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 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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