The nuclear export of cellular mRNAs is a complex process that requires the orchestrated participation of many proteins that are recruited during the early steps of mRNA synthesis and processing. This strategy allows the cell to guarantee the conformity of the messengers accessing the cytoplasm and the translation machinery. Most transcripts are exported by the exportin dimer Nuclear RNA export factor 1 (NXF1)–NTF2-related export protein 1 (NXT1) and the transcription–export complex 1 (TREX1). Some mRNAs that do not possess all the common messenger characteristics use either variants of the NXF1–NXT1 pathway or CRM1, a different exportin. Viruses whose mRNAs are synthesized in the nucleus (retroviruses, the vast majority of DNA viruses, and influenza viruses) exploit both these cellular export pathways. Viral mRNAs hijack the cellular export machinery via complex secondary structures recognized by cellular export factors and/or viral adapter proteins. This way, the viral transcripts succeed in escaping the host surveillance system and are efficiently exported for translation, allowing the infectious cycle to proceed. This review gives an overview of the cellular mRNA nuclear export mechanisms and presents detailed insights into the most important strategies that viruses use to export the different forms of their RNAs from the nucleus to the cytoplasm.

Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.

Fanleaf degeneration is a complex viral disease of Vitis spp. that detrimentally impacts fruit yield and reduces the productive lifespan of most vineyards worldwide. In France, its main causal agent is grapevine fanleaf virus (GFLV). In the past, field experiments were conducted to explore cross-protection as a management strategy of fanleaf degeneration, but results were unsatisfactory because the mild virus strain negatively impacted fruit yield. In order to select new mild GFLV isolates, we examined two old ‘Chardonnay’ parcels harbouring vines with distinct phenotypes. Symptoms and agronomic performances were monitored over the four-year study on 21 individual vines that were classified into three categories: asymptomatic GFLV-free vines, GFLV-infected vines severely diseased and GFLV-infected vines displaying mild symptoms. The complete coding genomic sequences of GFLV isolates in infected vines was determined by high-throughput sequencing. Most grapevines were infected with multiple genetically divergent variants. While no specific molecular features were apparent for GFLV isolates from vines displaying mild symptoms, a genetic differentiation of GFLV populations depending on the vineyard parcel was observed. The mild symptomatic grapevines identified during this study were established in a greenhouse to recover GFLV variants of potential interest for cross-protection studies.

Chez les métazoaires et leurs virus la majorité des ARNm est exportée du noyau par les exportines TAP-p15 et le complexe TREX-1, alors qu’une minorité est exportée par CRM1. Chez les plantes ce processus fondamental reste peu décrit voir inconnu pour les phytovirus comme le CaMV et ses ARNm 19S et 35S. Notre objectif a été de clarifier cette étape primordiale mais jamais étudiée du cycle de CaMV et de l'utiliser pour mieux comprendre l'export nucléaire des ARNm chez la plante modèle Arabidopsis thaliana. Nos principaux résultats montrent que le CaMV utilise les deux voies d’export, celle de TREX-1 et celle de CRM1, pour exporter ses ARN 35S et que le précurseur de sa protéase et transcriptase inverse, P5, est important pour l’export par TREX-1. Nous avons également démontré que la région leader de ces ARN viraux, et en particulier sa structure secondaire, est un élément reconnu par la machinerie d’export nucléaire.

Traditionally, to comprehensively assess the genetic diversity of a viral isolate, i.e. the population of variants, many molecular steps are necessary, mostly involving PCR amplification, cloning and Sanger sequencing. Lately, with its advent, high throughput sequencing (HTS) has become the method of choice. Both approaches, while extremely informative, may not be economically advantageous to use on a large scale, especially when dealing with highly complex viral populations. Here, we describe an Illumina-based amplicon sequencing (AmpSeq) approach, associated with an analytical workflow for rapid diagnostic, combining HTS quality screening at a more affordable cost. Our multi-primers assay was designed to identify a large diversity of both genomic RNAs (RNA1 and RNA2) of Nepovirus foliumflabelli (also known as Grapevine fanleaf virus, GFLV), compatible with the known genetic diversity of this bipartite virus down to detecting rare variants (i.e. present at less than 2% in an isolate). Beyond diagnostics, our approach can be used and adapted to characterize GFLV populations across vineyards as well as to support the development of GFLV cross-protected vines in France.