By Michael Gwarisa in Addis Ababa
Africa is increasingly becoming the frontline of global disease outbreaks. According to data from the Africa Centres for Disease Control and Prevention (Africa CDC), the continent recorded a 40% increase in outbreaks, from 152 in 2022 to 213 in 2024. In the past year alone, Africa has battled multiple health threats, including a deadly cholera outbreak in Southern Africa, escalating cases of Mpox in Central and East Africa, and Marburg and Ebola outbreaks in Rwanda, Tanzania, and Uganda respectively.
While many of these outbreaks have since been brought under control, and the Mpox outbreak, once declared a Public Health Emergency of Continental Security (PHECS), is on the verge of being downgraded, the risk remains high. Climate change, growing urbanization, and increased human-wildlife interaction continue to fuel the emergence and re-emergence of infectious diseases across the region.
When COVID-19 first struck, Africa had very limited genomic sequencing capacity. Only 7 of the 55 African Union Member States possessed next-generation sequencing (NGS) capabilities in their public health laboratories. The few existing laboratories were quickly overwhelmed, leaving the region vulnerable to undetected variants and delayed responses.
However, the pandemic served as a wake-up call, prompting massive investments in genomic sequencing infrastructure. By August 2022, 31 Member States had established NGS capacity, and by 2023, this number had risen to 40 countries. Across the continent, a total of 206 NGS devices have been identified, with significant concentrations in South Africa (79 devices), Kenya (28), and Morocco (18). This rapid expansion has laid the groundwork for a more resilient and proactive health security system, enabling African nations to better detect, monitor, and respond to emerging health threats.
Speaking to Journalists recently in Addis Ababa, Ethiopia, Dr. Collins K Tanui, the Principal Technical Officer – Pathogen Genomics in the Africa CDC said that before the COVID-19 pandemic, Africa’s capacity in genomics was minimal, but the situation has drastically improved.
Way back before COVID-19, we had very little in terms of Genomics but as we speak today, I can tell you for sure that the continent is being seen as one of the champions in genomics. A lot has been done and it’s not only on CIOVID-19 but other pathogens,” said Dr. Tanui.
The Africa CDC has a strategic plan where programmatic goal number 5 prioritises strengthening of clinical and public health laboratory system networks.
“For us to achieve this, there are a number of things that need to be done These include boosting surveillance and early warning systems for public health threats, enhancing timely detecting, characterisation and reporting of outbreaks and strengthening clinical services for both Communicable and Non-Communicable Diseases (NCDs).”
As part of its broader strategic objectives, the Africa CDC has prioritized the expansion of genomic surveillance under Objective 3 of its strategic plan, which focuses on enhancing molecular, genomics, and bioinformatics capabilities across member states. This objective aims to equip countries with the necessary infrastructure and expertise to conduct advanced outbreak detection, improve disease surveillance, and support research and clinical care. Strengthening these capacities is central to Africa CDC’s post-COVID-19 resilience strategy, recognizing that timely and accurate genomic data is crucial in identifying and tracking emerging pathogens. By investing in this pillar, Africa is not only building scientific independence but also ensuring a quicker, coordinated continental response to future health threats.
“Under this, especially for the molecular and genomics as well as Bioinformatics, there is a need to enhance that molecular, genomic and bioinformatics capacity among the member states. This was the areas that we were lagging behind especially before COVID-19. We are also for the aspect for the mapping and optimisation of seeing who is doing what at any given time on the continent,” said Dr. Tanui.
Since its launch in 2017, Africa CDC has rolled out key initiatives to strengthen health security across the continent. These include the Africa Pathogen Genomics Initiative (2020) to enhance genomic surveillance during COVID-19, and the Saving Lives and Livelihoods (SLL) initiative (2021) with Mastercard Foundation to boost vaccine access and build health capacity. In 2023, Phase 2 of SLL was launched to support pandemic preparedness through workforce development, improved laboratories, local manufacturing, and stronger public health institutions. The Africa CDC’s PGI Genomic Epidemiology Ecosystem outlines a comprehensive, eight-part framework to leverage genomics for public health impact across the continent.
“For us to achieve this, we ensure that we focus on the all-round ensuring sample collection all the way to making use of this data in public health.”
This ecosystem begins with the collection of specimens and associated metadata, followed by testing and sequencing, and continues through bioinformatics analysis. It then emphasizes the importance of data standards, curation, and sharing, before progressing to data analyses, integrating clinical and epidemiological insights, and interpretation. Finally, the data is used to inform public health decisions. Central to this ecosystem are key enablers: a skilled workforce, strategic planning, practical use-cases, robust supply chains, quality assurance mechanisms, and reliable connectivity, all essential for maximizing the benefits of pathogen genomics for disease detection, surveillance, and response in Africa.
The Africa PGI is premised on four strategic priorities which include foundational capacity and skilled workforce, integrating genomics into existing surveillance structure, Timely sharing of quality assured genomic data. We also enablers to ensure that we have an ecosystem, and sustainability mechanisms. As we continue to we need to ensure that there is a plan for ensuring that suitability.”
Building Lab Sustainability in Africa
Africa’s healthcare is faced with numerous challenges ranging from workforce attrition, lack of domestic financial investment, and weakened public healthcare system. Another major casue for concern is the heavy reliance of international and foreign donors for healthcare financing. The build sustainability for Genomic Sequencing, the Africa CDC is prioritising strengthening foundational capacity and retaining a skilled workforce.
“As we continue building the laboratories, we have to ensure that there is demand for ensuring that sustainability. During COVID-19, we saw that there was a need for a continental network to support multi-pathogen surveillance and we capaialised on all specialised Genomic and Biooinformtric Centres (SGBC) that was well established.”
Africa has been rapidly expanding its genomics capacity, as evidenced by available data. The Africa Pathogen Genomics Initiative (Africa PGI) has made significant strides in strengthening foundational capacity and building a skilled workforce. This includes establishing a continental network for multi-pathogen surveillance, with specialized genomics and bioinformatics centers (SGBCs) and regional sequencing hubs across the continent.
Key infrastructure investments, such as NextSeq, GridION, and MiSeq systems, alongside automated liquid handlers and high-performance computers, have bolstered the ability to detect and characterize outbreaks. Additionally, over 1,388 trainees from 54 member states, with 40% being female, have been trained, highlighting the initiative’s commitment to workforce development. The Africa CDC Laboratory Network Information Management System further supports these efforts by tracking samples, logistics, training, and quality assurance, ensuring efficient and coordinated operations.
