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 Xiphinema index. 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 X. index following nematodes feeding on roots. In this work, aviruliferous X. index 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 X. index tested positive for GFLV. Additionally, either pooled or single X. index 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 X. index as reservoirs of virus diversity.
Highlights
One of the main characteristics of RNA viruses is their high mutation rates
The main objective of this study was to decipher the genetic composition of Grapevine fanleaf virus (GFLV) variants retained in a single X. index following acquisition from naturally infected grapevines and to identify a putative genetic bottleneck imposed by X. index on GFLV populations during the acquisition/retention phase of the transmission process
The dataset was analyzed for the presence of variants of GFLV
Summary
One of the main characteristics of RNA viruses is their high mutation rates This is due to their highly error-prone RNA polymerase that produces mistakes during replication [1], stimulating the generation of divergent genotypes per infected cell and per cycle that surround a consensus genome sequence [2]. The dynamics of such highly polymorphic population as well as recombination, and reassortment enable the virus to adapt to ever-changing environments in the host and the vector, leading to selection/emergence of specific viral variants. Bottlenecks can occur from abiotic events such as deep freeze or drought and when a perennial plant is harvested and pruned at Viruses 2019, 11, 1139; doi:10.3390/v11121139 www.mdpi.com/journal/viruses
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