Detection of Multiple Variants of Grapevine Fanleaf Virus in Single Xiphinema index Nematodes

Abstract

Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode <i>Xiphinema index</i>. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in <i>X. index</i> following nematodes feeding on roots. In this work, aviruliferous <i>X. index</i> were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 <i>X. index</i> tested positive for GFLV. Additionally, either pooled or single <i>X. index</i> carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of <i>X. index</i> as reservoirs of virus diversity.