New genomic tool holds promise for rapid surveillance of Rift Valley fever virus

Scientists from the International Livestock Research Institute (ILRI) and colleagues have published a new study in BMC Genomics (Jul 2022) that describes the development of a computational tool for genomic surveillance of the Rift Valley fever virus that can aid in rapid detection and control of Rift Valley fever, a viral zoonotic disease affecting both humans and animals such as cows, sheep, goats and camels.

Genetic evolution of the Rift Valley fever virus in Africa has been shaped mainly by environmental changes in the last few decades such as abnormal rainfall patterns and climate change. Currently, 15 lineages of the Rift Valley fever virus have been identified to be circulating in sub-Saharan Africa.

Virus spillover events contribute to outbreaks of the disease, as was the case in the largest recorded Rift Valley fever epidemic of 1977 in Egypt during which about 200,000 people were infected. Genomic surveillance of the virus can help in early detection, prevention and control of disease outbreaks. 

The new computational tool can rapidly classify and assign lineages of Rift Valley fever isolates. The tool is based on the glycoprotein gene and whole genome sequences of the virus isolates. It is available both as a command line tool and a web application hosted at

Testing and validation of the tool for specificity, sensitivity and accuracy shows it to be useful in tracing the origin of disease outbreaks. It can therefore be used to support national and regional Rift Valley fever surveillance efforts.

Lead author John Juma is an ILRI PhD student registered with the South African National Bioinformatics Institute, University of Western Cape and is supported by the research-for-development project Boosting Uganda’s Investment in Livestock Development (BUILD) led by ILRI and funded by the German Federal Ministry of Economic Cooperation and Development. 

Sam Oyola (senior author and PhD supervisor) is a senior scientist at ILRI supported by the Rockefeller Foundation, the Africa Centers for Disease Control and Prevention and the CGIAR Research Program on Livestock. Dr Oyola works in collaboration with colleagues at the University of KwaZulu-Natal, Stellenbosch University, Universidade Federal de Minas Gerais, the Kenya Medical Research Institute, the Centre for the AIDS Programme of Research in South Africa, the University of Western Cape and the University of Washington.


Juma, J., Fonseca, V., Konongoi, S.L., Heusden, P. van, Roesel, K., Sang, R., Bett, B., Christoffels, A., Oliveira, T. de and Oyola, S.O. 2022. Genomic surveillance of Rift Valley fever virus: From sequencing to lineage assignment. BMC Genomics 23: 520.

Photo credit: Young goats in Hargeisa Market, Somaliland (Terra Nuova)