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European-African Initiative to Invest €22M to Support Pathogen Genomic Epidemiology Efforts


NEW YORK — The European Union and several partners will invest €22 million (about $22 million) into new projects that strengthen pathogen genomic epidemiology activities in Africa, including the use of genomic data to inform public health decision making.

The Global Health European and Developing Countries Clinical Trials Partnership Joint Undertaking (GH EDCTP3 JU) is overseeing the project, which recently closed a call for research proposals on "Genomic epidemiology for the surveillance and control of poverty-related and emerging/re-emerging infections in sub-Saharan Africa."

A spokesperson for the Global Health EDCTP3 said that proposals will now undergo an evaluation by independent experts, after which some will be selected for funding. Once grant agreements with selected projects are signed, the partnership will be able to provide more information about its scope and duration. According to the spokesperson, Global Health EDCTP3 believes that the EU might ultimately contribute about €5 million per project.

Global Health EDCTP3 was formed in May, at the same time it announced the call. The joint undertaking includes the EU as well as the European & Developing Countries Clinical Trials Partnership (EDCTP) Association. The latter has existed since 2003 and consists of institutions supported by 14 European and 18 African countries. In 2014, it was renewed for another decade.

Global Health EDCTP3 has a total budget of around €1.6 billion to finance various programs, of which roughly half comes from the EU's Horizon Europe program, according to the undertaking. The rest is derived from the EDCTP and various philanthropic organizations. In the case of the new genomic epidemiology call, the Gates Foundation is a contributing funder.

According to the Global Health EDCTP3 spokesperson, one catalyst for supporting new genomic epidemiology-related projects in Africa was the COVID-19 pandemic, which led to an "unprecedented expansion in global genomic sequencing capacity," including in Africa.

While capacity improved due to the pandemic, more investments are needed to harness its potential and to create the infrastructure to make any findings actionable, the spokesperson said.

One way to achieve this, according to a description of the program, is to better link pathogen genomic sequencing data to clinical and epidemiological data in order to create integrated surveillance systems to monitor infectious diseases in sub-Saharan Africa.

According to the spokesperson, GH EDCTP3 JU is specifically looking to fund proposals that will educate public health professionals and researchers in Africa, so that they have a better understanding of how to use genomic information related to infectious diseases in their surveillance and disease-control programs. Such public health authorities should also have better access to genomic data, and more researchers and public health officials should gain competency in genomic epidemiology. Projects should also focus on training the next generation of researchers and officials, so that they are comfortable with generating and using such data.

GH EDCTP3 JU is also looking to fund projects that will establish better cooperation between epidemiology sites, such as biobanks and clinical trial sites, and genomic sequencing labs within national public health institutes. In particular, the project description mentioned the Africa Pathogen Genomics Initiative as an example of the increased capacity for genomic sequencing in Africa.

Ultimately, the goal is to enable African countries to better understand the epidemiology of infectious pathogens, characterize pathogens, and support public health projects and intervention design and effectiveness monitoring.

Africa PGI did not respond to questions regarding its role in the new undertaking.

Other priorities outlined by the Global Health EDCTP3 include the creation of integrated data platforms for epidemiological, clinical, and genomic data; pilot projects for translational research that will use genomic data for decision making or product development purposes; and community building, resulting in increased genomics expertise in the region.

Yet another focus is the development of lower-cost solutions, such as diagnostics, therapies, and vaccines that can be deployed in low-resource settings. Global Health EDCTP3 is also looking to strengthen genomic epidemiology capacity within national and regional public health organizations in sub-Saharan Africa.

Proposals related to COVID-19 were not accepted for this specific program, given the investments to date in that area, though harmonization across other projects, including the European COVID-19 Data Platform, as well as the BY-COVID project, is being encouraged.

'Big step'

According to Anita Suresh, deputy director of genomics and sequencing at the Foundation for Innovative New Diagnostics (FIND), EDCTP routinely administers such calls as part of the Horizon Europe program focused on improving diagnostics and health systems in Africa. However, she said that the new call is the first ever devoted to genomic surveillance and "signals the increased interest and funding opportunities for genomics overall."

Suresh said that the Geneva, Switzerland-based nonprofit has been tracking next-generation sequencing investments and capacity built for the pandemic in collaboration with the New York-based Rockefeller Foundation's Pathogen Prevention Institute. FIND and PPI have undertaken capacity mapping via the Access to COVID-19 Tools Accelerator Genomic Surveillance Working Group, which is co-led by the World Health Organization.

"There has clearly been a significant increase in installed base and capacity for sequencing in Africa and globally," Suresh said of recent trends. Given this buildup in genomic capacity, she said that it is "critical" that sequencing resources and related data are linked and embedded in the overall epidemiological surveillance networks.

"Countries and implementers also want to make sure this built-up infrastructure and capacity is leveraged beyond COVID-19 for priority infectious diseases, starting with surveillance and eventually improved clinical care," Suresh added. As such, she called the new GH EDCTP3 JU program a "big step in the right direction" to ensure that the COVID-19 sequencing capacity is scalable and sustainable beyond the pandemic as a tool for surveillance and health systems.

Joe Fitchett, senior adviser for biotechnology at the Institut Pasteur de Dakar in Senegal, said that in general, sequencing pathogens for new and escalating threats is important in settings where access to care can be delayed and where fevers are common with a wider range of potential infections.

The value of sequencing, Fitchett said, is amplified by its integration with surveillance systems, including immunological platforms to assess host response to pathogens and links to clinical and epidemiological data. He said this is already routine in several African countries, including Senegal, and "should be a necessary standard going forward."

In addition to investing in genomic epidemiology data integration platforms, as well as improving expertise throughout the region, a reduction in the price of sequencing, as well as turnaround time, could also lead to more routine sequencing of pathogens, Fitchett pointed out.

"That reduction in cost is too slow but urgently needed to better characterize pathogens of concern regionally and globally," he stressed, "and to improve access to diagnostics in settings with a reduced number of laboratories."