Complete nucleotide sequences of the RNAs 2 of German isolates of grapevine fanleaf and Arabis mosaic nepoviruses

Characterization of a putative novel nepovirus from Aeonium sp

A virus was isolated from potted plants of an unidentified species of Aeonium, a succulent ornamental very common in Southern Italy, showing chlorotic spots and rings on both leaf surfaces. It was successfully transmitted by sap inoculation to a limited range of hosts, including Nicotiana benthamiana which was used for ultrastructural observations and virus purification. Virus particles are isometric, ca. 30nm in diameter, have a single type of coat protein (CP) subunits 54kDa in size, that encapsidate single-stranded positive-sense RNA species of 7549 (RNA1) and 4010 (RNA2) nucleotides. A third RNA molecule 3472 nts in size entirely derived from RNA2 was also found. The structural organization of both genomic RNAs and the cytopathological features were comparable to those of nepoviruses. In addition, amino acid sequence comparisons of CP and the Pro-Pol region (a sequence containing parts of the proteinase and polymerase) with those of other nepoviruses showed that the Aeonium virus belongs to the subgroup A of the genus Nepovirus and is phylogenetically close to, but serologically distinct from tobacco ringspot virus (TRSV). Based on the species demarcation criteria for the family Secoviridae, the virus under study appears to be a novel member of the genus Nepovirus for which the name of Aeonium ringspot virus (AeRSV) is proposed.

Complete nucleotide sequence of a South African isolate of Grapevine fanleaf virus and its associated satellite RNA

The complete sequences of RNA1, RNA2 and satellite RNA have been determined for a South African isolate of Grapevine fanleaf virus (GFLV-SACH44). The two RNAs of GFLV-SACH44 are 7,341 nucleotides (nt) and 3,816 nt in length, respectively, and its satellite RNA (satRNA) is 1,104 nt in length, all excluding the poly(A) tail. Multiple sequence alignment of these sequences showed that GFLV-SACH44 RNA1 and RNA2 were the closest to the South African isolate, GFLV-SAPCS3 (98.2% and 98.6% nt identity, respectively), followed by the French isolate, GFLV-F13 (87.3% and 90.1% nt identity, respectively). Interestingly, the GFLV-SACH44 satRNA is more similar to three Arabis mosaic virus satRNAs (85%–87.4% nt identity) than to the satRNA of GFLV-F13 (81.8% nt identity) and was most distantly related to the satRNA of GFLV-R2 (71.0% nt identity). Full-length infectious clones of GFLV-SACH44 satRNA were constructed. The infectivity of the clones was tested with three nepovirus isolates, GFLV-NW, Arabis mosaic virus (ArMV)-NW and GFLV-SAPCS3. The clones were mechanically inoculated in Chenopodium quinoa and were infectious when co-inoculated with the two GFLV helper viruses, but not when co-inoculated with ArMV-NW.

Complete sequence of RNA1 of grapevine Anatolian ringspot virus

The nucleotide sequence of RNA1 of grapevine Anatolian ringspot virus (GARSV), a nepovirus of subgroup B, was determined from cDNA clones. It is 7,288 nucleotides in length excluding the 3' terminal poly(A) tail and contains a large open reading frame (ORF), extending from nucleotides 272 to 7001, encoding a polypeptide of 2,243 amino acids with a predicted molecular mass of 250 kDa. The primary structure of the polyprotein, compared with that of other viral polyproteins, revealed the presence of all the characteristic domains of members of the order Picornavirales, i.e., the NTP-binding protein (1B(Hel)), the viral genome-linked protein (1C(VPg)), the proteinase (1D(Prot)), the RNA-dependent RNA polymerase (1E(Pol)), and of the protease cofactor (1A(Pro-cof)) shared by members of the subfamily Comovirinae within the family Secoviridae. The cleavage sites predicted within the polyprotein were found to be in agreement with those previously reported for nepoviruses of subgroup B, processing from 1A to 1E proteins of 67, 64, 3, 23 and 92 kDa, respectively. The RNA1-encoded polyprotein (p1) shared the highest amino acid sequence identity (66 %) with tomato black ring virus (TBRV) and beet ringspot virus (BRSV). The 5'- and 3'-noncoding regions (NCRs) of GARSV-RNA1 shared 89 % and 95 % nucleotide sequence identity respectively with the corresponding regions in RNA2. Phylogenetic analysis confirmed the close relationship of GARSV to members of subgroup B of the genus Nepovirus.

Population genetic analysis of grapevine fanleaf virus

Population genetic analysis of grapevine fanleaf virus (GFLV) was done on the basis of the virus movement protein (MP) gene sequences from the isolates detected and identified in this study and those of all previously reported GFLV strains/isolates. These revealed that the GFLV populations of Iran and Slovenia were highly distinct, whereas those of France, Germany, Italy and the USA were composed of multiple lineages. All populations were significantly differentiated from each other. However, two GFLV isolates from Tunisia, the only recorded GFLVs from that country, were not statistically distinct from the French, German and Italian populations. The ratio of non-synonymous nucleotide diversity to synonymous nucleotide diversity (Pi(a)/Pi(s)) was less than 1, suggesting that the MP gene has been under purifying selection. The neutrality tests were indicative of a balancing selection that is operating within Iranian and USA GFLV isolates, but they show a purifying selection within the other populations. Eleven recombination events were detected in a total of 50 isolates from France, Germany, Iran, Italy, Slovenia and the USA. The results from the recombination analysis were in agreement with those of the phylogenetic analysis. This study suggests that diversity among GFLV geographical populations resulted from possible host adaptation, recombination and founder effects.

Molecular Characterization of Phylogenetically Distinct Isolates of Grapevine fanleaf virus from Iran Based on 2A(HP) Gene

Movement and coat protein genes from Grapevine fanleaf virus (GFLV) isolates have been characterized previously from Iran. In this study, an optimized reverse transcription polymerase chain reaction protocol was established to amplify RNA2 genomic segment corresponding to the hypothetical protein (2A(HP)). The sequence of 2A(HP) was compared with that of previously reported GFLV strains/isolates from other countries which showed 82-86% sequence identities. The 2A(HP) gene from Iran appeared to be standing distinct from other isolates of GFLV when genetic distance- or parsimony-based phylogeneitc analyses were carried out. The present study for the first time reports characterization of Iranian isolate of GFLV based on 2A(HP) gene.

Grapevine deformation virus: completion of the sequence and evidence on its origin from recombination events between Grapevine fanleaf virus and Arabis mosaic virus

The complete nucleotide (nt) sequence of Grapevine deformation virus (GDefV) RNA-1 has been determined. It consists of 7386 nt, excluding the poly(A) tail, and contains a single open reading frame (ORF) encoding a polyprotein (p1) of 252 kDa. P1 comprises the 1A(Pro-cof) proteinase cofactor, the 1B(Hel) NTP-binding protein, the 1C(VPg) viral protein genome-linked, the 1D(Prot) proteinase and the 1E(Pol) RNA-dependent RNA polymerase, all of which are conserved domains in polyproteins of different members of the order Picornavirales. The amino acid (aa) sequence of GDefV RNA1 p1 has the highest identity with the homologous products of Grapevine fanleaf virus (GFLV, 86-88%) and Arabis mosaic virus (ArMV, 73-74%), two nepoviruses of subgroup A. Four cleavage sites for proteins processing were predicted (C/A, C/S, G/E and R/G) and found similar to those of GFLV RNA1. Phylogenetic trees constructed with the complete aa sequences of protein p1 and the RNA2-encoded protein p2 of GDeFV, GFLV and ArMV, showed an incongruent allocation of GDefV in these trees. Pairwise alignment and prediction of recombination sites of both RNA segments showed that GDefV RNA2 has a mosaic structure resulting from recombination events between GFLV and ArMV at the level of the 2A(HP) (homing protein), 2B(MP) (movement protein), 2C(CP) (capsid protein) and the 3'NCR (non coding region). This strongly suggests that GDefV originated from the interspecific recombination between isolates of GFLV and ArMV.

Genetic structure and molecular variability of Grapevine fanleaf virus populations

To gain insights into the evolutionary mechanisms of Grapevine fanleaf virus (GFLV) from the genus Nepovirus, family Secoviridae, the sequences of the complete coding region of RNA2, including genes 2A(HP), 2B(MP) and 2C(CP), and partial sequence from the RNA1-encoded gene 1E(Pol) of 14 GFLV isolates from three naturally infected California vineyards were characterized. Phylogenetic analyses suggested two to three evolutionarily divergent lineages that did not reflect the vineyard origin of the isolates or an association with rootstock genotype or scion cultivar. Examination of the genetic variability of the California isolates alongside isolates worldwide, for which three RNA1 and 44 RNA2 coding sequences are available, revealed similar patterns of molecular evolution for the different regions within the GFLV genome but distinct selection constraints with the strongest pressure exerted on genes 2C(CP) and 2B(MP), an intermediate level of pressure exerted on gene 1E(Pol), and the weakest pressure exerted on gene 2A(HP). Some of the California isolates resulted from interspecies recombination events between GFLV and Arabis mosaic virus with crossover sites suspected in gene 1E(Pol) and identified in genes 2A(HP) and 2B(MP); and intraspecies recombination events inferred in the four target genes but most frequently observed within gene 2C(CP). This study suggested that purifying selection and recombination are important evolutionary mechanisms in the genetic diversification of GFLV.

Genome diversity and intra- and interspecies recombination events in Grapevine fanleaf virus

ABSTRACT Grapevine fanleaf virus (GFLV) was documented in self-rooted vines of four grapevine (Vitis vinifera) cultivars in eastern Washington. GFLV was found as mixed infection in cvs. Pinot Noir, Chardonnay, and Cabernet Franc and as single infections in cv. Merlot. Fanleaf disease symptoms were only observed in the first two cultivars. The spatial distribution of GFLV-infected grapevines was random, suggesting primary spread through planting virus-infected cuttings rather than infield transmission. RNA1 sequences of Washington isolates showed 87 to 89% nucleotide sequence identity between them and with strain F13. RNA2 of Washington isolates was variable in size, showing 85 to 99% sequence identity between them and 81 to 92% with other isolates. As in other GFLV isolates, three conserved putative stem-loop structures were present in the 5' noncoding regions of both RNAs of Washington isolates. Phylogenetic incongruence of GFLV isolates from Washington in 2A(HP)- and 2B(MP)-based trees and identification of putative recombination events suggested that their genomic RNA2 originated from inter- and intraspecies recombination events between GFLV, Grapevine deformation virus, and Arabis mosaic virus. These results confirm interspecies recombination in RNA2 of grapevine-infecting nepoviruses as an important strategy for GFLV evolution.

Gene silencing and virus resistance based on defective interfering constructs in transgenic Nicotiana benthamiana is not linked to accumulation of siRNA

RNA interference (RNAi) was established in Nicotiana benthamiana plants by introducing constructs containing a defective interfering (DI) sequence from Tomato bushy stunt virus (TBSV) in combination with a conserved sense-sequence from the target Grapevine fanleaf virus (GFLV). Silencing in plants was confirmed by Agrobacterium-mediated infiltration of a GFP-sensor containing the GFLV-derived target sequence. The transgene-induced RNAi led to silencing of the GFP-sensor and GFP fluorescence was absent post-infiltration. In plants without GFP fluorescence after infiltration with the GFP-sensor, siRNA specific to GFP and the target virus sequence could not be detected. In contrast, infiltrated leaves of wild type and transgenic plants showing GFP fluorescence after infiltration revealed accumulation of siRNA specific to the sequence of the sensor. Silencing could be inhibited by co-infiltration using a p19 silencing suppressor construct together with the GFP-sensor, which always resulted in bright GFP fluorescence. In parallel, virus resistance of transgenic Nicotiana benthamiana was investigated via challenge inoculation with GFLV. Our results indicate that efficient RNAi in transgenic plants does not necessarily lead to a detectable accumulation of siRNA.

Genetic structure and variability of virus populations in cross-protected grapevines superinfected by Grapevine fanleaf virus

Recombination was assessed in a vineyard site in which grapevines cross-protected with mild strains GHu of Grapevine fanleaf virus (GFLV) or Ta of Arabis mosaic virus (ArMV) were superinfected with GFLV field isolates following transmission by the nematode vector Xiphinema index. The genetic structure and variability within RNA2 of isolates from grapevines co-infected with GFLV field isolates and either GFLV-GHu or ArMV-Ta were characterized to identify intra- and interspecies recombinants. Sequence analysis and phylogenetic relationships inferred intraspecies recombination among GFLV field isolates but not between field isolates and GFLV-GHu. SISCAN analysis confirmed a mosaic structure for two GFLV field isolates for which recombination sites were located in the movement protein and coat protein genes. One of the recombinants was found in eight grapevines that were in close spatial proximity within the vineyard site, suggesting its transmission by X. index. No interspecies recombination was detected between GFLV field isolates and ArMV-Ta. Altogether, our findings suggest that mild protective strains GFLV-GHu and ArMV-Ta did not assist the emergence of viable recombinants to detectable level during a 12-year cross-protection trial. To our knowledge, this is the first extensive characterization of the genetic structure and variability of virus isolates in cross-protected plants.

Comparisons of complete RNA-2 sequences, pathological and serological features among three Japanese isolates of Arabis mosaic virus

Arabis mosaic virus lily and narcissus isolates (ArMV-Li and ArMV-Na) induced severe necrotic spots on Chenopodium quinoa, whereas ArMV butterbur isolate (ArMV-Bu) caused symptomless infection in the plant. The accumulation level of ArMV-Bu in upper non-inoculated leaves of C. quinoa was comparable to that of ArMV-Li or -Na. The agar gel double-diffusion test using an antiserum against ArMV-Li showed ArMV-Li was closely related to ArMV-Na, but not to ArMV-Bu. The RNAs-2 of ArMV-Li, -Na, and -Bu consist of 3707, 3709, and 3789 nucleotides, and they contain one open reading frame encoding a putative polyprotein of 1083, 1084, and 1122 amino acids, respectively. The overall identity of RNA-2 of ArMV-Li displayed more than 90% with ArMV-Na, but less than 70% with ArMV-Bu. A phylogenetic analysis of 2A sequences from ArMV isolates revealed ArMV-Bu was not categorized in any cluster. ArMV-Bu is a unique isolate from the point of view of pathological and serological features, and nucleotide sequence.

Diversity of Grapevine fanleaf virus isolates from Iran

Enzyme-linked immunosorbent assay (ELISA) testing of 126 grapevine samples, from vineyards in the northwest region of Iran, detected Grapevine fanleaf virus (GFLV) in 33 samples. Total RNA from eight of the infected samples were subjected to reverse transcription polymerase chain reaction (RT-PCR) analysis using primers which corresponded to the virus coat protein and 3' non coding region of RNA 2. An expected 1620 bp DNA fragment was amplified from all the tested samples. PCR products from isolates B5, S1 and SH3 were cloned and the nucleotide sequences of three clones from each isolate were determined. The sequences showed that a DNA fragment of 1623 bp from isolate S1 and 1629bp from isolates B5 and SH3 were amplified. The fragments covered 1481 nucleotides of the 3' proximal region of the CP gene plus 142 or 148 nucleotides of the 3' non coding region. Alignment of the sequences revealed over 99% identities among clones from each isolate and 83-93% among clones from different isolates. Identities of 83-94% were found between the isolates from Iran and previously reported GFLV strains/isolates. Phylogenetic analysis based on CP sequences showed that isolates S1 and SH3 formed a distinct cluster but isolate B5 clustered with previously reported GFLV strains. This is the first report on sequence analysis of nearly full-length CP cDNA clones of GFLV isolates from Iran.

Development of degenerate and species-specific primers for the differential and simultaneous RT-PCR detection of grapevine-infecting nepoviruses of subgroups A, B and C

Based on the nucleotide sequence homology of RNA-1 and RNA-2 of nepoviruses isolated from grapevines, three sets of degenerate primers, one for each of the three subgroups of the genus (A, B and C), were designed and proved effective for RT-PCR detection of subgroups in infected grapevines and herbaceous hosts. Primers designed specifically for detecting subgroup A species amplified a fragment of 255 bp from samples infected by Grapevine fanleaf virus (GFLV), Arabis mosaic virus (ArMV), Tobacco ringspot virus (TRSV) and Grapevine deformation virus (GDefV), but not from samples infected by other nepovirus species. Similarly, primers for detection of subgroup B nepoviruses amplified a 390 bp product from samples infected by Grapevine chrome mosaic virus (GCMV), Tomato black ring virus (TBRV), Grapevine Anatolian ringspot virus (GARSV) and Artichoke Italian latent virus (AILV). The third set of primers amplified a 640 bp fragment, only from samples infected by subgroup C nepoviruses, i.e Tomato ringspot virus (ToRSV) Grapevine Bulgarian latent virus (GBLV), and Grapevine Tunisian ringspot virus (GTRSV). These primers were able to detect simultaneously all viral species belonging to the same subgroup and to discriminate species of different subgroups. Multiplex-PCR detection of subgroup A and B nepoviruses was obtained using a specific primer (sense for subgroup A and antisense for subgroup B) for each of the species of the same subgroup in combination with the degenerate subgroup-specific primers. In this way it was possible to detect four different viral species in single samples containing mixtures of viruses of the same subgroup. In particular, for viruses of subgroup A (TRSV, GFLV, ArMV and GDefV) amplicons of 190, 259, 301 and 371 bp were obtained, whereas amplicons of 190, 278, 425 and 485 bp, respectively, were obtained from samples infected with viruses of subgroup B (GCMV, AILV, GARSV and TBRV).

A RT/PCR-partial restriction enzymatic mapping (PREM) method for the molecular characterisation of the large satellite RNAs of Arabis mosaic virus isolates

The satellite RNA of the grapevine isolate NW of Arabis mosaic virus (ArMV) was cloned and sequenced, and showed 75% identity at the nucleotide level to the satellite RNA of the lilac isolate of ArMV. In order to survey ArMV isolates from various geographical origins and natural hosts for the presence of large satellite RNAs and analyse their degree of variability, a RT/PCR-partial restriction enzymatic mapping (PREM) method was developed. The method is based on the incorporation of 5-methyl-dCTP in the RT/PCR reaction, and the subsequent digestion of the RT/PCR products by methyl-sensitive restriction enzymes. Satellites RNAs were detected by RT/PCR in eight isolates out of 47, six of them originating from grapevine, one from hop and one from lilac. The partial restriction digestion patterns allowed to distinguish six different types of satellites. Cloning and sequencing of the different satellites confirmed these results, the PREM proving able to discriminate sequences with 96% identity. The sizes of the different satellites varied between 1092 and 1139 nucleotides, their encoded proteins between 338 and 360 amino acids. Conserved domains were found in the amino and carboxy-termini between the sequences of the proteins encoded by the satellites of the different isolates of ArMV.

Characterization of a naturally occurring recombinant isolate of Grapevine fanleaf virus

The naturally occurring Grapevine fanleaf virus (GFLV) recombinant isolate A17b was recovered from its grapevine host by sap inoculation and serial passages onto Gomphrena globosa, a pseudo local lesion herbaceous host, and Chenopodium quinoa, a systemic herbaceous host, to characterize some of its biological properties. Sequence analysis of the CP gene, in which a recombinational event was previously detected, demonstrated the genetic stability of recombinant isolate A17b over a 5-year period in its natural host as well as in C. quinoa. Also, recombinant isolate A17b was graft transmissible, as shown by an in vitro heterologous approach, and transmitted by the nematode Xiphinema index as readily as nonrecombinant GFLV isolates. Furthermore, despite a lower pathogenicity on Chenopodium amaranticolor, recombinant isolate A17b had a similar host range and induced similar symptoms in type and severity to nonrecombinant GFLV isolates. Interestingly, the use of infectious chimeric RNA2 transcripts in combination to RNA1 transcripts of GFLV strain F13 suggested no implication of the recombination event in the CP gene of isolate A17b in the reduced pathogenicity on C. amaranticolor. Altogether, recombinant isolate A17b had similar biological properties to GFLV nonrecombinant isolates.

Complete Nucleotide Sequence of the RNA-2 of Grapevine Deformation and Grapevine Anatolian Ringspot Viruses

The nucleotide sequence of RNA-2 of Grapevine Anatolian ringspot virus (GARSV) and Grapevine deformation virus (GDefV), two recently described nepoviruses, has been determined. These RNAs are 3753 nt (GDefV) and 4607 nt (GARSV) in size and contain a single open reading frame encoding a polyprotein of 122 kDa (GDefV) and 150 kDa (GARSV). Full-length nucleotide sequence comparison disclosed 71-73% homology between GDefV RNA-2 and that of Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV), and 62-64% homology between GARSV RNA-2 and that of Grapevine chrome mosaic virus (GCMV) and Tomato black ring virus (TBRV). As previously observed in other nepoviruses, the 5' non-coding regions of both RNAs are capable of forming stem-loop structures. Phylogenetic analysis of the three proteins encoded by RNA-2 (i.e. protein 2A, movement protein and coat protein) confirmed that GDefV and GARSV are distinct viruses which can be assigned as definitive species in subgroup A and subgroup B of the genus Nepovirus, respectively.

RT-PCR-RFLP for genetic diversity analysis of Tunisian Grapevine fanleaf virus isolates in their natural host plants

Genetic diversity was characterized in 20 isolates of Grapevine fanleaf virus (GFLV) recovered from naturally infected grapevine plants (Vitis vinifera) in the North of Tunisia. Viral RNAs were isolated by oligoprobe capture, and a 605 bp fragment containing a part of the viral coat protein gene was amplified by RT-PCR. Sequence variation among isolates was characterized by restriction fragment length polymorphism (RFLP) analysis and confirmed by sequencing. The GFLV infections are found as a complex mixture of closely related genomes. In further studies, RFLP analyses of virus isolates using AluI showed that GFLV populations in Tunisian vineyards consist of two restrictotypes corresponding to distinct sub-populations Sp1 and Sp2. The relative field distribution of these sub-populations showed that Sp2 was more abundant. Individual genomes were recovered by cloning the RT-PCR products. The sequences were found to vary from each other by as much as 11%. Cloning from mixed infections showed that Sp2 are also predominant.

Sensitive and reliable detection of grapevine fanleaf virus in a single Xiphinema index nematode vector

Grapevine fanleaf virus (GFLV) is specifically transmitted from plant to plant by the ectoparasitic nematode Xiphinema index. A sensitive and reliable procedure was developed to readily detect GFLV in a single viruliferous X. index, regardless of the nematode origin, i.e. greenhouse rearings or vineyard soils. The assay is based on bead milling to disrupt nematodes extracted from soil samples, solid-phase extraction of total nematode RNAs, and amplification of a 555bp fragment of the coat protein (CP) gene by reverse transcription-polymerase chain reaction with two primers designed from conserved sequences. This procedure is sensitive since the CP gene fragment is amplified from an artificial sample consisting of one viruliferous nematode mixed with 3000 aviruliferous individuals. In addition, StyI RFLP analysis of the CP amplicon enables the GFLV isolate carried by a single viruliferous X. index to be characterized. This GFLV detection assay opens new avenues for epidemiological studies and for molecular investigations on the mechanism of X. index-mediated GFLV transmission.

Isolate-Specific Detection of Grapevine fanleaf virus from Xiphinema index Through DNA-Based Molecular Probes

ABSTRACT Tests with a real-time reverse transcription-polymerase chain reaction (RT-PCR) were performed on specimens of Xiphinema index collected from the rhizosphere of Grapevine fanleaf virus (GFLV)-infected grapevines at Palagiano, Italy. A 1,157-bp fragment of the GFLV RNA-2 coat protein (CP) gene was amplified and sequenced. A fluorescent Scorpion probe was designed to detect a highly conserved CP region. A second region with isolate-specific multiple nucleotide polymorphisms was used to detect GFLV isolates using molecular beacons (MB). The Scorpion probe allowed quantitative estimation of GFLV RNA-2 in single nematodes, using a dilution series of a 692-nucleotide transcript of the CP gene. The assay allowed detection of GFLV RNA-2 in individual X. index, with a minimum template threshold of 800 fg or 2.8 x 10(6) RNA-2 molecules per nematode. The CP fragment used for GFLV detection with the Scorpion probe appeared highly conserved among isolates. The probes were tested against other GFLV isolates, which were recognized by the species-specific Scorpion probe and by the corresponding MB specific to the particular isolate. Both tests appeared useful as diagnostic tools or for studies on GFLV in acquisition, retention, and transmission experiments.

Field safety assessment of recombination in transgenic grapevines expressing the coat protein gene of Grapevine fanleaf virus

One of the major environmental safety issues over transgenic crops containing virus-derived genes relates to the outcome of recombination events between viral transgene transcripts and RNAs from indigenous virus populations. We addressed this issue by assessing the emergence of viable Grapevine fanleaf virus (GFLV) recombinants in transgenic grapevines expressing the GFLV coat protein (CP) gene. Test plants consisted of nontransgenic scions grafted onto transgenic and nontransgenic rootstocks that were exposed over 3 years to nematode-mediated GFLV infection in two distinct vineyard sites. The CP gene of challenging GFLV isolates was amplified from scions by IC-RT-PCR, and characterized by RFLP and nucleotide sequencing using strain F13 as reference since it provided the CP transgene. Analysis of EcoRI and StyI RFLP banding patterns from 347 challenging GFLV isolates and sequence data from 85 variants revealed no characteristics similar to strain F13 and no difference in the molecular variability among isolates from 190 transgenic and 157 nontransgenic plants, or from plants within (253 individuals) or outside (94 individuals) of the two sites. Interestingly, five GFLV recombinants were identified in three nontransgenic plants located outside of the two field settings. This survey indicates that transgenic grapevines did not assist the emergence of viable GFLV recombinants to detectable levels nor did they affect the molecular diversity of indigenous GFLV populations during the trial period. This is the first report on safety assessment of recombination with a transgenic crop expressing a CP gene under field conditions of heavy disease pressure but low, if any, selection pressure against recombinant viruses.

Population structure and genetic variability within isolates of Grapevine fanleaf virus from a naturally infected vineyard in France: evidence for mixed infection and recombination

The nematode-borne Grapevine fanleaf virus, from the genus Nepovirus in the family Comoviridae, causes severe degeneration of grapevines in most vineyards worldwide. We characterized 347 isolates from transgenic and conventional grapevines from two vineyard sites in the Champagne region of France for their molecular variant composition. The population structure and genetic diversity were examined in the coat protein gene by IC-RT-PCR-RFLP analysis with EcoRI and StyI, and nucleotide sequencing, respectively. RFLP data suggested that 55 % (191 of 347) of the isolates had a population structure consisting of one predominant variant. Sequencing data of 51 isolates representing the different restrictotypes confirmed the existence of mixed infection with a frequency of 33 % (17 of 51) and showed two major predominant haplotypes representing 71 % (60 of 85) of the sequence variants. Comparative nucleotide diversity among population subsets implied a lack of genetic differentiation according to host (transgenic vs conventional) or field site for most restrictotypes (17 of 18 and 13 of 18) and for haplotypes in most phylogenetic groups (seven of eight and six of eight), respectively. Interestingly, five of the 85 haplotypes sequenced had an intermediate divergence (0·036–0·066) between the lower (0·005–0·028) and upper range (0·083–0·138) of nucleotide variability, suggesting the occurrence of homologous RNA recombination. Sequence alignments clearly indicated a mosaic structure for four of these five variants, for which recombination sites were identified and parental lineages proposed. This is the first in-depth characterization of the population structure and genetic diversity in a nepovirus.

Simultaneous RT/PCR detection and differentiation of arabis mosaic and grapevine fanleaf nepoviruses in grapevines with a single pair of primers

The movement protein genes from several isolates of ArMV and GFLV of different geographical origins were amplified by RT/PCR using degenerate primers, cloned and sequenced. A single pair of degenerate primers was designed from these sequences to allow the simultaneous amplification of parts of the movement protein genes of ArMV and GFLV. Their use in an immunocapture-RT/PCR for the detection of ArMV or GFLV in infected grapevines proved to be ten times more sensitive than the corresponding ArMV or GFLV ELISA tests. A Sph1 restriction site found in the sequences corresponding to the amplified products from the GFLV isolates, but not in the amplified products from the ArMV isolates, allowed the differentiation between ArMV and GFLV in the infected grapevines by a Sph1 restriction digestion of the amplified products.