Senegal Uses Advanced Genomics to Track Rift Valley Fever Outbreak

Following the successful sequencing of the first Senegalese RVF genomes, LNERV rapidly expanded its surveillance activities.

When an outbreak of Rift Valley fever (RVF) emerged in Senegal in September 2025, health and veterinary authorities faced an urgent challenge. The disease posed a serious threat to livestock, rural livelihoods and public health, particularly in regions where farming and animal husbandry are central to local economies.

With support from the International Atomic Energy Agency (IAEA) and the Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, scientists were able to rapidly identify and sequence the virus responsible for the outbreak, giving authorities critical information needed to guide control measures. The outbreak was concentrated in the Saint-Louis and Louga regions, affecting communities across several locations in the Senegal River Basin, including Fass, Gandon, Mpal, Dagana, Richard Toll and Podor, as well as Keur Momar Sarr.

Rift Valley fever is a viral disease that primarily affects cattle, sheep and goats. The disease can cause severe illness and significant pregnancy losses in livestock. Humans can become infected through mosquito bites or direct contact with infected animals. Most human infections cause mild symptoms, though some cases can lead to more serious health complications.

First In-House Genome Sequencing Marks Major Milestone

Samples collected during the outbreak were sent to the National Livestock Laboratory and Veterinary Research Institute (LNERV) in Dakar, where scientists confirmed the presence of the virus using quantitative polymerase chain reaction (qPCR) testing.

The breakthrough came when LNERV researchers successfully carried out whole genome sequencing of the virus using a next-generation sequencing (NGS) platform for the first time entirely within Senegal. The sequencing equipment had been supplied through the IAEA's Zoonotic Disease Integrated Action (ZODIAC) initiative, which aims to strengthen countries' abilities to detect and monitor emerging animal and human diseases. The advanced technology allowed scientists to identify the exact viral lineage responsible for the outbreak within days. Their analysis confirmed that the virus belonged to Lineage H, a strain known for its ability to replicate efficiently and one that has previously been linked to major outbreaks.

According to LNERV Director Dr Assane Gueye Fall, rapid genomic characterization provides essential information that helps authorities implement targeted disease control measures and make informed decisions during outbreaks. The speed of the analysis represented a significant improvement over conventional diagnostic approaches, which often require much longer timeframes to generate detailed genetic information.

IAEA Support Builds Regional Disease Surveillance Capacity

Scientists from LNERV participated in two intensive three-month training programmes funded through the IAEA technical cooperation programme. The training took place at the FAO/IAEA Animal Production and Health Laboratory in Seibersdorf, Austria, where researchers learned how to operate advanced sequencing systems and analyse complex genomic data. The achievement has strengthened LNERV's position as one of the few veterinary laboratories in Africa equipped with advanced pathogen sequencing capabilities.

Support provided through ZODIAC and the Veterinary Laboratory Network (VETLAB) included equipment, laboratory reagents and specialized training. These resources have enabled the laboratory to generate high-quality genomic data that can be used to support disease surveillance and outbreak response. Senior LNERV scientist Dr Mame Thierno Bakhoum said the assistance has significantly enhanced the laboratory's ability to detect zoonotic diseases and monitor viral evolution in real time.

Senegal Emerges as a Regional Hub for Outbreak Response

Following the successful sequencing of the first Senegalese RVF genomes, LNERV rapidly expanded its surveillance activities. The laboratory is now sequencing virus samples collected from across Senegal and supporting neighbouring countries facing similar challenges.

Mauritania, which has also experienced Rift Valley fever outbreaks, is now sending samples to Senegal for genomic analysis. This cross-border collaboration is helping strengthen regional disease surveillance and improve understanding of how the virus spreads across West Africa. VETLAB continues to provide essential reagents that support both virus detection and ongoing sequencing activities, ensuring the laboratory can maintain its response efforts during critical periods.

Experts say regional laboratories capable of quickly identifying outbreaks and characterizing pathogens are becoming increasingly important as countries face growing threats from emerging infectious diseases. The experience in Senegal demonstrates how investments in advanced scientific infrastructure, training and international cooperation can dramatically improve outbreak preparedness and response. By generating critical genetic information locally, scientists can help authorities act faster, contain outbreaks more effectively and reduce the risks posed by diseases that affect both animals and people.