Genomic Analysis and Development of Infectious Clone of a Novel Carlavirus Infecting Blueberry

A new blueberry virus was discovered using high-throughput sequencing. Using sequence identity values, phylogenetics, and serological and biological properties, we propose the virus, putatively named blueberry virus S (BluVS), to be a distinct species within the genus Carlavirus (family Betaflexiviridae). The genome was analyzed in depth, and an infectious clone was developed to initiate studies on virus pathogenicity. Agroinfiltration of the binary vector construct produced severe systemic symptoms in Nicotiana occidentalis. Back-inoculation using sap from agroinfiltrated N. occidentalis produced identical symptoms to the recipient plants (N. occidentalis), and virus purification yielded flexuous carlavirus-like particles. However, unlike blueberry scorch virus (BlScV), BluVS caused symptomless infection in Chenopodium quinoa and reacted weakly to BlScV antibodies in an enzyme-linked immunosorbent assay. Collectively, the results provide evidence for the distinct speciation of BluVS. The availability of an infectious clone provides tools for future studies on the biology of the virus.

Subcellular localization and interactions among TGB proteins of cowpea mild mottle virus

Cowpea mild mottle virus (CPMMV) is a flexuous filamentous virus that belongs to the genus Carlavirus (family Betaflexiviridae). The CPMMV genome contains six open reading frames (ORFs), among which the triple gene block (TGB), encoded by ORFs 2 to 4, has been reported to encode movement proteins for different viruses. The subcellular localization of the TGB proteins of CPMMV isolate CPMMV:BR:MG:09:2 was analysed by transient expression of each protein fused to a fluorophore. Overall, the accumulation pattern and interactions among CPMMV TGB proteins (TGBp) were similar to those of their counterparts from the potex-like group. Considering these similarities, we evaluated the potential interactions between the TGB proteins of CPMMV and of potato virus X, which could complement cell-to-cell movement. The TGBp2 and TGBp3 of PVX had an effect on CPMMV TGBp1, directing it to the plasmodesmata, but the reverse was not true.

First complete genome sequence of carnation latent virus, the type member of the genus Carlavirus

The genus Carlavirus (family Betaflexiviridae, order Tymovirales) currently includes 53 species recognized by the ICTV. The NCBI GenBank database has 43 full-length carlavirus genome sequences (7,890 to 9,073 nt). Surprisingly, the type species Carnation latent virus is not associated with a complete genome sequence of a carnation latent virus (CLV) isolate; GenBank only has accessions with 1313 or fewer nucleotides. The goal of this study was to determine the full-length genome sequence of CLV. Naturally infected greenhouse-grown 'Kiwi Lace' carnation plants that tested positive for CLV by ELISA and RT-PCR were used as source plants for high-throughput sequencing, completed by 5' and 3' RACE and validated by Sanger sequencing of CLV-specific RT-PCR-generated amplicons. The complete CLV-KL sequence (MN450069) was determined to be 8,513 nt in length. In pairwise analysis, the genome shares 40-46% identity with recognized carlaviruses and the six in silico-translated proteins have 15-62% amino acid sequence identity to their respective carlavirus orthologs. The CLV-KL coat protein shares 98.4% identity with the NCBI reference sequence CLV-UK. In phylogenetic analysis, CLV clusters with butterbur mosaic virus, coleus vein necrosis virus, and garlic common latent virus. This is the first report of the full genome sequence of an isolate of carnation latent virus, the type member of the genus Carlavirus.

Characterization of the virome of shallots affected by the shallot mild yellow stripe disease in France

To elucidate the etiology of a new disease of shallot in France, double-stranded RNAs from asymptomatic and symptomatic shallot plants were analyzed using high-throughput sequencing (HTS). Annotation of contigs, molecular characterization and phylogenetic analyses revealed the presence in symptomatic plants of a virus complex consisting of shallot virus X (ShVX, Allexivirus), shallot latent virus (SLV, Carlavirus) and two novel viruses belonging to the genera Carlavirus and Potyvirus, for which the names of shallot virus S (ShVS) and shallot mild yellow stripe associated virus (SMYSaV), are proposed. Complete or near complete genomic sequences were obtained for all these agents, revealing divergent isolates of ShVX and SLV. Trials to fulfill Koch's postulates were pursued but failed to reproduce the symptoms on inoculated shallots, even though the plants were proved to be infected by the four viruses detected by HTS. Replanting of bulbs from SMYSaV-inoculated shallot plants resulted in infected plants, showing that the virus can perpetuate the infection over seasons. A survey analyzing 351 shallot samples over a four years period strongly suggests an association of SMYSaV with the disease symptoms. An analysis of SMYSaV diversity indicates the existence of two clusters of isolates, one of which is largely predominant in the field over years.

Molecular characterization and detection of two carlaviruses infecting cactus

Two large contigs with sequence similarities to different carlaviruses were identified by high-throughput sequencing in samples from a cactus plant. The complete genomes of the two viruses, tentatively named "cactus carlavirus 1" (CCV-1) and "cactus carlavirus 2" (CCV-2), were determined to be 8,441 and 8,396 nucleotides long, respectively, excluding the poly(A) tail. These viruses have the typical genomic organization of members of the genus Carlavirus. CCV-1 appears to be a cactus isolate of the carlavirus HSO-2016a, with 90.1% nucleotide sequence identity between the two virus genomes, whereas CCV-2 may be classified as a member of a new species. The sequences of CCV-2 and other carlaviruses are 48.9-60.0% identical at the whole-genome level.

Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences

Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus.

Construction and characterization of an infectious cDNA clone of potato virus S developed from selected populations that survived genetic bottlenecks

BACKGROUND

Infectious cDNA clones are a powerful tool for studies on RNA viruses using reverse genetics. Potato virus S (PVS) is a carlavirus with a worldwide distribution. Although the complete genome sequences of many PVS isolates have been reported, the construction of an infectious cDNA clone of PVS is yet to be reported. The aim of this study is the development and molecular characterization of an infectious cDNA clone of PVS.

METHODS

A full-length cDNA clone pPVS-H-FL-AB was constructed by connecting eight cDNA clones of PVS isolate H95. Capped RNA transcripts from pPVS-H-FL-AB and a modified clone pPVS-H-FL-H, containing the consensus genome sequence of PVS-H95, proved to be non-infectious. Therefore, a full-length cDNA clone pPVS-H-FL-β was reconstructed from PVS-H00, isolated from PVS-H95 populations by repeating a single local lesion isolation in Chenopodium quinoa three times; PVS-H00 appeared to be a selected variant that survived genetic bottlenecks. The sequence of cDNA clone pPVS-H-FL-β was determined as the genome sequence of PVS-H00 and compared with the consensus sequence of PVS-H95 genome.

RESULTS

All Nicotiana occidentalis plants inoculated with ≥0.2 μg capped RNA transcripts from pPVS-H-FL-β developed symptoms on upper leaves, as observed with PVS-H00 inoculation. Similar levels of viral genomic and subgenomic RNAs and coat protein were detected in systemically infected leaves. Sequence comparison of PVS-H95 and PVS-H00 revealed 370 nucleotide polymorphisms (4.4% of the entire genome sequence), causing 91 amino acid substitutions in six open reading frames (ORFs). The infectivity of chimeric RNAs derived from recombinants between the two cDNA clones revealed that the lack of infectivity of pPVS-H-FL-H transcripts was due to ORF1, which encodes replicase and harbors 80 amino acid substitutions compared with pPVS-H-FL-β. Approximately 71.3% amino acid substitutions in replicase were located within the variable region of unknown function between the putative methyltransferase and ovarian tumor-like protease domains.

CONCLUSIONS

This is the first report of the development of an infectious cDNA clone of PVS. Our analyses suggest that PVS population within a plant exists as quasispecies and the replicase sequence diversity of PVS obstruct the construction of a full-length infectious cDNA clone.

Phylogenetic relationships of two Ukrainian tomato isolates of potato virus M and genetic variability analysis of its population

The aim of this study was to investigate biological and molecular properties of two Ukrainian tomato isolates of potato virus M (PVM), K-16 and Pol-14, to determine their phylogenetic relationships and the genetic variability of PVM isolates. Study of phylogenetic relationships of two Ukrainian tomato PVM isolates with 35 isolates represented in GenBank was conducted. It was found that the coat protein (CP) gene sequence identity between two Ukrainian PVM isolates is 94.3% at the nucleotide level and 100% at the amino acid level. The highest level of the sequence identity (97.0% and 96.5% nt and 100% aa) have the isolates K-16 and Pol-14 with the German potato isolate DSMZ PV0273, Indian potato isolates Del 123, Del 134, Del 147, M 34 and Chinese isolate from pepino GS-6-2 (isolate K-16), which testifies about their common origin. Ukrainian tomato isolates K-16 and Pol-14 belong together with all European, Chinese, Iranian, Indian isolates to PVM-o clade or group I. It was found that the nucleotide substitutions in the capsid protein gene of all tomato PVM isolates (except the Italian) are synonymous. Analysis showed that the global dN/dS ratio for the entire CP gene sequences used in the study was 0.041 (p Keywords: potato virus M; Solanum lycopersicum; phylogenetic analysis; genetic variability; selection pressure.

The Biology and Phylogenetics of Potato virus S Isolates from the Andean Region of South America

Biological characteristics of 11 Potato virus S (PVS) isolates from three cultivated potato species (Solanum spp.) growing in five Andean countries and 1 from Scotland differed in virulence depending on isolate and host species. Nine isolates infected Chenopodium quinoa systemically but two others and the Scottish isolate remained restricted to inoculated leaves; therefore, they belonged to biologically defined strains PVS^A and PVS^O, respectively. When nine wild potato species were inoculated, most developed symptomless systemic infection but Solanum megistacrolobum developed systemic hypersensitive resistance (SHR) with one PVS^O and two PVS^A isolates. Andean potato cultivars developed mostly asymptomatic primary infection but predominantly symptomatic secondary infection. In both wild and cultivated potato plants, PVS^A and PVS^O elicited similar foliage symptoms. Following graft inoculation, all except two PVS^O isolates were detected in partially PVS-resistant cultivar Saco, while clone Snec 66/139-19 developed SHR with two isolates each of PVS^A and PVS^O. Myzus persicae transmitted all nine PVS^A isolates but none of the three PVS^O isolates. All 12 isolates were transmitted by plant-to-plant contact. In infective sap, all isolates had thermal inactivation points of 55 to 60°C. Longevities in vitro were 25 to 40 days with six PVS^A isolates but less than 21 days for the three PVS^O isolates. Dilution end points were 10^-3 for two PVS^O isolates but 10^-4 to 10^-6 with the other isolates. Complete new genome sequences were obtained from seven Andean PVS isolates; seven isolates from Africa, Australia, or Europe; and single isolates from S. muricatum and Arracacia xanthorhiza. These 17 new genomes and 23 from GenBank provided 40 unique sequences; however, 5 from Eurasia were recombinants. Phylogenetic analysis of the 35 nonrecombinants revealed three major lineages, two predominantly South American (SA) and evenly branched and one non-SA with a single long basal branch and many distal subdivisions. Using least squares dating and nucleotide sequences, the two nodes of the basal PVS trifurcation were dated at 1079 and 1055 Common Era (CE), the three midphylogeny nodes of the SA lineages at 1352, 1487, and 1537 CE, and the basal node to the non-SA lineage at 1837 CE. The Potato rough dwarf virus/Potato virus P (PVS/PRDV/PVP) cluster was sister to PVS and diverged 5,000 to 7,000 years ago. The non-SA PVS lineage contained 18 of 19 isolates from S. tuberosum subsp. tuberosum but the two SA lineages contained 6 from S. tuberosum subsp. andigena, 4 from S. phureja, 3 from S. tuberosum subsp. tuberosum, and 1 each from S. muricatum, S. curtilobum, and A. xanthorrhiza. This suggests that a potato-infecting proto-PVS/PRDV/PVP emerged in South America at least 5,000 years ago, became endemic, and diverged into a range of local Solanum spp. and other species, and one early lineage spread worldwide in potato. Preventing establishment of the SA lineages is advised for all countries still without them.

Complete nucleotide sequence of a new carlavirus in chrysanthemums in China

A new virus causing a serious stunt disease of chrysanthemum was identified in China by high-throughput sequencing (HTS) and named chrysanthemum virus R (CVR). The complete sequence of CVR was determined by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The genomic RNA of CVR consists of 8,874 nucleotides (nt), excluding the poly(A) tail, contains six putative open reading frames (ORFs), and has a genomic organization typical of members of the genus Carlavirus. BLAST analysis of the full genome sequence showed low similarity (38%-56% sequence identity) to other members of the genus Carlavirus. BLAST analysis and phylogenetic analysis based on the amino acid (aa) sequences of the CVR replicase and coat protein (CP) confirmed that CVR is a distinct member of the genus Carlavirus.

Simultaneous detection of three lily viruses using Triplex IC-RT-PCR

Viruses commonly infecting lily (Lilium spp.) include: Lily symptomless virus (LSV), Cucumber mosaic virus (CMV) and Lily mottle virus (LMoV). These viruses usually co-infect lilies causing severe economic losses in terms of quantity and quality of flower and bulb production around the world. Reliable and precise detection systems need to be developed for virus identification. We describe the development of a triplex immunocapture (IC) reverse transcription (RT) polymerase chain reaction (PCR) assay for the simultaneous detection of LSV, CMV and LMoV. The triplex IC-RT-PCR was compared with a quadruplex RT-PCR assay. Relative to the quadruplex RT-PCR, the specificity of the triplex IC-RT-PCR system for LSV, CMV and LMoV was 100% for field samples. The sensitivity of the triplex IC-RT-PCR system was 99.4%, 81.4% and 98.7% for LSV, CMV and LMoV, respectively. Agreement (κ) between the results obtained from the two tests was 0.968, 0.844 and 0.984 for LSV, CMV and LMoV, respectively. This is the first report of the simultaneous detection of LSV, CMV and LMoV in a triplex IC-RT-PCR assay. In particular we believe this convenient and reliable triplex IC-RT-PCR method could be used routinely for large-scale field surveys or crop health monitoring of lily.

Construction of a full-length infectious cDNA clone of Cowpea mild mottle virus

Infectious cDNA clones are an important tool to study the molecular and cellular process of RNA virus infection. In vitro and in vivo transcription systems are the two main strategies used in the generation of infectious cDNA clones for RNA viruses. This study describes the first generation of a full-length infectious cDNA clone of Cowpea mild mottle virus (CPMMV), a Carlavirus. The full-length genome was synthesized by Overlap Extension PCR of two overlapping fragments and cloned in a pUC-based vector under control of the SP6 RNA polymerase promoter. After in vitro run-off transcription, the produced RNA was mechanically inoculated into soybean plants cv. CD206. The systemic infection was confirmed by RT-PCR and further sequencing of amplified cDNA fragments. To simplify the transfection process, the complete genome was subcloned into a binary vector under control of the 35S promoter of cauliflower mosaic virus by the Gibson Assembly protocol. The resulting clones were inoculated by particle bombardment onto soybean seedlings and the recovery of the virus was confirmed 2 weeks later by RT-PCR. Our results indicate the constructs of the full-length cDNA of CPMMV are fully infectious in both in vitro and in vivo transcription strategies.

The complete nucleotide sequence and genome organization of pea streak virus (genus Carlavirus)

Pea streak virus (PeSV) is a member of the genus Carlavirus in the family Betaflexiviridae. Here, the first complete genome sequence of PeSV was determined by deep sequencing of a cDNA library constructed from dsRNA extracted from a PeSV-infected sample and Rapid Amplification of cDNA Ends (RACE) PCR. The PeSV genome consists of 8041 nucleotides excluding the poly(A) tail and contains six open reading frames (ORFs). The putative peptide encoded by the PeSV ORF6 has an estimated molecular mass of 6.6 kDa and shows no similarity to any known proteins. This differs from typical carlaviruses, whose ORF6 encodes a 12- to 18-kDa cysteine-rich nucleic-acid-binding protein.

Nucleotide sequence and genome organization of atractylodes mottle virus, a new member of the genus Carlavirus

The complete genome sequence of a member of a distinct species of the genus Carlavirus in the family Betaflexiviridae, tentatively named atractylodes mottle virus (AtrMoV), has been determined. Analysis of its genomic organization indicates that it has a single-stranded, positive-sense genomic RNA of 8866 nucleotides, excluding the poly(A) tail, and consists of six open reading frames typical of members of the genus Carlavirus. The individual open reading frames of AtrMoV show moderately low sequence similarity to those of other carlaviruses at the nucleotide and amino acid sequence levels. Pairwise comparison and phylogenetic analysis suggest that AtrMoV is most closely related to chrysanthemum virus B.

Molecular variability of cowpea mild mottle virus infecting soybean in Brazil

Molecular variability was assessed for 18 isolates of cowpea mild mottle virus (CPMMV, genus Carlavirus, family Betaflexiviridae) found infecting soybean in various Brazilian states (Bahia, Goiás, Maranhão, Mato Grosso, Minas Gerais, Pará) in 2001 and 2010. A variety of symptoms was expressed in soybean cv. CD206, ranging from mild (crinkle/blistering leaves, mosaic and vein clearing) to severe (bud blight, dwarfing, leaf and stem necrosis). Recombination analysis revealed only one CPMMV isolate to be recombinant. Pairwise comparisons and phylogenetic analysis were performed for partial genomes (ORF 2 to the 3' terminus) and for each ORF individually (ORFs 2 to 6), showing the isolates to be distinct. The topology of the phylogenetic tree could be related to symptoms, but not to the year of collection or geographical origin. Additionally, the phylogenetic analysis supported the existence of two distinct strains of the virus, designated CPMMV-BR1 and CPMMV-BR2, with molecular variations between them.

RNA viral metagenome of whiteflies leads to the discovery and characterization of a whitefly-transmitted carlavirus in North America

Whiteflies from the Bemisia tabaci species complex have the ability to transmit a large number of plant viruses and are some of the most detrimental pests in agriculture. Although whiteflies are known to transmit both DNA and RNA viruses, most of the diversity has been recorded for the former, specifically for the Begomovirus genus. This study investigated the total diversity of DNA and RNA viruses found in whiteflies collected from a single site in Florida to evaluate if there are additional, previously undetected viral types within the B. tabaci vector. Metagenomic analysis of viral DNA extracted from the whiteflies only resulted in the detection of begomoviruses. In contrast, whiteflies contained sequences similar to RNA viruses from divergent groups, with a diversity that extends beyond currently described viruses. The metagenomic analysis of whiteflies also led to the first report of a whitefly-transmitted RNA virus similar to Cowpea mild mottle virus (CpMMV Florida) (genus Carlavirus) in North America. Further investigation resulted in the detection of CpMMV Florida in native and cultivated plants growing near the original field site of whitefly collection and determination of its experimental host range. Analysis of complete CpMMV Florida genomes recovered from whiteflies and plants suggests that the current classification criteria for carlaviruses need to be reevaluated. Overall, metagenomic analysis supports that DNA plant viruses carried by B. tabaci are dominated by begomoviruses, whereas significantly less is known about RNA viruses present in this damaging insect vector.

Stepwise artificial evolution of a plant disease resistance gene

Genes encoding plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins confer dominant resistance to diverse pathogens. The wild-type potato NB-LRR protein Rx confers resistance against a single strain of potato virus X (PVX), whereas LRR mutants protect against both a second PVX strain and the distantly related poplar mosaic virus (PopMV). In one of the Rx mutants there was a cost to the broad-spectrum resistance because the response to PopMV was transformed from a mild disease on plants carrying wild-type Rx to a trailing necrosis that killed the plant. To explore the use of secondary mutagenesis to eliminate this cost of broad-spectrum resistance, we performed random mutagenesis of the N-terminal domains of this broad-recognition version of Rx and isolated four mutants with a stronger response against the PopMV coat protein due to enhanced activation sensitivity. These mutations are located close to the nucleotide-binding pocket, a highly conserved structure that likely controls the "switch" between active and inactive NB-LRR conformations. Stable transgenic plants expressing one of these versions of Rx are resistant to the strains of PVX and the PopMV that previously caused trailing necrosis. We conclude from this work that artificial evolution of NB-LRR disease resistance genes in crops can be enhanced by modification of both activation and recognition phases, to both accentuate the positive and eliminate the negative aspects of disease resistance.

Discovery and Characterization of a Novel Carlavirus Infecting Potatoes in China

A new carlavirus, tentatively named Potato virus H (PVH), was found on potato plants with mild symptoms in Hohhot, Inner Mongolia Autonomous Region, China. PVH was confirmed by genome sequencing, serological reactions, electron microscopy, and host index assays. The PVH particles were filamentous and slightly curved, with a modal length of 570 nm. Complete RNA genomic sequences of two isolates of PVH were determined using reverse transcription-PCR (RT-PCR) and the 5' rapid amplification of cDNA ends (5' RACE) method. Sequence analysis revealed that PVH had the typical genomic organization of members of the genus Carlavirus, with a positive-sense single-stranded genome of 8410 nt. It shared coat protein (CP) and replicase amino acid sequence identities of 17.9-56.7% with those of reported carlaviruses. Phylogenetic analyses based on the protein-coding sequences of replicase and CP showed that PVH formed a distinct branch, which was related only distantly to other carlaviruses. Western blotting assays showed that PVH was not related serologically to other potato carlaviruses (Potato virus S, Potato virus M, and Potato latent virus). PVH systemically infected Nicotianaglutinosa but not Nicotiana tabacum, Nicotianabenthamiana, or Chenopodiumquinoa, which is in contrast with the other potato carlaviruses. These results support the classification of PVH as a novel species in the genus Carlavirus. Preliminary results also indicated that a cysteine-rich protein encoded by the smallest ORF located in the 3' proximal region of the genome suppressed local RNA silencing and enhanced the pathogenicity of the recombinant PVX.

[Detection and molecular characterization of Potato virus S (PVS, Carlavirus) from Colombia]

In Colombia, potato crops are affected by a wide variety of viruses such as PVY, PLRV, PVX, PMTV and PVS. Unfortunately, there are very few studies on the biology, distribution and pathogenicity of these viruses; this situation is even worse for the latent virus PVS. In this work, we evaluated the presence ofPVS in four Colombian provinces (Antioquia, Boyacá, Cundinamarca, Nariño) by the use of ELISA. We also studied the degree of molecular variation by sequence comparison of a segment of the gene encoding for the viral coat protein. In average, PVS was detected in 40% of 320 analyzed samples of potato leaves; the highest levels were observed in the East ofAntioquia (49%) and Pasto (Nariño) (47%), while in the other regions ranged between 35% and 42%. Analysis of sequence revealed the presence of two PVS strains in Colombia: three isolates were associated to PVSo (Ordinary) and twelve belonged to PVSA (Andean). A high diversity was observed among PVSA strains with percent identities in the range of 88-99%. These findings highlight the importance of strengthening seed certification programs and quarantine measures in Colombia for viruses like PVS, which can cause losses of up to 20% in potato crops and even higher in mixed virus infection.

An RNA virus-encoded zinc-finger protein acts as a plant transcription factor and induces a regulator of cell size and proliferation in two tobacco species

Plant viruses cause a variety of diseases in susceptible hosts. The disease symptoms often include leaf malformations and other developmental abnormalities, suggesting that viruses can affect plant development. However, little is known about the mechanisms underlying virus interference with plant morphogenesis. Here, we show that a C-4 type zinc-finger (ZF) protein, p12, encoded by a carlavirus (chrysanthemum virus B) can induce cell proliferation, which results in hyperplasia and severe leaf malformation. We demonstrate that the p12 protein activates expression of a regulator of cell size and proliferation, designated upp-L (upregulated by p12), which encodes a transcription factor of the basic/helix-loop-helix family sufficient to cause hyperplasia. The induction of upp-L requires translocation of the p12 protein into the nucleus and ZF-dependent specific interaction with the conserved regulatory region in the upp-L promoter. Our results establish the role of the p12 protein in modulation of host cell morphogenesis. It is likely that other members of the conserved C-4 type ZF family of viral proteins instigate reprogramming of plant development by mimicking eukaryotic transcriptional activators.

Sequence and structure prediction of RNA-dependent RNA polymerase of lily symptomless virus isolated from L. × 'Casablanca'

The DNA sequence of the RNA-dependent RNA polymerase (RdRp) gene of lily symptomless virus (LSV), a lily-infecting member of the genus Carlavirus, was determined from nine overlapping cDNA fragments of different sizes. The complete sequence of this RdRp gene (HM070294) consisted of 5,847 nucleotides coding for a protein of 220 kDa. It had 97-98% sequence identity with RdRps of other known isolates at both the DNA and the amino acid level. Phylogenetic analysis indicated that this RdRp (designated as RdRp-DL) was closely related to the RdRp of the Korean isolate (AM516059), as well as to the RdRps from Passiflora latent virus (PLV) and Kalanchoe latent virus (KLV) of the genus Carlavirus. Hydrophobic analysis of RdRp-DL revealed a hydrophobic N-terminus and a hydrophilic C-terminus. Helices and Loops were the major secondary structures of RdRp-DL. In addition, RdRp-DL also had three coil structures. Four conserved domains were identified: typoviral methyltransferase, RNA-dependent RNA polymerase, P-loop-containing nucleoside triphosphate hydrolases and carlavirus endopeptidase. A model of the tertiary structure predicted by I-TASSER was obtained for each of these conserved domains. This is the first report of a detailed phylogenetic analysis of LSV RdRp with those of other members of the genus Carlavirus, and the first to predict the domain structures of LSV RdRp.

Genomic variability in potato virus M and the development of RT-PCR and RFLP procedures for the detection of this virus in seed potatoes

Potato virus M (PVM, Carlavirus) is considered to be one of the most common potato viruses distributed worldwide. Sequences of the coat protein (CP) gene of several Canadian PVM isolates were determined. Phylogenetic analysis indicated that all known PVM isolates fell into two distinct groups and the isolates from Canada and the US clustered in the same group. The Canadian PVM isolates could be further divided into two sub-groups. Two molecular procedures, reverse transcription - polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP) were developed in this study for the detection and identification of PVM in potato tubers. RT-PCR was highly specific and only amplified PVM RNA from potato samples. PVM RNAs were easily detected in composite samples of 400 to 800 potato leaves or 200 to 400 dormant tubers. Restriction analysis of PCR amplicons with MscI was a simple method for the confirmation of PCR tests. Thus, RT-PCR followed by RFLP analysis may be a useful approach for screening potato samples on a large scale for the presence of PVM.

Complementation analysis of triple gene block of Potato virus S (PVS) revealed its capability to support systemic infection and aphid transmissibility of recombinant Potato virus X

Triple gene block (TGB) sequences derived from isolates of ordinary Potato virus S (PVS-O) and Chenopodium-systemic (PVS-CS) were analyzed. Although the TGB sequences did not reveal any specific difference within the 7K protein, some specific differences within the 25K and 12K ORFs were found. In order to investigate a possible functional divergence of PVS-O and PVS-CS TGB variants, these genes were propagated in chimeric Potato virus X (PVX). Both PVS TGB variants partly complemented PVX TGB in Nicotiana benthamiana. The recombinant viruses multiplied to lower titer than the wild-type PVX in N. benthamiana showed attenuated symptoms. Whereas the recombinant PVX variants were also propagated systemically in Nicotiana glutinosa, Celosia argentea, Nicotiana occidentalis and chimeric PVX bearing TGB from PVS-O in Solanum lycopersicum, neither were propagated systemically in Chenopodium quinoa nor in Nicotiana tabacum cv. Samsun nn and the PVX-resistant Solanum tuberosum cv. Szignal. The potential for recombinant viruses to be transmitted by the aphid Myzus persicae was investigated. Aphid transmission in the recombinant virus was obtained by replacing PVX TGB by TGB from the PVS-CS isolate. These results show the potential function of Carlavirus TGB in aphid transmissibility and underlines the possible biological risks from certain recombinant virus variants.

Role of the zinc-finger and basic motifs of chrysanthemum virus B p12 protein in nucleic acid binding, protein localization and induction of a hypersensitive response upon expression from a viral vector

The genomes of carlaviruses encode cysteine-rich proteins (CRPs) of unknown function. The 12 kDa CRP of chrysanthemum virus B (CVB), p12, has been shown previously to induce a hypersensitive response (HR) when expressed from potato virus X (PVX). This study demonstrated that a p12-induced HR was preceded by induction of a number of genes related to pathogenesis, stress and systemic acquired resistance. p12 localized predominantly to the nucleus. Interestingly, it was found that p12 bound both RNA and DNA in vitro, but notably exhibited a preference for DNA in the presence of Zn(2+) ions. Mutational analysis of the p12 conserved sequence motifs demonstrated that the basic motif is required for p12 translocation to the nucleus, thus representing part of the protein nuclear localization signal, whereas the predicted zinc finger motif is needed for both Zn(2+)-dependent DNA binding and eliciting an HR in PVX-infected leaves. Collectively, these results link, for the first time, nuclear localization of the protein encoded by a cytoplasmically replicating virus and its DNA-binding capacity with HR induction. Furthermore, these data suggest that p12 may mediate induction of the host genes by binding to the plant genomic DNA, and emphasize that CVB p12 is functionally distinct from other known nuclear-localized proteins encoded by the plant positive-stranded RNA viruses.

Complete nucleotide sequence of a Japanese isolate of Chrysanthemum virus B (genus Carlavirus)

The complete nucleotide sequence of a Chrysanthemum virus B isolate from Japan (CVB-S) has been determined. The genomic RNA of CVB-S is 8,990 nucleotides long, excluding the poly(A) tail and, like that of other carlaviruses, contains six open reading frames (ORFs). Multiple alignment and phylogenetic analyses indicated that the phylogenetic relationship among members of the genus Carlavirus is very diverse, with phlox virus S being the closest relative of CVB. In aphid transmission tests, CVB-S was transmitted at a very low rate by Aphis gossypii, a new vector of the virus.

Sequence analysis of the entire RNA genome of a sweet potato chlorotic fleck virus isolate reveals that it belongs to a distinct carlavirus species

Since the paucity of information on sweet potato chlorotic fleck virus (SPCFV) had precluded its classification, we have determined the complete nucleotide sequence of the single-stranded RNA genome of a Ugandan isolate of SPCFV. The genome is 9104 nucleotides long (excluding the poly(A) tail) and potentially includes six open reading frames (ORFs). Based on genomic organisation and sequence similarity, SPCFV appears to be a member of the genus Carlavirus (family Flexiviridae). However, SPCFV is distantly related to typical carlaviruses, as most of its putative gene products share amino acid sequence identities of <40% with those of typical carlaviruses. Its closest relative is melon yellowing-associated virus, a proposed carlavirus from Brazil, with which it shares ORF5 and ORF6 amino acid sequence identities of 61 and 46%, respectively.

The complete nucleotide sequence of Passiflora latent virus and its phylogenetic relationship to other carlaviruses

A virus identified as Passiflora latent virus (PLV) was isolated from passion fruit plants. Particle morphology, host range and serological properties suggested that this virus belongs to the genus Carlavirus. The complete genomic sequence of PLV was determined by sequencing overlapping cDNA fragments. The genome consisted of 8386 nt, excluding the poly (A) tail and contained six open reading frames, typical of carlaviruses. The overall similarities of the predicted amino acid sequence of PLV to those of other carlaviruses ranged from 25 to 73%. Phylogenetic analysis indicated that PLV was closely related to lily symptomless virus and blueberry scorch virus. This is the first report of the complete nucleotide sequence and genome structure of PLV.

Narcissus symptomless virus: a new carlavirus of daffodils

A filamentous virus, with particles 600-650 nm long, was purified from Narcissus pseudonarcissus (daffodil) in Hangzhou and an antiserum prepared. After mechanical inoculation, the virus could be detected serologically in Narcissus species but not in some commonly used virus indicators. Infection was symptomless. The complete sequence of the genomic RNA (8281 nt) showed six predicted ORFs typical of carlaviruses. Pairwise comparisons of gene sequences and phylogenetic analysis demonstrated that the new virus should be classified as a carlavirus but that it was not closely related to members of any current species. We propose the name Narcissus symptomless virus (NSV).

Potato chromosomes IX and XI carry genes for resistance to potato virus M

Two new loci for resistance to potato virus M (PVM), Gm and Rm, have been mapped in potato. The gene Gm was derived from Solanum gourlayi, whereas, Solanum megistacrolobum is the source of the gene Rm. Gm confers resistance to PVM infection after mechanical inoculation. Rm induces a hypersensitive response in potato plants. Two diploid populations segregating for Gm and Rm, bulked segregant analysis (BSA) using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), and available potato molecular maps were instrumental for mapping the resistance loci. The novel locus Gm was mapped to a central region on potato chromosome IX. The locus Rm was placed on the short arm of chromosome XI, close to the marker loci GP250 and GP283, where a hotspot for monogenic and polygenic resistance to diverse pathogens is located in the potato and tomato genome.

Complete nucleotide sequence and affinities of the genomic RNA of Narcissus common latent virus (genus Carlavirus)

The complete sequence of an isolate of Narcissus common latent virus (NCLV) from Zhangzhou city, Fujian, China was determined from amplified fragments of purified viral RNA. Excluding the poly(A) tail, the genomic RNA of NCLV was 8539 nucleotides (nt) long and had the typical organization for a member of the genus Carlavirus. The most closely related species were Potato virus M, Hop latent virus and Aconitum latent virus, which had 58-59% nt identity to NCLV in their entire genomes. These relationships were confirmed by a phylogenetic analysis using a composite nucleotide alignment of all the open reading frames.

[Interaction of cysteine-rich protein of Carlavirus with plant defense system]

Viruses of genus Carlavirus encode a small cysteine-rich protein (CRP) of unknown function. To investigate the role of CRP of carlavirus chrysanthemum virus B (CVB), a recombinant potato virus X (PVX) genome was constructed, which carried the CVB CRP gene. Expression of CVB CRP in the PVX genetic background drastically changed the PVX symptom phenotype in N. benthamiana. Instead of symptomless infection and mild mosaic, which are characteristic of PVX in this plant host, the recombinant virus expressing CVB CRP induced formation of necrotic local lesions on inoculated leaves and necrosis of the apical leaves. In N. tabacum, the infection pattern depended on the host genotype: the recombinant PVX was able to spread systemically only in N gene-carrying plants. In agroinfiltration-mediated transient expression assay, CVB CRP did not exhibit the properties of avirulence factor in N. benthamiana and was unable to suppress post-transcriptional gene silencing. Thus, CVB CRP is the viral pathogenicity determinant controlling the virus interaction with plant hosts in a manner which depends on plant defense mediated by resistance genes such as the N gene.

Genome structure and complete sequence of genomic RNA of Daphne virus S

The complete genomic nucleotide sequence and structure of Daphne virus S (DVS), a daphne-infecting member of the genus Carlavirus, were determined. The genome of DVS was 8,739 nucleotides long, excluding the poly (A) tails. The genome of DVS contained six open reading frames coding for proteins of Mr 227 kDa (viral replicase), 25 kDa, 11 kDa and 7 kDa (triple gene block TGB) proteins 1, 2 and 3), 35 kDa (coat protein; CP), and 12 kDa from the 5' to 3' ends; respectively. This is the typical genome structure of members of the genus Carlavirus. Overall amino acid sequence similarities for the six ORFs of DVS were from 58.5% to 13.2% to those of the other carlaviruses. The 227 kDa replicase of DVS shared 45.5-39.2% amino acid similarities to that of 8 other known carlaviruses. Results from phylogenetic analyses of viral replicases and CPs demonstrated that DVS is a close relative of Helenium virus S and Chrysanthemum virus B. A total of 13 isolates of DVS shared 100-95.9% identities for the amino acid level and 99.5-81.0% identities for the nucleotide level. This is the first report of the complete genome sequence and structure of DVS and supports the conclusion that DVS is a typical species of the genus Carlavirus.

Evaluation of a simple membrane-based nucleic acid preparation protocol for RT-PCR detection of potato viruses from aphid and plant tissues

A rapid and simple protocol for preparing viral RNA from aphids (Myzus persicae) and potato (Solanum tuberosum L.) tissue (leaves, sprouts, and tubers) for reverse transcription-polymerase chain reaction (RT-PCR) was developed. The four-step method involves: (1) preparing plant crude sap or aphid macerates in a buffered detergent (Triton XL-80N) solution; (2) immobilizing clarified sap on a nitrocellulose membrane; (3) performing reverse transcription using eluted water extract from cut-out spot from membrane; and (4) amplifying cDNA through PCR. The entire procedure from tissue grinding to RT-PCR can be completed within 6h. The protocol was applied successfully for the detection of individual potato viruses: carlavirus Potato virus S (PVS), potexvirus Potato virus X (PVX), potyvirus Potato virus Y (PVY), and polerovirus Potato leafroll virus (PLRV). PLRV was also detected from individual viruliferous aphids or composites of viruliferous and healthy aphids. PVY and PLRV were detected from extracts immobilized on nitrocellulose membranes, stored for more than 65-273 days at room temperature (25 degrees C). The protocol was companed with the 'long protocols' involving enzyme and phenol extraction for aphids or sodium sulfite and phenol extraction for tubers. The simplified protocol was found comparable in sensitivity to these long procedures, and is especially suitable for those regions where specialized PCR laboratories are only available in centralized locations. Viral RNA immobilized membranes can be mailed out for detection by RT-PCR to these centralized laboratories from remote areas of the country.

Complete nucleotide sequence of the genomic RNA of poplar mosaic virus (Genus Carlavirus)

The complete nucleotide sequence of the Poplar mosaic virus (PopMV) genome was determined. The genomic RNA of PopMV is 8,742 nucleotides in length. Comparative sequence analysis supports earlier research suggesting that this virus is a member of the genus Carlavirus. For example, as is the case for all carlaviruses, there are 6 predicted ORFs in the PopMV genome. The first ORF, ORF1, encodes a predicted helicase/replicase, which corresponds to ORF1 from other carlaviruses, while ORF2, ORF3, ORF4, ORF5 and ORF6 encode the three triple block proteins, the coat protein, and a putative nucleic acid-binding protein respectively.

Complete nucleotide sequence and molecular probing of potato virus S genome

Complete genomes of three isolates of Potato virus S (PVS) were cloned and sequenced. The PVS ORF-1 was characterized for the first time. It encodes a putative replication protein (RPT) that shares the highest homology (about 52%) with that of Blueberry scorch virus (BlScV). ORF-1 motifs, characteristic for carlaviruses were found for methyltransferase (MTR), helicase (HEL) and RNA-dependent RNA polymerase (RdRp). The complete sequence of PVS genome enabled to develop an immunocapture RT-PCR probing of the PVS genome. Using this system, the sequence variability of 11 genome zones was examined for 34 PVS isolates including 15 PVS-CS variants that caused a systemic infection in Chenopodium quinoa. A broad variability between PVS isolates and diverse sequence variants was found. cDNA fragments covering the coat protein (CP) leader and CP-coding region (approx. 420 bp) were pooled for PVS-O and Chenopodium-systemic PVS isolates (PVS-CS) and corresponding cDNA libraries were screened for sequence variants. Both cDNA pools differred mainly in the 5'-end of the CP gene. Methionine at the position 17 in combination with serine at the position 34 were frequently associated with the CS character of PVS. In general, hydrophobic and polar amino acids were characteristic for the positions 17 and 34, respectively in PVS-CS isolates. Genome probing and evolutionary distances suggested that the PVS-CS isolates analyzed were close to the ordinary European isolates of ordinary strain of PVS (PVS-O) but distant to the original Andean strain of PVS (PVS-A).

Construction and properties of a gene-silencing vector based on Poplar mosaic virus (genus Carlavirus)

A gene-silencing vector based on a full-length genomic clone of Poplar mosaic virus (PopMV) was constructed, with coat protein and movement protein genes removed, and containing instead, the coding sequence for green fluorescent protein (GFP). This paper demonstrates that the PopMV-derived gene-silencing vector was able to silence GFP expression in GFP transgenic Nicotiana benthamiana plants. The full-length genome of an Oxford isolate of PopMV (PV275) was cloned and sequenced. A full-length PopMV clone, under transcriptional control of the 35SCaMV promoter was then constructed, and the clone was able to replicate locally in Nicotiana species. Several autonomous plant RNA and DNA viruses have been converted into vectors and implemented for virus-induced gene-silencing (VIGS) of transgenes and endogenous genes [Burton, R., Gibeaut, D., Bacic, A., Findlay, K., Roberts, K., Hamilton, A., Baulcombe, D., Fincher, G., 2000. Virus-induced silencing of a plant cellulose synthase gene. Plant Cell 12, 691-706; Dalmay, T., Horsefield, R., Braunstein, T.H., Baulcombe, D.C., 2001. SDE3 encodes an RNA helicase required for post-transcriptional gene silencing in Arabidopsis. EMBO J. 20, 2069-2077; Gossele, V., Fache, I., Meulewaeter, F., Cornelissen, M., Metzlaff, M., 2002. SVISS--a novel transient gene silencing system for gene function discovery and validation in tobacco plants. Plant J. 32, 859-866; Holzberg, S., Brosio, P., Gross, C., Pogue, G.P., 2002. Barley stripe mosaic virus-induced gene silencing in a monocot plant. Plant J. 30, 315-327; Ratcliff, F., Martin-Hernandez, A., Baulcombe, D., 2000. Tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J. 25, 237-245; Ruiz, M., Vionnet, O., Baulcombe, D., 1998. Initiation and maintenance of virus-induced gene silencing. Plant Cell 10, 937-946]. The use of a virus that naturally infects trees as a gene-silencing vector has not been demonstrated before. The ability to systemically silence a plant transgene following the production of a gene-silencing signal from a locally replicating viral-construct derived from a carlavirus has not to our knowledge been shown before.

Characterization of the 3'-terminal nucleotide sequence of two Korean isolates of Daphne virus S support its placement as a distinct species of the genus Carlavirus

This study determined the 3'-terminal nucleotide sequences of two Korean isolates of Daphne virus S (DVS), a tentative member of the genus Carlavirus, causing leaf distortion and chlorotic spot disease symptoms in daphne plants. The 3'-terminal 1,465 nucleotide sequences of the two isolates contained two open reading frames coding for proteins of 36 kDa viral coat protein (CP) and 12 kDa from the 5'-3' end, which is a typical genome structure of the 3'-terminal region of carlaviruses. Both DVS isolates were 98.1% and 93.6% amino acid identical in the CP and 12 kDa, respectively. The CP gene of DVS shares 25.2-55.2% and 42.9-56.1% similarities with that of 19 other carlaviruses at the amino acid and nucleotide levels, respectively. The 3'-proximal 12 kDa gene of DVS shares 20.2-57.8% amino acid identities with that of 18 other members of the genus. The 3' noncoding region of DVS consists of 73 nucleotides with long excluding poly A tract, and shares 69.1-77.1% identities to the known carlaviruses. In the phylogenetic analyses of the two proteins, DVS was closely related to Helenium virus S and Chrysanthemum virus B. This is the first sequence information for the DVS, and further confirms the classification of DVS as a distinct member of the genus Carlavirus.

The complete nucleotide sequence of the genome RNA of Lily symptomless virus and its comparison with that of other carlaviruses

The complete genomic nucleotide sequence and genome structure of Lily symptomless virus (LSV), a lily-infecting carlavirus, have been obtained. The genome of the Korean strain of LSV, LSV-Kr, was 8394 nucleotides long and contained six open reading frames (ORFs) coding for proteins of Mr 220 kDa (1948 aa), 25 kDa (228 aa), 12 kDa (106 aa), 7 kDa (64 aa), 32 kDa (291 aa) and 16 kDa (140 aa) from the 5' to 3' end, respectively, which is typical of carlaviruses. Genetic heterogeneity was observed in the ORF1 gene. A total of 221 of 5,847 nucleotides (nt) were heterologous in the ORF1 of replicase; 162 nt portions were silent and 59 nt resulted in amino acid changes. This heterogeneity indicates that the LSV-infecting lily plants contained a genetically heterogeneous population of LSV (quasispecies). Overall similarities to those of other carlaviruses for the six ORFs of LSV were from 76.1% to 31.6% and from 87.3% to 13.7%, at nucleotide and amino acid levels, respectively. The ORF1 replicase gene of LSV shares 40.9% to 56.8% and 48.9% and 58.6% identities with that of 5 other carlaviruses at the amino acid and nucleotide levels, respectively. LSV was closest to Blueberry scorch virus (BlScV) in this ORF, among the carlaviruses for which sequence information is available. The three triple gene blocks (ORF2-4), ORF5 (coat protein) and 3'-proximal 16 kDa ORF6 genes were further analyzed, and phylogenetic trees for the coding regions indicate that the LSV was the most closely related to Kalanchoe latent virus and BlScV. This is the first report of the complete nucleotide sequence and genome structure of LSV.

Occurrence and sequences of Lily mottle virus and Lily symptomless virus in plants grown from imported bulbs in Zhejiang province, China

Degenerate primers were used to amplify virus sequences from imported lilies in Zhejiang province, China. Two viruses, Lily mottle virus (LMoV, genus Potyvirus) and Lily symptomless virus (LSV, genus Carlavirus) were detected, purified and completely sequenced from a mixed infection in a plant raised from bulbs imported from the Netherlands. The sequence of LMoV was 9644 nt long and encoded a polyprotein of 3095 amino acids with a calculated M(r) of 351.0 kDa that had only 45.1-54.4% identity to other completely sequenced potyviruses. Phylogenetic analysis of the complete polyproteins of members of the genus demonstrated that LMoV was distantly grouped with LYSV, BYMV and ClYVV. Two partial LMoV sequences from different cultivars were identical to one another and very similar (98.3% identical nucleotides) to the corresponding region of the complete sequence. Analysis of the coat protein sequences of LMoV isolates revealed two subgroups, corresponding to the earlier "Tulip breaking virus lily strain" and "Tulip band breaking virus" isolates. Our newly-determined isolates showed an extremely close relationship to the first of these. The LSV sequence was 8393 nucleotides long and had the typical carlavirus genome organization. The ORF1 protein was most closely related to that of Blueberry scorch virus (57.2% identical amino acids). Sequences of 1796 nt at the 3'-end of three additional LSV isolates from different cultivars were very similar (>98% identical nucleotides) to the corresponding region of the complete sequence. This is the first report of complete sequences for LMoV and LSV.

[Complete sequence analysis on potato virus M infecting Solanum muricatum]

The complete sequence of Potato virus M from Solanum muricatum was determined. The liner, single-strand and positive sense genomic RNA was 8526 nucleotides long and six open reading frames were identified. The genome organization was typical feature of genus Carlavirus. Sequence analysis showed that PVM isolates shared 62.5% - 97.2% nucleotide and 60.9% - 97.4% amino acid identities. The coat protein gene was most conserved and TGB3 gene was greatly variable. Phylogenetic tree analysis suggested that the Idaho potato isolate (PVM-Id) was a distant strain, and other 4 isolates were grouped discriminatively based on CP and NABP amino acid sequences respectively. This is the first report of PVM from Solanum muricatum.

Characterization of a distinct carlavirus isolated from Verbena

Avirus was isolated from Verbena plants that bore virus-like symptoms. The virus, for which the name Verbena latent virus (VeLV) is proposed, was consistently isolated from these plants, both with and without disease symptoms. Electron microscopy studies of ultrathin sections of infected Verbena tissues revealed the presence of elongated flexuous virus particles, ca. 650 nm in length. Its experimental host range was limited to Verbena spp. and Nicotiana clevelandii. No inclusion bodies or specific cytopathological effects, were observed. Electrophoresis of dissociated purified virus preparation in sodium dodecyl sulfate-polyacrylamide gel revealed a major protein component with a molecular mass of 38.9 kDa. Polyclonal antibodies which could specifically bind to virus particles were produced. A portion of the viral RNA was cloned and sequenced; it comprised 2503 nucleotides and contained part of three open reading frames (ORFs) which from the 5' to the 3'-ends, potentially encode for 489 amino acids (ORF1), a 25.8-kDa protein (ORF2) and a 12-kDa protein (ORF3). Comparison of the predicted amino acid sequence with those of other plant viruses revealed 40-60% identity with several carlaviruses. In the light of particle morphology, absence of specific cytopathological effects in ultrathin sections, and genomic and serological properties, it is suggested that this virus belongs to the genus Carlavirus.

Complete genome sequence of garlic latent virus, a member of the carlavirus family

The complete genome sequence of the garlic latent virus (GLV) has been determined. The whole GLV genome consists of 8,353 nucleotides, excluding the 3'-end poly(A)+ tail, and contains six open-reading frames (ORFs). Putative proteins that were encoded by the reading frames contain the motifs that were conserved in carlavirus-specific RNA replicases, NTP-dependent DNA helicases, two viral membrane-bound proteins, a viral coat protein, and a zinc-finger. Overall, the GLV genome shows structural features that are common in carlaviruses. An in vitro translation analysis revealed that the zinc-finger protein is not produced as a transframe protein with the coat protein by ribosomal frameshifting. A Northern blot analysis showed that GLV-specific probes hybridized to garlic leaf RNA fragments of about 2.6 and 1.5 kb long, in addition to the 8.5 kb whole genome. The two subgenomic RNAs might be encapsidated into smaller viral particles. In garlic plants, 700 nm long flexuous rod-shaped virus particles were observed in the immunoelectron microscopy using polyclonal antibodies against the GLV coat proteins.

Characterisation of some carla- and potyviruses from bulb crops in China. Brief report

Conserved carla- and potyvirus primers were used in RT-PCR to amplify virus fragments from garlic and other bulb crops in China and the fragments were subsequently sequenced and compared in phylogenetic analyses. Garlic plants from Henan, Hubei, Jiangsu, Shangdong and Yunnan provinces all contained at least one isolate each of Garlic latent virus (genus Carlavirus), Onion yellow dwarf virus (OYDV, genus Potyvirus) and Leek yellow stripe virus (LYSV, genus Potyvirus). The complete sequence of a Zhejiang isolate of LYSV was also determined, providing the first complete sequence of this virus. The genome was 10142 nucleotides long excluding the poly(A) tail and had the typical features of the genus Potyvirus, although some of the amino acids surrounding the polyprotein cleavage sites were unusual. Shallot yellow stripe virus (SYSV) was amplified from bunching onion (Allium fistulosum var. caespitosum) in Zhejiang province, providing the first record of SYSV in China. Lily mottle virus was amplified from dragon-teeth lily (Lilium brownii var. viridulum).

Complete nucleotide sequence of the genomic RNA of Aconitum latent virus (genus Carlavirus) isolated from Delphinium sp

We determined the complete nucleotide sequence of Aconitum latent virus (AcLV-D) isolated from Delphinium sp. The genomic RNA of AcLV-D is 8,657 nucleotides in length, excluding the poly (A) tail. Based on computer analysis, six open reading frames (ORFs) were identified as for other carlaviruses. Although each ORF differs from those of previously reported carlaviruses, the coat protein of AcLV and Potato virus M (PVM) shows a high level of identity. The results suggest that AcLV is a distinct carlavirus species but closely related to PVM.

Molecular characterization of Hop mosaic virus: its serological and molecular relationships to Hop latent virus

The 3'-terminal sequence of hop mosaic virus (HpMV) genomic RNA was determined. A cDNA of approximately 1.8 kbp was amplified from the HpMV genome by 3' RACE using a degenerate primer, which was designed to anneal to the overlapping region of open reading frames (ORFs) 2 and 3 of eight carlavirus genomes. The sequence contained three ORFs, encoding proteins of 7-, 34-, and 11-kDa, which corresponded to ORFs 4, 5, and 6 of the carlavirus genome, respectively. The amino acid sequence of ORF 5, encoding the coat protein (CP) of HpMV, shows the highest identity (67%) to that of Hop latent virus (HpLV). The HpMV CP N-terminal sequence differs from that of HpLV, but the central and C-terminal sequences of the CP of both viruses are similar. The sequence similarity possibly causes the cross-reaction of heterologous antibodies of HpMV and HpLV. Phylogenetic analyses based on the CP amino acid and 3' non-coding region sequences indicate close relationships among HpMV, HpLV, and Potato virus M. We report here the first molecular characterization of HpMV genomic RNA.

Molecular characterisation of a complex mixture of viruses in garlic with mosaic symptoms in China

Degenerate primers were used to detect and amplify cDNA of viruses of the genera Carlavirus, Allexivirus and Potyvirus from garlic plants with mosaic symptoms growing in Zhejiang province, China. Plants contained a complex mixture of viruses and strains. Three distinct stains of Garlic latent virus were detected; the most frequent one was completely sequenced and partial sequences were obtained for the other two. The complete sequence (8363 nt) was 76.4% identical to a Korean isolate. Two allexiviruses were detected and completely sequenced. One (8319 nt) was identified as Garlic virus X and comparisons showed that a published Korean isolate (which had 90.2% identical nucleotides) had an N-terminal deletion in the serine-rich ORF4. The other isolate (8451 nt), tentatively named Garlic virus E, appeared to be a new member of the genus. Phylogenetic analyses of the different viral proteins and distinctive conserved sequence motifs within the genus are discussed. This is the first report of allexiviruses from China. Using potyvirus primers, three distinct isolates of Onion yellow dwarf virus and one of Leek yellow stripe virus were detected and the 3'-terminal sequences of their genomes were determined. In a coat protein phylogenetic analysis, the new isolates were most closely related to other published isolates from Japan and China.