Occurrence of Grapevine fanleaf virus in Algerian vineyards, and complete genome sequencing

Abstract

Prevalence and genetic diversity of Grapevine fanleaf virus (Nepovirus foliumflabelli, GFLV) were determined in vineyards and grape varieties in Algeria. Samples (414) from different cultivars and viticulture areas were screened using DAS-ELISA and partially confirmed by RT-PCR, revealing 21% infection incidence. In Ahmer Bou Amer the greatest incidence of infection was recorded (61%). Some vines, confirmed to be GFLV-infected, had characteristic symptoms of leaf yellowing, chloroses, and mosaic patterns, reducing vine vigour and fruit quality. High throughput sequencing and bioinformatics analyses of a single GFLV-infected accession obtained a nearly complete grapevine fanleaf virus RNA1 consensus sequence of 5,979 nt, and an RNA2 with complete consensus sequence of 3,711 nt. Grapevine yellow speckle viroid, Hop stunt viroid and other viruses were also identified in the ‘background’ virome. Phylogenetic analyses of an amplified fragment of the GFLV coat protein gene from some of the accessions indicated close genetic relationships between Algerian and Russian/United States of America GFLV isolates, suggesting potential shared origins or transmission pathways. These results emphasize the need for implementing strict phytosanitary measures (e.g. use of virus-free planting material) to mitigate GFLV spread and its detrimental effects on grapevine production in Algeria.