Publication Highlight: Targeted sequencing of Rift Valley fever virus (RVFV) on Oxford Nanopore MinION platform

A new study by our GenPath Africa colleagues Sam Oyola and John Juma from the International Livestock Research Institute (ILRI) provides a targeted sequencing approach of Rift Valley fever virus (RVFV) on the portable MinION platform and marks a significant innovation in RVFV genomic surveillance.

What is this publication about?

This study uses a targeted amplicon sequencing protocol, designed to recover complete RVFV genomes directly from clinical samples without the need for virus culture. Inspired by similar protocols used for sequencing SARS-CoV-2, the team designed a set of overlapping primers based on publicly available RVFV genomes. This method was successfully applied to outbreak samples collected from livestock, generating high-coverage viral genomes.

Why is this important?

RVFV is a high-priority pathogen due to its epidemic potential. Genome sequencing plays a critical role in tracking virus transmission, detecting mutations, and informing public health responses. However, traditional genome recovery techniques rely on culturing the virus in biosafety level 3 (BSL-3) laboratories - a resource many research institutions in endemic regions lack. By eliminating the need for virus cultivation, this new method greatly reduces turnaround time, enhances safety, and broadens the accessibility of genomic surveillance tools.

“Rift Valley fever is a zoonotic, climate-aggravated disease that poses serious threats to both public health and food security,” said Sam Oyola, lead scientist on the project. “Our method allows rapid sequencing of the virus genome in the field, without requiring high-containment laboratories.”

How can this make a difference?

This sequencing protocol, when combined with epidemiological data, can strengthen early warning systems and improve response strategies during RVF outbreaks. Its portability and adaptability make it especially valuable for resource-limited settings across Africa and beyond.

“This approach is a game-changer for outbreak response,” said John Juma, co-author of the study. “It allows us to bring genomics directly to the field, enabling near real-time monitoring of RVFV during outbreaks.”

John Juma, Samson Konongoi, Reuben Kimenji, Collins Muli, Paul Dobi, Shebbar Osiany, Edward Kiritu, Bernard Bett, Samuel Oyola, “Targeted sequencing of Rift Valley fever virus (RVFV) on Oxford Nanopore MinION platform.” Protocols.io, 28 April 2025. doi: 10.17504/protocols.io.rm7vz6y3xgx1/v1.