TY - JOUR T1 - High throughput amplicon sequencing to assess within- and between-host genetic diversity in plant viruses JF - bioRxiv DO - 10.1101/168773 SP - 168773 AU - Sylvain Piry AU - Catherine Wipf-Scheibel AU - Jean-François Martin AU - Maxime Galan AU - Karine Berthier Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/07/26/168773.abstract N2 - Molecular epidemiology approaches at the landscape scale require to study the genetic diversity of viral populations from numerous hosts and to characterize mixed infections. In such a context, high-throughput amplicon sequencing (HTAS) techniques create interesting opportunities as they allow identifying distinct variants within a same host while simultaneously genotyping a high number of samples. Validating variants produced by HTAS may, however, remain difficult due to biases occurring at different steps of the data-generating process (e.g. environmental contaminations and sequencing error). Here, we focused on Endive necrotic mosaic virus (ENMV), a member of family Potyviridae, genus Potyvirus to develop an HTAS approach and to characterize the genetic diversity at the intra- and inter-host levels from 430 samples collected over an area of 1660 km2 located in south-eastern France. We demonstrated how it is possible, by incorporating various controls in the experimental design and by performing independent sample replicates, to estimate potential biases in HTAS results and to implement an automated and robust variant calling procedure.HighlightsHigh-throughput amplicon sequencing to assess plant virus genetic diversityEstimating bias in high throughput amplicon sequencing resultsAutomated variant calling procedure for robust high throughput amplicon sequencing ER -