Detecting DNA in molecular diagnostics: dead or alive?

Invasive organisms pose a threat to native European forests through their introduction via global trade of living plants or plant parts. The analysis of samples from such traded plants, for example with molecular diagnostic tools, provides information about their infection status. However, standard routine assays do not indicate if the identified pests are alive or dead. In this project, we are testing a new method of Oxford Nanopore Technologies (ONT) sequencing, in which a trained AI model infers viability of the sequenced material from raw sequencing signals. We will sequence living and damaged/dead cultures of different fungal pathogens that we regularly use in our lab and compare the results to understand how this technology may be employed in the early detection and monitoring of invasive pathogens.