Mobile, instant diagnosis of viruses

Science at work 9 January 2019
In a first for plant virology, a team from CIRAD recently used nanopore technology to sequence the entire genomes of two yam RNA viruses. This as yet little-used but promising molecular biology technique paves the way for new tools for field diagnosis of plant, animal and human diseases. A godsend for developing countries…
A new technique will make it possible to detect viruses in the field. In this case, a yam plot in Guadeloupe © D. Filloux, CIRAD

A new technique will make it possible to detect viruses in the field. In this case, a yam plot in Guadeloupe © D. Filloux, CIRAD

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

Reference

Filloux D., Fernandez E., Loire E., Claude L., Galzi S., Candresse T., Winter S., Jeeva ML., Makeshkumar T., Martin D.P., Roumagnac P., 2018. Nanopore-based detection and characterization of yam viruses. Nature - Scientific Reports 8:17879

How does nanopore sequencing work?

The DNA molecule to be sequenced is captured by an unwinding enzyme that slowly extrudes the single-strand DNA through the nanopore. As it passes through, the DNA is constricted by the nanopore, which slows it down. This makes it possible to "read" the nucleotide bases by measuring the intensity of the electric current passing through the nanopore at a given time.

Illustration © Kerstin Göpfrich

Illustration © Kerstin Göpfrich

See also