Fellows from Senegal, Indonesia and Tunisia received three months of training in next generation sequencing at the Animal Production and Health Laboratory of the Joint FAO/IAEA Centre in 2022. (Photo: H. Ouled Ahmed Ben Ali/IAEA)
An outbreak of Rift Valley fever in Senegal in September 2025 threatened the health and livelihoods of people and livestock throughout the country and its neighbours. With IAEA support through the Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture , scientists in the two most affected regions were able to rapidly sequence the virus, enabling the authorities to quickly respond to the outbreak.
Rift Valley fever (RVF) is a devastating viral zoonotic disease that primarily affects livestock such as cattle, sheep and goats. In some instances, it can infect humans through mosquito bites or contact with the blood or organs of infected animals. In animals, RVF can cause serious illness and pregnancy loss, while human cases range from mild, flu-like symptoms to more severe complications in a small proportion of patients.
Faster Gene Sequencing Enables Rapid Response
The outbreak in Senegal was concentrated in two regions: Saint-Louis, particularly the Senegal River Basin areas of Fass, Gandon, Mpal, Dagana, Richard Toll and Podor; and Keur Momar Sarr the Louga region.
Samples were collected and sent to the National Livestock Laboratory and Veterinary Research Institute (LNERV) in Dakar, where qPCR testing confirmed the presence of the virus. With skills enhanced through training supported by the IAEA technical cooperation programme , LNERV scientists performed whole genome sequencing using a next-generation sequencing (NGS) sequencer in-house for the very first time. The NGS sequencer, supplied through the IAEA's Zoonotic Disease Integrated Action (ZODIAC) initiative , enabled the scientists to rapidly determine the viral lineage driving the outbreak, providing critical insights to public health authorities within days, far faster than conventional diagnostic methods. This analysis confirmed the virus as Lineage H.
"Quick genomic characterization is essential to tailor response to disease outbreaks and implement efficient control measures," said Dr. Assane Gueye Fall, Director of LNERV. The identification of Lineage H was important due to its previous association with larger epidemics and its known efficiency in viral replication.
Establishing LNERV as a Regional Genomic Hub
The successful sequencing of these initial Senegalese strains marked an important step in expanding LNERV's role in regional genomic surveillance. Supported by the Joint FAO/IAEA Centre and its Veterinary Laboratory Network (VETLAB), LNERV is now one of Africa's few veterinary laboratories equipped with advanced sequencing technology.
Through ZODIAC, whole genome sequencing hubs are being established around the world to localize pathogen detection and characterization capacity, enabling countries to respond rapidly to disease outbreaks and mitigate the risk of pandemics. "Support from ZODIAC and VETLAB including equipment, reagents and training has empowered LNERV to strengthen zoonotic disease detection and surveillance, enabling the timely generation of RVF virus genomes," said Dr. Mame Thierno Bakhoum, senior scientist at LNERV.
This success was built on preparation. LNERV staff completed two intensive three-month training sessions, funded through the IAEA technical cooperation programme, at the FAO/IAEA Animal Production and Health Laboratory in Seibersdorf, Austria, where they gained the practical expertise to operate the Ion S5 sequencer and analyse the resulting data.
Leading the West African Response
Following the successful sequencing of the first local virus genome, LNERV quickly expanded its operations. The laboratory is now sequencing RVF virus genomes from across Senegal and supporting regional efforts by receiving and sequencing virus samples from neighbouring Mauritania, which is managing its own RFV outbreaks. VETLAB promptly provided reagents for RVF detection and ongoing sequencing campaigns that are critical for identifying the virus and generating genetic data needed to guide outbreak response. This ensures continuity in the laboratory's response efforts at a critical moment.
"Capable regional laboratories that can quickly confirm outbreaks and rapidly characterize pathogen sequences are essential for informed decision-making and effective disease control," said Charles Lamien, Animal Health Technical Officer at the Joint FAO/IAEA Centre.
About the ZODIAC Initiative
The IAEA's ZODIAC initiative strengthens the capacity of countries to rapidly detect and respond to zoonotic diseases. A key component of this initiative is equipping high-potential laboratories with whole genome sequencing technology, which produces a precise genomic blueprint for pathogens, providing critical insights into their biological and epidemiological characteristics.
Nine ZODIAC National Laboratories in Africa, Asia and the Pacific, Europe and Latin America received a complete next-generation sequencing package, including short read sequencing platforms, equipment, laboratory supplies and intensive training.
