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Genetic diversity analysis of grapevine fanleaf virus (GFLV) isolates, using a corpus of 40 ORF1 (left panel) and 80 ORF2 (right panel) nucleotide sequences. Graphics represent π (substitutions) and Tajima’s D (DT) for evolution along the ORF1 and ORF2 sequences. Bars and # and * correspond to statistically validated regions (P-values at 0.05 and 0.001), respectively
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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 demarca...
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High-throughput sequencing has provided the capacity of broad virus detection for both known and unknown viruses in a variety of hosts and habitats. It has been successfully applied for novel virus discovery in many agricultural crops, leading to the current drive to apply this technology routinely for plant health diagnostics. For this, efficient...
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... Overall, the similarity in sequences within the same host and year of nding, irrespectively of location, substantiates that TRSV was spread by vegetative propagation. Additionally, the fact that genotypes differ between different plant species indicates that TRSV had been able to enter the Netherlands on multiple occasions.The observed difference in clustering of RNA1 and 2 of TRSV is in line withHily et al. (2021), who recently showed that the phylogenetic relationship between the Nepovirus subgroups was different when looking at either RNA1 or RNA2. While the division between subgroup A, B and C was clear when comparing RNA1 sequences, this was less clear for RNA2. ...
Occasional findings of Tobacco ringspot virus (TRSV) in the Netherlands since 1997, were reason for large-scale surveys for TRSV in vegetatively propagated ornamental plants and for its vector, Xiphinema americanum sensu lato. In total, TRSV was identified in ten ornamental species, comprising over 30 cultivars, while X. americanum s.l. was not found. In addition, TRSV was identified in four ornamental species originating from outside the Netherlands. This report describes a newly designed and validated real time RT-PCR and gives an overview of TRSV findings and interceptions, including phylogenetic analyses of (nearly) complete genome sequences from available isolates and NCBI GenBank accessions in relation to their metadata of host and origin. Overall, the results suggest that TRSV entered the Netherlands on multiple occasions and was further spread by vegetative propagation. Furthermore, TRSV seems to be more widespread in the European Union (EU) than previously assumed, indicating that the current regulatory measures do not fully safeguard the absence of TRSV. Alternative strategies to protect the crops at risk are discussed, and reconsideration of the regulatory status of TRSV in the EU is recommended.
... In this context, our study predicted several different potential recombination sites involving the AILV genomes of different hosts, and, in particular, those of grapevine (AILV-V), artichoke (AILV-C), and chard (AILV-B). This recombination, and particularly in these host types, was almost expected, since these are plant species that often share the same agricultural habitats and in consideration of the fact that recombination events are quite frequent in nepoviruses [33]. It is likely that these recombinations are due to the existence of common vectors in nature, which could facilitate the encounter of different AILV isolates in the same plant. ...
Despite its first description in 1977 and numerous reports of its presence in various plant species in many countries, the molecular information available in GenBank for artichoke Italian latent virus (AILV) is still limited to a single complete genome sequence (RNA1 and 2) of a grapevine isolate (AILV-V) and a partial portion of the RNA2 sequence from an isolate of unknown origin and host. Here, we report the results of molecular analyses conducted on the RNA2 of some AILV isolates, sequenced for the first time in this study, together with the first-time identification of AILV in a new host plant species, namely chard (Beta vulgaris subsp. vulgaris), associated with vein clearing and mottling symptoms on leaves. The different AILV isolates sequenced were from artichoke (AILV-C), gladiolus (AILV-G), Sonchus (AILV-S), and chard (AILV-B). At the molecular level, the sequencing results of the RNA2 segments showed that AILV-C, AILV-G, AILV-S, and AILV-B had a length of 4629 nt (excluding the 3′ terminal polyA tail), which is one nt shorter than that of the AILV-V reported in GenBank. A comparison of the RNA2 coding region sequences of all the isolates showed that AILV-V was the most divergent isolate, with the lowest sequence identities of 83.2% at the nucleotide level and 84.7% at the amino acid level. Putative intra-species sequence recombination sites were predicted among the AILV isolates, mainly involving the genomes of AILV-V, AILV-C, and AILV-B. This study adds insights into the variability of AILV and the occurrence of recombination that may condition plant infection.
... AhNV identi ed in a non-vascular plant encoded a MP with the characteristic 'LPL' motif, similar to the ones encoded by nepoviruses of vascular plants (Mifsud et al., 2022). As nepovirus MP facilitates the cell-to-cell movement of viruses in vascular plants (Hily et al., 2021), identi cation of such MP homolog in yet another nepovirus of non-vascular plant warrants further studies to con rm their function in viruses of non-vascular plants (Mifsud et al., 2022). ...
... However, viruses in sub-groups A and C were scattered in distinct clades in both Pro-Pol and polyprotein 2-based phylogenetic trees, and further sub-grouping within sub-groups A and C was di cult. Hily et al. (2021) observed scattering of sub-group A and C nepoviruses as distinct clades in ORF2 nucleotide sequence-based phylogenetic tree. Increasing discoveries of novel nepoviruses increase the phylogenetic diversity of nepoviruses, which warrants revisiting of the nepovirus sub-grouping. ...
Secoviridae family contains single stranded RNA genome-containing viruses that infect plants. In the present study, we mined publicly available plant transcriptomes and identi ed sixty-one putative novel secoviral sequences in various plant species ranging from bryophytes to trees, which increased the known secoviral diversity by approximately 0.5-fold. Of the identi ed viral sequences, 13 were monopartite and 48 were bipartite, and sequences of 52 secoviruses were coding-complete and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization, sequence similarity to known members, phylogeny and secovirus species demarcation criteria, all but three identi ed novel secoviruses were assigned to different secoviral genera-Cheravirus (3), Comovirus (2), Fabavirus (5), Nepovirus (29), Sadwavirus (3), Sequivirus (1), Stralarivirus (1), Torradovirus (4) and Waikavirus (10). Genome organization of two of the identi ed waika-like viruses resembled that of the recently identi ed waika-like virus-Triticum aestivum secovirus. Phylogenetic analysis revealed the host-waikavirus co-evolution pattern in a few waika-and waika-like viruses, the increased phylogenetic diversity of nepoviruses and the phylogenetic clustering of waika-like viruses. The study paves way for further studies on understanding the biological properties of identi ed novel secoviruses.
... It is the first time that genetic differentiation between vineyard sites within a same vine-growing region is described for GFLV. Indeed, while differential geographic structuration of GFLV populations between countries have been previously described [17,86], no genetic differentiation was observed between populations from three naturally GFLV-infected Californian vineyard sites [26]. Additionally, in France in 2004, the comparison of 85 sequences of the 2C CP coding region of GFLV isolates from two vineyard parcels located 500 m apart in the Champagne region showed no genetic differentiation according to the parcel [18]. ...
... Regarding GFLV, this feature appears essential as this virus exists as a population of numerous and sometimes unique (this study) genetically distant molecular variants within a vineyard site [18,20,26,55,87,88]. In the Pa and Py vineyards, the overall nucleotide sequence diversity (π) was similar to the one observed for GFLV sequences from all around the world either for ORF1 or ORF2 sequences [17]. As previously observed [17,18,55,[88][89][90], intra-species recombination events were predicted in this study. ...
... In the Pa and Py vineyards, the overall nucleotide sequence diversity (π) was similar to the one observed for GFLV sequences from all around the world either for ORF1 or ORF2 sequences [17]. As previously observed [17,18,55,[88][89][90], intra-species recombination events were predicted in this study. Mixed infection with more than one genetically divergent molecular variant of each GFLV genomic RNA were found in most vines in the Pa and Py vineyard sites. ...
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.
... Since plants are the only known hosts of nepoviruses and these viruses are typically transmitted through pollen [5], one can speculate about a possible pollen and plant origin of Hobart nepovirus 3. Among the betterdescribed nepoviruses, our novel nepovirus isolates are closest to melon mild mottle virus, grapevine deformation virus, and petunia chlorotic mottle virus based on RNA1 sequences, all of which are subgroup A nepoviruses [11]. On the other hand, based on the phylogenic tree generated using the partial MP coding region of RNA2, the new bean nepovirus isolates were closest to caraway yellows virus, a recently described subgroup C nepovirus from caraway (Carum carvi) in Germany [12] (data not shown). ...
Two common bean leaf samples from Ethiopia that had shown chlorotic fleck and veinal mosaic symptoms but tested ELISA-negative for known viruses were mechanically transmitted to herbaceous hosts to obtain virus isolates ET-773/4 and ET-779. Virus purification from Chenopodium quinoa systemically infected with ET-773/4 yielded icosahedral particles measuring ~ 30 nm in diameter and containing a single capsid protein of ~ 58 kDa, suggesting a nepovirus infection. Analysis of nucleotide sequences generated from RNA1 and RNA2 of the isolates indicated that they represent a distinct virus species in the genus Nepovirus. Surprisingly, the most closely related sequence in the GenBank database was that of Hobart nepovirus 3, an incompletely described metagenomic sequence obtained from honey bees in Tasmania. This new nepovirus from Ethiopia is provisionally named "bean chlorotic fleck virus".
Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.
Viral RNAs can be uridylated in eucaryotic hosts. However, our knowledge of uridylation patterns and roles remains rudimentary for phytoviruses. Here, we report global 3’ terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses. We detected uridylation in all 47 viral RNAs investigated here, revealing its prevalence. Yet, uridylation levels of viral RNAs varied from 0.2% to 90%. Unexpectedly, most poly(A) tails of grapevine fanleaf virus (GFLV) RNAs, including encapsidated tails, were strictly mono-uridylated, which corresponded to an unidentified type of viral genomic RNA extremity. This mono-uridylation appears beneficial for GFLV because it becomes dominant when plants are infected with non-uridylated GFLV transcripts. We found that GFLV RNA mono-uridylation is independent of the known TUTases HEN1 SUPPRESSOR 1 (HESO1) and UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) in Arabidopsis (Arabidopsis thaliana). By contrast, both TUTases uridylate other viral RNAs like turnip crinkle virus (TCV) and turnip mosaic virus (TuMV) RNAs. Interestingly, TCV and TuMV degradation intermediates were differentially uridylated by HESO1 and URT1. Although the lack of both TUTases did not prevent viral infection, we detected degradation intermediates of TCV RNA at higher levels in a Arabidopsis heso1 urt1 mutant, suggesting that uridylation participates in clearing viral RNA. Collectively, our work unveils an extreme diversity of uridylation patterns across phytoviruses and constitutes a valuable resource to further decipher pro- and anti-viral roles of uridylation.
