Methodological guidelines for accurate detection of viruses in wild plant species

Supplemental material for this article may be found at http://dx.doi.org/10.1128/AEM.03538-15.

International audience

English. Ecological understanding of disease risk, emergence, dynamics and the efficacy of control strategies relies heavily on efficient tools for microorganism identification and characterization. Misdetection, such as the misclassification of infected hosts as healthy, can strongly bias estimates of disease prevalence and lead to inaccurate conclusions. In natural plant ecosystems, interest in assessing microbial dynamics is increasing exponentially, but guidelines for detection of microorganisms in wild plants remain limited, particularly so for plant viruses. To address this gap, we explored issues and solutions associated with virus detection by serological and molecular methods in non-crop plant species as applied to the globally important Barley yellow dwarf virus-PAV species (Luteoviridae), which infects wild native plants as well as crops. With ELISA, we demonstrate how virus detection in a perennial wild plant species may be much greater in stems than in leaves, although leaves are most commonly sampled, and may also vary among tillers within an individual, thereby highlighting the importance of designing effective sampling strategies. With RT-PCR, we demonstrate how inhibitors in tissues of perennial wild hosts can suppress virus detection but can be overcome with methods and products that improve isolation and amplification of nucleic acids. These examples demonstrate the paramount importance of testing and validating survey designs and virus detection methods for non-crop plant communities to ensure accurate ecological surveys and reliable inference about virus dynamics in wild hosts.