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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Over the past few years, Africa CDC through the Africa Pathogen Genomics Initiative (Africa PGI) has led the implementation of capacity building initiatives for pathogen genomics sequencing including an aggressive training agenda through short courses on SARS-COV-2 sequencing and data analytics. Through this effort, most Member States have now in-country sequencing capacity, and with continued support, they are ready to apply genome sequencing for the surveillance of priority diseases in Africa. The COVID-19 pandemic has accelerated the adoption of pathogen genomics to inform public health decision-making in Africa but has also highlighted the need for a well-trained workforce to realize the power of next-generation sequencing for other public health functions. Building on existing efforts and to further expand genomics capacity beyond COVID-19, the Africa CDC in partnership with the African Society for Laboratory Medicine (ASLM), and regional centers of excellence has developed and launched the Africa PGI Pathogen Genomics & Bioinformatics Fellowship Program.

“Africa continues to face a growing risk of infectious disease outbreaks. The recent Ebola, Cholera, Marburg, and other outbreaks highlight the urgent need for effective implementation and utilization of pathogen genomics across Africa. It is imperative to strengthen African public health institutions through capacity building and workforce development as the major pillars of the New Public Health Order. This fellowship program is a step forward in our effort to leapfrog outbreak detection and disease surveillance in Africa,” said Dr. Ahmed Ogwell, Acting Director General of the Africa CDC. “The public health benefits of next-generation sequencing can only be realized through a well-trained workforce. We are very excited to partner with the Africa CDC in capacity and capability building for pathogen genomics and bioinformatics in Africa,” said Nqobile Ndlovu, Chief Executive Officer of ASLM.

The fellowship program

The Africa PGI – Pathogen Genomics and Bioinformatics Fellowship Program has 3 tracks; a wet-lab track (Next-Generation Sequencing of pathogens), a dry-lab track (Public health bioinformatics data analytics, interpretation, and reporting), and a track on genomic epidemiology to be included at a later stage. Overall, the fellowship program aims to support technical experts and future leaders in public health pathogen genomics and bioinformatics in Africa.

“Lessons from the COVID-19 pandemic were identified across the pathogen genomics ecosystem, and we are working with our partners to address them. We are extremely excited about this fellowship program, as it is designed to ensure the availability of a qualified workforce that can design, generate, analyze, and interpret genomic data in public health institutions – the need has never been greater or more apparent,” said Dr. Yenew Kebede, Head Division of Laboratory Systems and Networks at the Africa CDC.

Over the course of the fellowship, participants will be trained on core competencies with a focus on genomics and data analytics for outbreak detection, viral and bacterial disease surveillance, antimicrobial resistance, and malaria surveillance. The fellowship will also provide opportunities for alumni and institutional networks to foster future collaborations across Africa.

Call for the application for the fellowship program is open today – 03 April 2023 for the first cohort of 25 fellows. Africa CDC welcomes applications from all qualified persons from all AU Member States. The fellowship program will prioritize women, youth, and those Member States with limited genomics and bioinformatics capacity.

More information about the fellowship can be found in the Call for applications.

-END-

For more information, contact:

Africa CDC

Dr. Sofonias Tessema:  Sofoniast@africa-union.org
Dr. Gerald Mboowa: MboowaG@africa-union.org

ASLM
Edwin Shumba:  EShumba@aslm.org

About Africa CDC

The Africa Centres for Disease Control and Prevention (Africa CDC) is a continental Public Health agency of the African Union that supports Member States in their efforts to strengthen health systems and improve surveillance, emergency response, prevention, and control of diseases.

For more information: https://africacdc.org/

About the African Society for Laboratory Medicine (ASLM)

ASLM is an independent, international, not-for-profit organization founded in March 2011 in Addis Ababa that coordinates, galvanizes, and mobilizes relevant stakeholders at the local, national, and international levels to improve local access to world-class diagnostic services and ensure healthy African communities now and for the long-term. ASLM is the first pan-African society for laboratory professionals, endorsed by the African Union (AU) and supported by multiple African Ministers of Health through its Ministerial Call for Action. ASLM is the implementing partner for the Africa CDC Saving Lives and Livelihoods Initiative. For more information: https://aslm.org

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The emergence and spread of drug-resistant malaria, mutated parasites that skip detection by commonly used rapid diagnostic tests, and the resurgence of malaria transmission in multiple countries are major threats to the control and ultimate elimination of malaria. A recent expansion of malaria genomics in Africa has enormous potential to help tackle these problems, but there is an urgent need to expand the workforce for the generation, analysis, interpretation and utilization of malaria molecular surveillance (MMS) data to fully realize this potential. To fill this gap, Africa CDC collaborated with IDRC, UCSF and JHU to develop and deploy an interactive, hands-on workshop, bringing together programmatic and research personnel to understand the uses of malaria genomics in augmenting public health surveillance, discuss the challenges in implementing such technology, and work together across institutions and countries to identity practical solutions.

“This training was a unique opportunity to bring together researchers and officers from the national malaria control program to support the expansion of malaria molecular surveillance to monitor the spread of drug and diagnostic resistance variants across Africa”, said Dr. Yenew Kebede, Head Division of Laboratory Systems and Networks and Acting Head of Division of Disease Surveillance and Intelligence at the Africa CDC. He further added, “The training will act as one of the avenues to bridge the gap between researchers who develop tools and generate data and the program officers who apply data to inform malaria control and elimination”.

“The knowledge and skills gained from this training workshop have the potential to further expand MMS in public health settings by facilitating networking and exchange of ideas between those working in programmatic and research settings.” said Bryan Greenhouse, Associate Professor and Co-director of the EPPIcenter program at the University of California, San Francisco.

“We hope that this training will inspire researchers and programs to work together to achieve the goal of integrating MMS into routine surveillance in their countries, with the longer-term goal of increased regional collaboration to prevent and respond to the spread of drug and diagnostic resistance,” said Jessica Briggs, Assistant Professor also from the University of California, San Francisco, who led development and delivery of the course.

The participants of this training were equipped with knowledge and skills required for the application of malaria genomic data for programmatic needs. The interactive modules in the present training workshop comprised of introduction to malaria epidemiology, molecular genomics, data management, bioinformatics and data analysis tools, translation of data into meaningful results, and ways to disseminate these results in multiple forums, along with the current state of high priority threats in the region. Trainers from the KEMRI-Wellcome Trust Research Programme in Kenya, the Armauer Hansen Research Institute (AHRI) in Ethiopia, and Brown University were also involved in the workshop.

For more information, contact:

Africa CDC – Africa PGI
Dr Sofonias Tessema
Program Lead – Africa PGI
Africa Centers for Disease Control and Prevention sofoniast@africa-union.org

University of California, San Francisco

Dr Bryan Greenhouse

Associate Professor and Co-director of the EPPIcenter

University of California, San Francisco bryan.greenhouse@ucsf.edu

The post Strengthening the Malaria Genomics Workforce in East Africa appeared first on Africa CDC.

The scientific publication includes over 300 authors from Africa and abroad who worked together to describe and analyze over 100,000 genomes and characterize SARS-CoV-2 variants in real-time. This was the largest consortium of African scientists and public health institutions working together to support data-driven COVID-19 response in Africa.

This publication shows how the large investment, collaboration and capacity building in genomic surveillance on the African continent enabled real-time public health response. Particularly it describes the setting up of the Africa Centre for Disease Control and Prevention (Africa CDC) – Africa Pathogen Genomics Initiative (Africa PGI) and the development of the continental network by the Africa CDC and the Regional Office for the World Health Organization in Africa (WHO) to expand access to sequencing and cover surveillance blind spots, in parallel with the growth of the number of countries that are able to sequence SARS-CoV-2 with in the country.

“The publication highlights that sustained investment for diagnostics and genomic surveillance in Africa was needed to not only combat SARS-CoV-2 on the continent, but establish a platform to address the emerging, re-emerging, endemic infectious disease threats, such as Ebola, HIV/AIDS, TB and Malaria. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.” said Dr. Yenew Kebede, Head Division of Laboratory Systems Acting Head for Surveillance and Disease Intelligence at the Africa CDC

This study was led by two labs that setup the network for genomics surveillance in South Africa, the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University and the KwaZulu Natal Research and Innovation Sequencing Platform (KRISP) at the University of KwaZulu-Natal, in close coordination with the Africa CDC, WHO AFRO and 300 other institutions across the continent.

“The enormous leap Africa made in genomic surveillance during the past two years is the silver lining in the COVID-19 pandemic,” said Dr Matshidiso Moeti, WHO Regional Director for Africa. “The continent is now better prepared to face down both old and emerging pathogens. This is a model of how when Africans are in the driving seat we can come up with lasting change and stay a step ahead of dangerous diseases.”

“It has been an inspiring experience to share knowledge, support and learn from colleagues in all parts of the continent continuously during the pandemic. We witnessed small

countries with no previous genomics experience become empowered in sequencing and bioinformatics methods, and start to actively participate in regular pathogen genomic surveillance for SARS-CoV-2. I think it will be a real model of how scientists and public health officials across countries can have a unified front against infectious diseases in the future.”, says Houriiyah Tegally, Bioinformatician at KRISP and CERI and first-author on this publication.

The results also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most relevant being the detection of Beta and various Omicron subvariants. The publication highlights that most of the SARS-CoV-2 variants causing epidemic in Africa were introduced from abroad.

The scientists proceeded carefully in analysing genomic and epidemiological data collected in over 50 countries that experienced quite heterogenous epidemics in order to reconstruct transmission dynamics of the virus in the most accurate way. “The phylogeographic methods that we employ to investigate the movement of the SARS-CoV-2 virus and its variants into, out of, and within the African continent account for uneven testing and sampling proportions across countries, arising from the realities of doing genomic sequencing in the middle of a pandemic, often in low resourced settings.”, explains Dr. Eduan Wilkinson, head of bioinformatics at CERI at Stellenbosch University and senior author on this publication.

The initial waves of infections in Africa were primarily seeded by multiple introductions of viral lineages from abroad (mainly Europe). The Alpha variant that emerged in Europe in the end of 2020 ended up causing infections in 43 countries with evidence of community transmission in Ghana, Nigeria, Kenya, Gabon and Angola. For Delta, the bulk of introductions was attributed to India (~72%), mainland Europe (~8%), the UK (~5%), and the US (~2.5%). Viral introductions of Delta also occurred between African countries in 7% of inferred introduction. For Omicron the scientific results indicate more reintroductions of the variant back into Africa, at least 69 (95% CI: 60 – 78) from Europe and 102 (95% CI: 92 – 112) from North America than from other African countries. This was amplified for Omicron BA.2; the results suggest at least 99 separate introduction or reintroduction events of BA.2 into African countries, ~65% of which are from Europe and ~30% from Asia.

“The ironical part of these results is that most of the introductions of variants in Africa were from abroad, but Africa was the most discriminated and penalized continent in the world with travel bans. Instead of unscientific and inappropriate reactions, we should be building on the infrastructure established in Africa so that the continent can rapidly pivot to other epidemics without the fear of being punished” said Prof. Tulio de Oliveira, Director of the two institutes, CERI and KRISP, that lead the consortium analysis with the Africa CDC and WHO AFRO.

“This study is a testament to Africa CDC’s impact in rapidly expanding access to sequencing technologies by African Union Member States, and creating a platform for coordination and collaboration by all stakeholders.” said Dr. Ahmed Ogwell, Acting Director of the Africa CDC

About Africa Pathogen Genomic Initiative (Africa PGI)

In 2020, the Africa Centres for Disease Control and Prevention (CDC) launched a multi-sectoral partnership –Africa Pathogen Genomics Initiative (Africa PGI) to integrate pathogen genomics and bioinformatics into public health surveillance, outbreak investigations, and improved disease control and prevention in Africa. Africa PGI is a collaboration between the Africa CDC Institute of Pathogen Genomics, ASLM, US CDC, the Bill & Melinda Gates Foundation, Microsoft, Illumina Inc, Oxford Nanopore Technologies, and others.

About the Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University.

CERI primary goal is to challenge the status quo on epidemic response and innovation in Africa and allows Africa to control its own epidemics and pandemics. Our vision is to effectively respond to epidemics through pathogen genomic surveillance to enhance biomedical discovery, improve the treatment, diagnosis and prevention of human diseases in Africa. CERI is a centre of Stellenbosch University and its state-of-the-art laboratory are based at the new Biomedical Research Institute Building at the Faculty of Medical and Health Sciences campus.

About the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at University of KwaZulu-Natal (UKZN).

KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Council (SAMRC). KRISP is based on a state-of-art building at Nelson R Mandela School of Medicine at UKZN, Durban. KRISP has one of the world’s most advanced genetic sequencing systems in order to enable and support world-class genomics research in Africa. Our objective is to use Next Generation sequencing and bioinformatics to answer scientific questions that are of local, national and international importance.

About World Health Organization (WHO) African Region (WHO AFRO)

World Health Organization contributes to a better future for people everywhere. Good health lays the foundation for vibrant and productive communities, stronger economies, safer nations and a better world. As the lead health authority within the United Nations system, our work touches people’s lives around the world every day. In Africa, WHO serves 47 Member States and works with development partners to improve the health and well-being of all people living here. The WHO Regional Office for Africa is located in Brazzaville, Congo. Learn more at www.afro.who.int and follow us on Twitter, Facebook and YouTube

For media enquiries to Africa CDC – Africa PGI, please contact:

Dr. Sofonias K Tessema
Program Lead, Africa PGI
+251962458542
sofoniast@africa-union.org

For media enquiries to CERI and KRISP, please contact:

Paul Harris
Communication Officer

CERI – Centre for Epidemic Response and Innovation
Stellenbosch University
KRISP – KZN Research Innovation and Sequencing Platform
Nelson R Mandela School of Medicine, UKZN, Durban.
+27 31 260 4898
+27 82 806 6290
paul@htagmedia.co.za

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