The Integrated Genomic Surveillance and Data Sharing Platform and Integrated Genomic Surveillance for Outbreak Detection were officially announced on 24 April.

“These projects are poised to strengthen laboratory detection and surveillance of emerging, re-emerging, and endemic diseases, as well as antimicrobial-resistant pathogens in Africa,” said Dr Jean Kaseya, Director General of the Africa CDC. 

“The increasing number of outbreaks is driven by complex ecological, climatic, political, economic, and social factors, all of which are becoming more exacerbated on our continent,” he said. 

“In the face of ongoing global health challenges…Fortifying multi-pathogen molecular detection and sequencing capabilities in the African Union is essential for global health security,” said Laurent Muschel, Acting Director General of the European Commission Health Emergency Preparedness and Response Authority (HERA).

The Africa CDC, HERA, the European Health and Digital Executive Agency, the African Society for Laboratory Medicine and the Africa Public Health Foundation are collaborating in the projects. Together with our partners, we’re building a collaborative network that strengthens our ability to respond to health threats in Africa.

The European Union-funded projects feed into the Africa Pathogen Genomics Initiative (Africa PGI 2.0) which, is a transition from emergency response to building an optimized, resilient, and integrated molecular diagnostic and genomic surveillance ecosystem.

Nqobile Ndlovu, Chief Executive Officer of ASLM, said the launch of the two projects is pivotal in devising scalable and sustainable approaches for integrating molecular diagnostics and sequencing within Africa’s routine surveillance structures. 

“We are eager to collaborate with the Africa CDC and HERA to strengthen laboratory systems ensuring effective responses to current and future health threats,” Ndlovu said.

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The kick-off meeting, convened at the Africa CDC Office in Addis Ababa, Ethiopia, signified a pivotal moment in the collaboration between the African CDC and the European Commission Health Emergency Preparedness and Response Authority (HERA) to strengthen outbreak detection and disease surveillance throughout Africa.

Through these projects implemented by the European Health and Digital Executive Agency (HaDEA), Africa CDC, and HERA, in partnership with African Union (AU) Member States, the African Society for Laboratory Medicine (ASLM) and the Africa Public Health Foundation (APHF), will strengthen national and regional capacities to promptly detect outbreaks, support the integration of AMR genomic surveillance, and facilitate swift and high-quality data sharing for public health decision-making.

His Excellency Dr Jean Kaseya, Director General of the Africa CDC, emphasized the significance of this partnership stating, “The increasing number of outbreaks is driven by complex ecological, climatic, political, economic, and social factors, all of which are becoming more exacerbated on our continent. These projects are poised to strengthen laboratory detection and surveillance of emerging, re-emerging, and endemic diseases, as well as antimicrobial-resistant pathogens in Africa. They also highlight the strategic partnership between Africa CDC and the European Commission.”

Laurent Muschel, Acting Director General of HERA, emphasized, “In the face of ongoing global health challenges, Africa CDC and HERA are taking together concrete actions to strengthen detection of outbreaks, AMR genomic surveillance, and timely data sharing across Africa. Fortifying multi-pathogen molecular detection and sequencing capabilities in the African Union is essential for global health security.”

Africa CDC’s shift towards Africa PGI 2.0 signifies a transition from emergency response to building an optimized, resilient, and integrated molecular diagnostic and genomic surveillance ecosystem. It is critical and timely to incorporate lessons from the COVID-19 pandemic, and empower national and regional reference laboratories to expand their capabilities to detect and characterize epidemic and pandemic-prone diseases. As demonstrated in previous outbreaks, molecular detection and genomic sequencing improves early detection and response to public health emergencies. Mr. Nqobile Ndlovu, CEO of ASLM, remarked, “The launch of the two projects is pivotal in devising scalable and sustainable approaches for integrating molecular diagnostics and sequencing within Africa’s routine surveillance structures. We are eager to collaborate with the Africa CDC and HERA to strengthen laboratory systems ensuring effective responses to current and future health threats”.

“APHF will continue to strengthen collaboration with the Africa CDC and HERA to support the flagship Pathogen Genomics Initiative (Africa PGI) and advance public health laboratory systems for pandemic preparedness and response.” Said Dr. Ebere Okereke, CEO of APHF

The Africa CDC is working with ASLM, APHF, Member States, the Africa Laboratory Technical Working Group, and other partners to ensure the effective and successful implementation of the two projects.

# #

For more information:

Dr. Sofonias Tessema, Program Lead, Africa PGI |Africa CDC| sofoniast@africacdc.org

Media inquiries:

Ms. Margaret Muigai Edwin, Director, Communication & Public Information Directorate: Africa CDC |

Tel: +255 742 635 592 | Email: edwinm@africacdc.org

About Africa CDC

The Africa Centres for Disease Control and Prevention (Africa CDC) is the continental autonomous Health agency of the African Union that strengthens the capacity and capability of Africa’s public health institutions as well as partnerships to detect and respond quickly and effectively to disease threats and outbreaks, based on data-driven interventions and programmes. Learn more at: http://www.africacdc.org 

About Health Emergency Preparedness and Response Authority

The Health Emergency Preparedness and Response Authority (HERA) is a directorate-general of the European Commission with a mission to prevent, detect, and rapidly respond to health emergencies. HERA aims to assess potential health threats, promote research and development, manufacturing, procurement, and equitable distribution of key medical countermeasures to strengthen the EU’s health emergency preparedness and response. Learn more at https://commission.europa.eu

About Africa Public Health Foundation 

The Africa Public Health Foundation exists to forge partnerships and mobilize resources to support critical public health initiatives across the continent, in support of the Africa Centres for Disease Control and Prevention (Africa CDC). Learn more at https://aphf.africa/

About African Society for Laboratory Medicine (ASLM) The African Society for Laboratory Medicine (ASLM) is a pan-African professional body working to advocate for the critical role and needs of laboratory medicine and networks throughout Africa. ASLM aims to strengthen healthcare systems through collaborative efforts with governments, local and international organizations, implementing partners, and the private sector. Learn more at www.aslm.org

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About the Project
Approximately 700,000 deaths occur globally annually due to infections caused by antimicrobial-resistant (AMR) pathogens. In Africa, western sub-Saharan Africa,
is disproportionately affected by AMR relative to other regions. The pervasiveness of AMR in this region threatens to reverse health gains made over the past years,
curtailing the achievement of sustainable development goals. Thus, a robust surveillance system to the emergence and spread of AMR, particularly in bloodstream
infections (BSIs) which are associated with high morbidity and mortality is much needed. In this project, genomic sequencing technologies will be employed to rapidly analyse genomic sequences, identify markers of resistance, and facilitate timely data sharing to support evidence-based decision-making for public health
interventions.

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About the Project
In 2023, 166 outbreaks and public health events were reported in Africa. This calls for a resilient laboratory systems for timely detection and reporting of current and future outbreaks. This project aims to scale up molecular diagnostic and genomic sequencing-based detection and characterization of outbreaks.
Africa CDC is working with Member States to develop guidance, diagnostic algorithm, training and capacity building to enable outbreak detection, and reporting to inform public health response.

The post The Africa Pathogen Genomics Initative (Africa PGI) Integrated Genomic Surveillance for Outbreak Detection (DETECT) appeared first on Africa CDC.

Timely and efficient data transfer through the internet plays a critical role in establishing a real-time public health genomic surveillance system. However, limited bandwidth internet access remains a significant challenge in Africa, hindering the timely transfer of data and effective utilization of cloud-based or open-source web-based bioinformatics solutions and databases. To address this issue, the Africa PGI, in collaboration with ASLM, BMGF, and SpaceX, initiated a pilot project in September 2023. The primary objective of this project is to enhance access to high-speed satellite-based internet, enabling real-time, or near-real-time, transfer of pathogen genomic data and facilitating access to cloud-based resources. This high-speed internet service will not only improve data transfer but also enhance other internet-based operations such as communication, e-learning, virtual meetings, video conferences, and various other activities. The pilot project is being implemented in all Member States that have obtained regulatory approval for the operation of SpaceX’s satellite-based internet.

With the continuous expansion of the Africa CDC laboratory network, digital transformation becomes imperative to enhance efficiency. In November 2023, the Africa CDC introduced a laboratory network information management system (NIMS – https://www.pgi-nims-africacdc.org/) to monitor and facilitate informed decision-making on network operations. The NIMS system serves as a valuable resource for Africa CDC, centers of excellence, regional and national laboratories, enabling efficient tracking of biological sample shipments and ensuring their integrity during transit from referral sites to destination facilities across the network. This system also supports cross-border sample referrals for testing and sequencing. The NIMS system has undergone successful piloting for cross-border sample referral in four sites and is currently being implemented for in-country sample referral in one site. The integration of connectivity, digitization, and innovative solutions in public health genomics in Africa will contribute significantly to the detection, response, and control of infectious diseases. By strengthening genomics capacity, improving internet access, and digitizing laboratory operations, Africa is poised to harness the full potential of genomics for public health surveillance and outbreak management.

For media enquiries please contact:

Dorothy Njagi | Senior Communication Officer- Communication & Public Information directorate | Africa Centres for Disease Control and Prevention| African Union| email: email: njagid@africacdc.org  | Website: www.africacdc.org| Addis Ababa| Ethiopia| Facebook | Twitter

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The initiative is built upon four strategic priorities. The first priority is to enhance foundational capacities by developing skilled workforce, and networks in the fields of molecular diagnostics, genomics and bioinformatics. The second priority is to strengthen data management, analysis, sharing and translation to inform public health response. The third priority is the implementation of high priority genomic use-cases for public health through an integrated genomic surveillance system. Finally, the fourth priority is to advocate for sustainability and enabling mechanisms through a collaborative community approach involving the whole community.

Through Africa PGI 2.0, Africa CDC is shifting its focus from emergency response to building an optimized, resilient, and integrated molecular diagnostic and genomic surveillance ecosystem.

Collaboration is at the heart of Africa PGI 2.0. as Africa CDC aims to strengthen the pivotal public-philanthropic-private partnerships and create the synergy needed to maximize the impact of genomics for disease control and prevention in Africa. By prioritizing capacity-building, data management, genomic surveillance, and collaboration, Africa PGI 2.0 sets the stage for leveraging genomics to address current and future public health challenges in Africa. Through this initiative, Africa is equipping itself with the necessary tools and expertise to lead the way in disease control and prevention through genomics.

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The visit presented a timely opportunity to unveil the state-of-the-art Reference Laboratory at Africa CDC Office buildings constructed through the support of the People’s Republic of China. The unveiling ceremony presented a chance to showcase the laboratory’s capabilities and its anticipated contributions to healthcare advancement in Africa.

H.E Dr. Jean Kaseya the Director General of Africa CDC while welcoming his counterpart from China CDC on his first official visit to Africa, appreciated the Peoples Republic of China for their generous support in advancing public health in Africa. “The Africa CDC and China CDC are keen to enhance their collaboration in multiple areas, and the reference laboratory aligns with Africa CDC’s strategic priorities, enhancing its capacity to respond promptly and effectively to various public health threats. It represents a key milestone in our vision to transform Africa CDC into a world-class, agile and self-sustaining organization,” emphasized Dr. Kaseya.

The Laboratory facility which has two biosafety level (BSL)-I, four BSL-II, two specialized BSL-II (BSL-II plus) and two high containment laboratories (BSL-III) aims to address significant gaps in laboratory systems in Africa. Currently, less than 5% of African laboratories possess fully developed and sustainable capacity for diagnosing the priority diseases within their countries, properly transporting specimens, and adhering to international standards and regulatory requirements. Against this backdrop, expanding clinical and public health laboratory systems and networks in Africa is one of Africa CDC’s top priorities for the period 2023-2027. This laboratory will play a crucial role in achieving this goal by ensuring the expansion of laboratory services and in conducting pathogen research and epidemiology in Africa.

The Africa CDC Reference Laboratory named after Chinese Scientist Dr. Wu Lien-teh, who is a pioneer of modern medicine in China, is fully equipped and will promote collaboration on capacity building of Member States to have strong laboratory systems and networks to improve clinical care, support surveillance and outbreak response and facilitate technology transfer to African institutions.  

H.E Ambassador Hu Changchun, the Head of China Mission to the African Union noted that the inauguration of the Africa CDC new headquarters and the unveiling of Dr. Wu Lien-teh Laboratory will certainly open a new chapter in public health in Africa and inject new momentum into the deepening of China-Africa health cooperation. “President Xi Jinping put forward three major initiatives (i) supporting Africa’s industrialization, (ii) agricultural modernization, and (iii) China-Africa cooperation on talent development. These will provide new opportunities for our friendship and win-win cooperation,” said Ambassador Hu Changchun.

The facility will serve as training and quality assurance center, will provide support for evaluation and validation of diagnostic technologies and tools, facilitate research and development and play important role in outbreak confirmation. The facility will work in close collaboration with National Public Health Institutes/National Reference Laboratories of Member States as continent laboratory network.

“One hundred years ago, Dr. Wu Lien-teh launched a large-scale, systematic campaign to prevent and control plague in China, initiating the modernization of China’s public health system. China CDC will inherit Dr. Wu’s professional attitude and internationalism and will cooperate with Africa CDC to contribute to the health and safety of the people in Africa and the world,” stated Dr. Shen Hongbing the Director General of China National Disease Control and Prevention.

As a Centre of Excellence, the laboratory will house antimicrobial susceptibility testing for surveillance of antimicrobial resistance (AMR) across the continent, biochemical analysis, multiplex molecular diagnosis capacity, bio-banking, advanced pathogen genomic sequencing including metagenomic sequencing capacity for identification of unknown pathogens.

About Africa CDC

Africa CDC is an autonomous health agency of the African Union which supports Member States in their efforts to strengthen health systems and improve surveillance, emergency response, prevention and control of diseases. Learn more at: http://www.africacdc.org 

About China CDC

The Chinese Center for Disease Control and Prevention (or the China CDC) is a national-level technical organization under the National Health Commission that specializes in disease control and prevention and public health https://en.chinacdc.cn/

For media enquiries please contact:

Dorothy Njagi | Senior Communication Officer- Policy, Health Diplomacy & Communication | Africa Centres for Disease Control and Prevention| African Union| email: email: njagid@africacdc.org  | Website: www.africacdc.org| Addis Ababa| Ethiopia| Facebook | Twitter

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La cérémonie de remise a eu lieu au Laboratoire national de santé publique à Yaoundé, au Cameroun. Elle s’est déroulée en présence de S.E. Dr Manaouda Malachie, Dr Benjamin Djoudalbaye, représentant d’Africa CDC et de dignitaires du ministère de la santé. La cérémonie de remise est suivie d’une formation technique d’une semaine sur le séquençage génomique et la bio-informatique pour le personnel du Laboratoire national de santé publique.

L’équipement de séquençage fait partie de l’initiative de génomique des pathogènes d’Africa CDC (Africa PGI) visant à établir un réseau de laboratoires de référence régionaux pour le séquençage génomique et la bioinformatique en Afrique. Cette initiative vise à améliorer la détection et la caractérisation des nouveaux variants du SRAS-CoV-2, de la RAM, du paludisme, du choléra, d’Ebola, de Marburg et d’autres agents pathogènes prioritaires, et à soutenir la recherche et le développement de diagnostics, de vaccins et de thérapies.

Africa CDC a exprimé sa gratitude à S.E. Dr Manaouda Malachie et au Ministère de la Santé du Cameroun pour leur collaboration et leur engagement à faire progresser la santé publique en Afrique. Africa CDC se réjouit de travailler avec le Cameroun et d’autres États membres pour tirer parti des technologies génomiques afin de rendre le continent plus sain et plus sûr.

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À propos du CDC Afrique
Africa CDC est une agence de santé continentale autonome de l’Union africaine créée pour soutenir les initiatives de santé publique des États membres et renforcer la capacité de leurs institutions de santé publique à détecter, prévenir, contrôler et répondre rapidement et efficacement aux menaces de maladies.
Pour plus d’informations, veuillez consulter: http://www.africacdc.org
Follow Africa CDC on Twitter, Facebook, and LinkedIn

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The handover ceremony occurred at the National Public Health Laboratory in Yaoundé, Cameroon. It was attended by H.E Dr Manaouda Malachie, Dr Benjamin Djoudalbaye, Representative of Africa CDC and dignitaries from the Ministry of Health. The handover ceremony is followed by a one week technical training on genomic sequencing and bioinformatics for the National Public Health Laboratory personnel.

The sequencing equipment is part of the Africa CDC’s Pathogen Genomics Initiative (Africa PGI) to establish a network of regional reference laboratories for genomic sequencing and bioinformatics in Africa. The initiative aims to improve the detection and characterization of new variants of SARS-CoV-2, AMR, Malaria, Cholera, Ebola, Marburg and other priority, pathogens and to support the research and development for diagnostics, vaccines and therapeutics.

The Africa CDC expressed gratitude to H.E Dr Manaouda Malachie and the Ministry of Health of Cameroon for their collaboration and commitment to advancing public health in Africa. The Africa CDC looks forward to working with Cameroon and other Member States to leverage genomic technologies for a healthier and safer continent.

— END —

About Africa CDC
Africa CDC is a continental autonomous health agency of the African Union established to support public health initiatives of Member States and strengthen the capacity of their public health institutions to detect, prevent, control, and respond quickly and effectively to disease threats.
For more information, please visit: http://www.africacdc.org
Follow Africa CDC on Twitter, Facebook, and LinkedIn

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Who should apply:
The program is open to National public health institutes (NPHIs) and National Reference Laboratories (NRLs) personnel who wish to gain experience in NGS sequencing or analyzing pathogen genomic sequence data. Applicants should have a minimum of BSc degree and be a citizen of the African Union Member States.

Fellowship Program:

• The fellowship has two tracks – i) a wet-lab track focusing of end-to-end protocols for next-generation sequencing of pathogens; and ii) a dry-lab track with a focus on public health bioinformatics data analytics, interpretation, and reporting.
• The fellowship program aims to support technical experts and future leaders in public health pathogen genomics and bioinformatics in Africa.
• Training led by continent-based educational and professional subject matter experts
• Training at State-of-the-art facilities across the continent
• Multilingual fellowship program

The fellowship program has the following objectives:

• To train pathogen genomics and bioinformatics workforce to improve outbreak detection, investigation & disease surveillance in Africa
• To contribute to strengthening the prevention, preparedness, surveillance, and control of infectious diseases while supporting the implementation of Africa’s New Public Health Order
• To contribute to knowledge and technology transfers and capacity building within and between African Union Member States

Potential candidates and host institutions:

• We are anticipating at least 25 fellows for the 2023 cohort
• 15 host institutions across Africa. Applicants should provide evidence of the host institution’s agreement to accept the fellow for the duration of the fellowship period. Africa CDC and ASLM will support fellows to identify host institutions.
• Only complete applications shall be evaluated by an independent selection committee and the outcome communicated to the applicants

Before applying read the documents below:

More details on the fellowship program

• Information Booklet – Arabic
• Information Booklet – English
• Information Booklet – French
• Information Booklet – Portuguese

How to apply:

• All interested participants should fill in the online application form based on the selected languages:
• Application form – English – https://bit.ly/3KrHk9P
• Application form – French – https://bit.ly/3Mi6sRJ

Application deadline: Friday, May 05, 2023, 5:00 PM (EAT)

Start of the fellowship: June 2023

Contact Information: For all inquiries, please contact: Africa CDC – Africa PGI Help Desk

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