Illumina wants to ensure that "costs aren't an element" to the initiative. "Over the years, Illumina has been dedicated to driving down the cost of sequencing," he said, adding that as the initiative matures and the 2030 goals are achieved, "I am fully confident that we will continue to see the cost of sequencing reduced so that there can be sustainability."

Mark Ihimoyan, Microsoft's director of business development for the Middle East and Africa, did not disclose the firm's exact contribution, but said the company will provide access to the Microsoft Azure cloud ecosystem, "to support pathogen genomics data sharing and bioinformatics." Microsoft will also contribute technical resources to support the design and construction of the initiative's data architecture and the integration of bioinformatics software packages on Azure, as well as help build the Africa-owned data archive and repository for pathogen genomics and provide training on Azure as part of the NGS Academy.

Greg Armstrong, director of the advanced molecular detection program at the US CDC, noted during the webinar that the US began incorporating sequencing into public health pathogen surveillance and detection about seven years ago and about three years ago started conversations with the Gates Foundation around bringing the technology to low- and middle-income countries.

Armstrong emphasized the importance of having a robust network of labs and public health institutes working together, as well as the importance of collaboration between academic groups and government. The US CDC will provide technical expertise to the Africa PGI, Armstrong said. "In addition to that, I anticipate in the near future that we'll also be in the position to provide financial assistance," he said.

Febbo commented that technology needs the right ecosystem and stakeholder participation to be sustainable, and he underscored the importance of public-private partnerships.

"To achieve success, I think the Africa CDC has really brought together the right folks to make sure that trained professionals are ready to receive the instruments and technologies, [and] to make sure that there is service and support available if the machines go down," he said. "We want to make sure that this initiative builds an incredible group of investigators and laboratory scientists across Africa who can use next-generation sequencing to characterize emerging pathogens."