A new high-throughput, miniature, portable sequencing technique* has been developed in recent years, for human and animal health purposes. It uses mobile laboratories to diagnose viruses such as Ebola or Zika almost instantly, in the field. Diagnosis is both quick and early, which avoids the need to transfer contaminated samples.

"The technology is characterized by the production of long nucleotide sequences, which makes it possible to sequence the entire viral genome," Philippe Roumagnac, a virologist with CIRAD, explains. CIRAD was one of the first laboratories in the world to test and validate its use in plant virology. "Using a diseased yam plant, it took us just a few hours to sequence the entire genome of two single-strand RNA viruses, a macluravirus and a potyvirus" , his colleague Denis Filloux adds.

Mobile, instant diagnosis of plant viruses, to back up epidemiosurveillance networks

As with human virology, the fact that the technique has now been validated in a plant virology laboratory paves the way for real-time, mobile detection of chronic, seasonal or emerging plant viruses, even in isolated areas. By shortening the time that elapses between sampling and diagnosis, the technology will help epidemiosurveillance networks detect harmful organisms at an earlier stage.

This work, by an international team including CIRAD and European, Indian and South African partners, was funded by Agropolis Fondation under a flagship project, E-SPACE (Improving epidemiosurveillance of Mediterranean and tropical plant diseases).

* Oxford Nanopore MinION