When conventional testing fails: identifying Maize Lethal Necrosis in Eastern Africa

Maize Lethal Necrosis disease (MLN) had been devastating crops across East Africa. Farmers described it spreading through their fields like a fire — rapid, destructive and difficult to contain. The disease is caused by the introduction of maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV), and efforts to limit its spread depended on accurate, timely diagnosis.

The problem was that standard diagnostic methods weren't working. Samples collected from plants showing classic MLN symptoms were repeatedly testing negative using ELISA and PCR — the techniques routinely used for MCMV and SCMV. Either the tools were missing something, or the picture in the field was more complicated than anyone had assumed.

Fera's plant virology team applied high throughput sequencing (HTS) to the same field samples that conventional methods had failed to characterise. Rather than testing for specific known pathogens, HTS examines the full genetic material present in a sample — making it capable of detecting both known and previously undescribed viruses simultaneously.

The results changed the picture entirely. SCMV was found to be significantly more prevalent than targeted diagnostics had suggested. More importantly, the samples were infected with a range of other viruses — seven of which had never been described before. Maize yellow mosaic virus (MYMV), previously unrecorded in the region, was the most prevalent virus after MCMV itself.

The findings demonstrated a fundamental limitation of targeted diagnostics when dealing with emerging diseases: if you don't know what you're looking for, you won't find it. NGS removes that constraint.

A further challenge was deployability. High-end HTS platforms are largely unavailable in Sub-Saharan Africa due to equipment costs, service infrastructure and reagent expenses. Even more accessible tabletop sequencers such as the MiSeq remain confined to specialist centralised laboratories.

To address this, Fera explored the application of Oxford Nanopore Technology's MinION sequencer — a device that has reduced NGS instrument costs by 50x and relies on cloud-based analysis, removing the need for powerful on-site computing. The results demonstrated that the MinION could accurately diagnose known viruses, with the potential for future iterations to identify novel ones. Its portability and low cost make it a realistic option for deployment in resource-limited settings.

The work led to the development of a targeted seed test for MLN, now used by the Kenyan Government as part of its national response to the disease. Fera continues to work with governments and international partners to support the policy and diagnostic frameworks needed to manage emerging crop threats at scale.

Funded by: Defra Future Proofing Plant Health project (PH0469), the Oxford Nanopore MAP programme, the Global Plant Clinic, and the Swedish International Development Cooperation Agency (SIDA) through an award to the BecA-ILRI Hub.