| cherry virus a: cdna cloning of dsrna, nucleotide sequence analysis and serology reveal a new plant capillovirus in sweet cherry. | the nucleotide sequence (7383 nucleotides) of a newly identified member of the genus capillovirus, cherry virus a (cva), was obtained from cdna clones. the cdna was generated from dsrna extracted from plant tissue infected with little cherry virus (lcv). small amounts of lcv dsrna served as template nucleic acid and enabled the construction of a library of which, unexpectedly, 7.5% of the recombinant plasmids were specific for cva. the genome organization of cva resembles that of apple stem groo ... | 1995 | 7636482 |
| papain-like proteinase of turnip yellow mosaic virus: a prototype of a new viral proteinase group. | sequence comparisons predicted a potential papain-like proteinase domain in the n-terminal cleavage product (nrp) of the large nonstructural replicase polyprotein (rp) of turnip yellow mosaic virus (tymv). replacement of the predicted catalytic amino acids, cys-783 by ser, or of his-869 by glu, abolished cleavage of the 206k rp into a approximately 150 k nrp and a approximately 78 k c-terminal product in reticulocyte lysates, while other substitutions exerted no apparent influence on proteolysis ... | 1995 | 7710355 |
| nucleotide sequence and genome structure of grapevine rupestris stem pitting associated virus-1 reveal similarities to apple stem pitting virus. | rupestris stem pitting (rsp), a component of the rugose wood complex, is one of the most widespread graft-transmissible diseases of grapevines. here we report on the consistent association of a high molecular mass dsrna (ca. 8.7 kbp) with rsp. the dsrna was reverse-transcribed and cdnas generated were cloned into lambda zap ii. sequence analysis of the cdna clones showed that the dsrna was of viral origin and the putative virus was designated rupestris stem pitting associated virus-1 (rspav-1). ... | 1998 | 9714258 |
| cdna cloning and molecular characterization of cherry green ring mottle virus. | the complete nucleotide sequence of the cherry green ring mottle virus (cgrmv) genome was determined to be 8372 nt excluding a 3' poly(a) tail. based on computer analysis and sequence comparison, five open reading frames (orfs) were identified on the virion strand encoding: a putative rna-dependent rna polymerase, a triple gene block and a coat protein. two other orfs with mr values over 10,000 and internal to the helicase and coat protein genes, but of unknown function, were also identified. se ... | 1998 | 9747738 |
| apricot latent virus: a new species in the genus foveavirus. | extraction of viral double-stranded rna from peach leaves infected with apricot latent virus (alv) followed by molecular cloning of synthesized cdna and its sequencing, suggested that alv is a new virus, whose coat protein (cp) coding region contains apple stem pitting virus (aspv)-related sequences. the sequenced portion of the alv genome (1,444 nt) includes the putative cp gene and the 3' non-translated region. the 5' portion of this fragment (1-651 nt) is highly distinct whereas the 3' portio ... | 2000 | 11043942 |
| detection of four apple viruses by multiplex rt-pcr assays with coamplification of plant mrna as internal control. | two multiplex rt-pcr assays with specific coamplification of plant mrna as an internal control from total nucleic acids are described for the parallel detection of apple chlorotic leaf spot virus, apple stem pitting virus, apple mosaic virus and apple stem grooving virus. all are important economically and common pathogens in commercial apple and pear cultivars, except for apple mosaic virus. four virus specific primer pairs and one primer pair which allows the specific amplification of mrna of ... | 2002 | 11684306 |
| multiplex rt-pcr-elisa compared with bioassay for the detection of four apple viruses. | a sensitive and reliable multiplex rt-pcr-elisa technique for the detection of apple chlorotic leaf spot virus, apple stem pitting virus, apple mosaic virus and apple stem grooving virus was developed. this technique is compared with the method used commonly for indexing by woody indicators, which is time consuming and expensive. for the rt-pcr-elisa technique, the amplified products were labeled with digoxigenin during the rt-pcr by incorporation of a digoxigenin labeled primer. after hybridiza ... | 2003 | 12798242 |
| a rapid and effective rna release procedure for virus detection in woody plants by reverse transcription-polymerase chain reaction. | a rapid and effective rna release procedure (rna-rp) for detection of the apple stem pitting virus (aspv) and the apple stem grooving virus (asgv) in woody plants by reverse transcription-polymerase chain reaction (rt-pcr) was developed. rna-rp released rna into crude homogenate. rna-rp was compared with classical phenol/chlorophorm extraction of rna. the rt-pcr detection of aspv and asgv was shown to be similar by both the rna preparation procedures. rna-rp in contrast to the classical phenol/c ... | 2003 | 14658842 |
| simultaneous detection and identification of four pome fruit viruses by one-tube pentaplex rt-pcr. | a pentaplex reverse-transcription polymerase chain reaction (pentaplex rt-pcr) in a single tube was developed for the simultaneous detection of the pome fruit viruses: apple stem pitting virus (aspv), apple stem grooving virus (asgv), apple chlorotic leaf spot virus (aclsv) and apple mosaic virus (apmv). this is the first report of the simultaneous detection of all four viruses and host mrna as an internal specific control. pentaplex rt-pcr was applied successfully throughout the year, using dif ... | 2006 | 16337013 |
| analysis of the complete genome of peach chlorotic mottle virus: identification of non-aug start codons, in vitro coat protein expression, and elucidation of serological cross-reactions. | the entire genome of peach chlorotic mottle virus (pcmv), originally identified as prunus persica cv. agua virus (4n6), was sequenced and analysed. pcmv cross-reacts with antisera to diverse viruses, such as plum pox virus (ppv), genus potyvirus, family potyviridae; and apple stem pitting virus (aspv), genus foveavirus, family flexiviridae. the pcmv genome consists of 9005 nucleotides (nts), excluding a poly(a) tail at the 3' end of the genome. five open reading frames (orfs) were identified wit ... | 2007 | 17891331 |
| transgenic nicotiana occidentalis plants expressing the 50-kda protein of apple chlorotic leaf spot virus display increased susceptibility to homologous virus, but strong resistance to grapevine berry inner necrosis virus. | abstract the 50-kda protein (p50) encoded by the open reading frame 2 of apple chlorotic leaf spot virus (aclsv), a putative movement protein, was expressed in transgenic nicotiana occidentalis plants. p50 in transgenic plants was mainly detected in a modified form in the cell wall fraction, similar to that in infected leaves. the p50-expressing plants (p50 plants) complemented the systemic spread of the p50-defective mutants of an infectious cdna clone of aclsv (pclsf), indicating that p50 in t ... | 2000 | 18944625 |
| identification of sugarcane striate mosaic-associated virus by partial characterization of its double-stranded rna. | abstract sugarcane striate mosaic (scsm)-affected sugarcane leaves contain a disease-associated 9-kilobase (kb) double-stranded rna (dsrna), usually together with 6- and 2.6-kb dsrnas. the purified 9-kb dsrna was amplified by the randomly primed polymerase chain reaction (pcr) and cloned. the nucleotide sequences of three separate regions, representing about 2.55 kb (28%) of the dsrna sequence, were found to have significant similarities to viruses in the genera capillo-, carla-, fovea-, potex-, ... | 1999 | 18944730 |
| nucleotide sequence and rt-pcr detection of a virus associated with grapevine rupestris stem-pitting disease. | abstract grapevine rupestris stem pitting (rsp) is a graft-transmissible disease of unknown etiology. we have characterized a virus associated with this disease. the entire genomic sequence (genbank accession number af026278) consisted of 8,725 nucleotides excluding a poly(a) tail. six open reading frames (orf) were found. orf1 potentially encodes a polypeptide with a methyltransferase domain, a papain-like proteinase domain, a helicase domain, and a rna-dependent rna polymerase domain; orf2, or ... | 1998 | 18944859 |
| characterization of prunus-infecting apricot latent virus-like foveaviruses: evolutionary and taxonomic implications. | the complete genomic sequences of four prunus-infecting apricot latent virus (aplv) like isolates were determined and used to analyze the taxonomic position and variability of these viruses. the results indicate that all isolates show a typical foveavirus genetic organization. despite an average 23% nucleotide divergence, they show strong colinearity with only three regions of significant indel variability, in the internal and 3' non-coding regions and variable n-terminal half of the coat protei ... | 2010 | 21144869 |
| cydonia japonica, pyrus calleryana and p. amygdaliformis: three new ornamental or wild hosts of apple stem pitting virus. | japanese quince, ornamental and wild pear symptomless samples were infected with apple stem pitting virus (aspv). identification of aspv was achieved by different pcr assays that amplified either the rna polymerase or coat protein gene regions. for further confirmation, 312 bp amplicons within the polymerase gene were sequenced and compared with previously published aspv sequences and additional sequences of isolates from ancient italian cultivars. comparison of the partial sequences isolated fr ... | 2011 | 22006446 |
| determination of major viral and sub viral pathogens incidence in apple orchards in himachal pradesh. | apple is the major commercial horticulture crop in himachal pradesh and other hill states of jammu & kashmir, uttarakhand and some parts of northeastern states of india. in order to gather data on health status and incidence of virus and virus-like pathogens in apple orchards, survey was conducted in the month of june and september, 2010 in hatkoti, rohru, kuthara, jubbal and khadapathar areas of major apple producing shimla district of himachal pradesh. a total of 250 samples were collected and ... | 2011 | 23730008 |
| deep sequencing analysis of apple infecting viruses in korea. | deep sequencing has generated 52 contigs derived from five viruses; apple chlorotic leaf spot virus (aclsv), apple stem grooving virus (asgv), apple stem pitting virus (aspv), apple green crinkle associated virus (agcav), and apricot latent virus (aplv) were identified from eight apple samples showing small leaves and/or growth retardation. nucleotide (nt) sequence identity of the assembled contigs was from 68% to 99% compared to the reference sequences of the five respective viral genomes. sequ ... | 2016 | 27721694 |
| a multiple rt-pcr assay for simultaneous detection and differentiation of latent viruses and apscarviroids in apple trees. | apple chlorotic leaf spot virus (aclsv), apple stem grooving virus (asgv), and apple stem pitting virus (aspv) are three latent viruses frequently occurring in apple trees worldwide. in field orchards, these viruses are frequently found in a mixed infection with viroids in the genus apscarviroid, including apple scar skin viroid, and apple dimple fruit viroid. together these viruses and viroids could cause serious damage to apple fruit production worldwide. rapid and efficient detection methods ... | 2016 | 27054889 |
| cryotherapy as a method for reducing the virus infection of apples (malus sp.). | there is an urgent need in kazakhstan for virus-free nursery stock to reinvigorate the industry and preserve historic cultivars. an in vitro collection of apples could be used for virus testing and elimination and to provide virus-free elite stock plants to nurseries. | 2016 | 26964019 |
| a simplified strategy for studying the etiology of viral diseases: apple stem grooving virus as a case study. | a simple method to amplify infective, complete genomes of single stranded rna viruses by long distance pcr (ld pcr) from woody plant tissues is described in detail. the present protocol eliminates partial purification of viral particles and the amplification is achieved in three steps: (i) easy preparation of template rna by incorporating a pre processing step before loading onto the column (ii) reverse transcription by amv or superscript reverse transcriptase and (iii) amplification of cdna by ... | 2015 | 25486082 |
| simultaneous detection of major pome fruit viruses and a viroid. | a rapid and sensitive two-step rt-pcr protocol for simultaneous detection of major apple viruses, namely apple mosaic virus (apmv), apple stem pitting virus (aspv), apple stem grooving virus (asgv), apple chlorotic leaf spot virus (aclsv) and apple scar skin viroid (assvd), was developed. five specific primer pairs were tested and confirmed for these viruses and viroid together in a single tube, giving amplicons of ~198, ~330, ~370, ~547 and ~645 bp corresponding to asgv, assvd, aspv, apmv and a ... | 2014 | 25320423 |
| multiplex rt-pcr detection and distribution of four apple viruses in china. | apple trees are natural hosts of four economically important virus species in china. we used a simple, sensitive multiplex rt-pcr protocol with an internal control to simultaneously detect and differentiate four apple viruses: apple chlorotic leaf spot virus (aclsv), apple mosaic virus (apmv), apple stem pitting virus (aspv), and apple stem grooving virus (asgv). this multiplex rt-pcr could be used as an alternative to other routinely used detection methods. we used this protocol to evaluate the ... | 2013 | 24294957 |
| simultaneous detection and differentiation of three viruses in pear plants by a multiplex rt-pcr. | a multiplex rt-pcr (mrt-pcr) assay was developed for detection and differentiation of the apple stem pitting virus (aspv), apple stem grooving virus (asgv) and apple chlorotic leaf spot virus (aclsv), which are viruses frequently occurring in pear trees. different combinations of mixed primer pairs were tested for their specificity and sensitivity for the simultaneous detection of the three viruses. three primer pairs were used to amplify their fragments of 247bp, 358bp and 500bp, respectively. ... | 2014 | 24269332 |
| identification and characterization of an isolate of apple green crinkle associated virus involved in a severe disease of quince (cydonia oblonga, mill.). | a quince tree showing severe symptoms of a previously undescribed viral disease occurring in northern apulia (italy) was analysed using high-throughput sequencing of small rna libraries, leading to the identification of a new strain of apple green crinkle associated virus (isolate agcav-cyd) showing peculiar traits. rt-pcr with specific primers detected agcav-cyd in consistent association with symptoms in the surveyed orchards. molecular characterization of the reconstructed genome, together wit ... | 2017 | 27709400 |
| malus pumila 'spy 227' and apple stem pitting virus: graft incompatibility and epinasty. | apple stem pitting foveavirus (aspv) is one of the most important and widespread virus infecting apples in the world. of late, the virus has been found to be invariably associated with most of the apple plantations of shimla district of himachal pradesh based on das-elisa results. bioassay of viruses in vegetatively propagated crops including apple is considered to be an essential component in indexing programmes for the production of virus free propagating material. woody indicator malus pumila ... | 2015 | 26436128 |
| genetic diversity of a natural population of apple stem pitting virus isolated from apple in korea. | apple stem pitting virus (aspv), of the foveavirus genus in the family betaflexiviridae, is one of the most common viruses of apple and pear trees. to examine variability of the coat protein (cp) gene from aspv, eight isolates originating from 251 apple trees, which were collected from 22 apple orchards located in intensive apple growing areas of the north gyeongsang and north jeolla provinces in korea, were sequenced and compared. the nucleotide sequence identity of the cp gene of eight aspv is ... | 2014 | 25289003 |
| a double-imprinted diffraction-grating sensor based on a virus-responsive super-aptamer hydrogel derived from an impure extract. | the detection of viruses is of interest for a number of fields including biomedicine, environmental science, and biosecurity. of particular interest are methods that do not require expensive equipment or trained personnel, especially if the results can be read by the naked eye. a new "double imprinting" method was developed whereby a virus-bioimprinted hydrogel is further micromolded into a diffraction grating sensor by using imprint-lithography techniques to give a "molecularly imprinted polyme ... | 2014 | 24453117 |
| identification and complete genome analysis of a virus variant or putative new foveavirus associated with apple green crinkle disease. | a virus identified as "apple green crinkle associated virus" (agcav) was isolated from aurora golden gala apple showing severe symptoms of green crinkle disease. evidence was obtained of a potential causal relationship to the disease. the viral genome consists of 9266 nucleotides, excluding the poly(a) tail at the 3'-terminus. it has a genome organization similar to that of members of the species apple stem pitting virus (aspv), the type species of the genus foveavirus, family betaflexiviridae. ... | 2013 | 23553453 |
| homogeneous assay for evaluation of aptamer-protein interaction. | we introduce amplified luminescent proximity homogenous assay (alpha) to assess the k(d) value of aptamer-protein complexes as demonstrated through the study of apple stem pitting virus coat protein-specific aptamers. this method can be used as a simple, cost-effective method for screening aptamer-target protein interactions during aptamer selection. | 2012 | 22805733 |
| complete genomic sequence analyses of apple stem pitting virus isolates from china. | the complete genomic sequences of a chinese aspv isolates kl1 and kl9 were determined from ten overlapping cdna clones. the genomes of both isolates were 9265 nucleotides excluding the poly (a) tail and contained five open reading frames (orfs). the identities between two complete genomes were 92.5% at nt level. multiple alignment of the amino acid sequences showed that 110 aa variations between two genomic sequences and the variable domains mainly distributed in 5'-terminal of orf1, orf3, and o ... | 2012 | 21909953 |
| sequence diversity and potential recombination events in the coat protein gene of apple stem pitting virus. | the variability of the apple stem pitting virus (aspv) coat protein (cp) gene was investigated. the cp gene of ten virus isolates from apple and pear trees was sequenced. comparison of all sequenced virus isolates revealed high diversity of the cp gene (70.7-93.5% at the nucleotide level and 77.8-98.7% at the amino acid level). additionally, one or two deletions in the n-terminal part of the coat protein gene of the studied virus isolates were identified. the ratio of nonsynonymous to synonymous ... | 2011 | 21402110 |
| selection and versatile application of virus-specific aptamers. | although the significance of molecular diagnostics in routine plant virus detection is rapidly growing, the preferred methods are still antibody-based enzyme immunoassays. in the past decade, aptamers have been demonstrated to be viable alternatives of antibodies in many applications. we set out to select apple stem pitting virus (aspv)-specific aptamers and to apply them as antibody substitutes in various immunoassay methods. the applied systematic evolution of ligands by exponential enrichment ... | 2010 | 20624933 |
| evaluation of several rt-pcr primer pairs for the detection of apple stem pitting virus. | detection of apple stem pitting virus (aspv) using rt-pcr based methods was studied in infected apple and pear trees. three virus-specific primers (aspf1cp, aspf2cp, aspr3cp) were designed to target the most conservative regions of the coat protein gene of 10 virus isolates in poland and 7 other aspv sequences available in genbank. the suitability of the primer pairs aspf1cp-aspr3cp and aspf2cp-aspr3cp for detection of 19 virus isolates was checked. both new primer pairs initiated amplification ... | 2010 | 20447421 |
| aptamer-based biochips for label-free detection of plant virus coat proteins by spr imaging. | specific detection of virus strains by affinity-based bioassays is often limited by the availability of ligands able to differentiate among close homologues of virus coat proteins. as viruses are prone to mutation, the ligand generation should, in addition, be fast enough to allow rapid identification of new varieties. these two criteria are difficult to be fulfilled by antibodies; however, they open up opportunities for aptamer-based detection. here we report on the feasibility of selectively d ... | 2010 | 20419239 |
| rapid and sensitive detection of apple stem pitting virus in apple trees through rna amplification and probing with fluorescent molecular beacons. | abstract currently, detection of apple stem pitting virus (aspv; genus foveavirus) in apple trees for certification purposes occurs by woody indexing. this method requires a minimum of 12 to 24 weeks in greenhouse testing to up to 2 years in field testing. in this paper, the development of a single tube amplidet rna system for the rapid gel-free detection of aspv in apple tree tissues is described. the system relies on the specific amplification of the viral rna by nucleic acid sequence-based am ... | 2001 | 18943445 |
| foveavirus, a new plant virus genus. | foveavirus is a novel genus of plant viruses with helically constructed filamentous particles ca. 800 nm long, typified by apple stem pitting virus (aspv). virions do not contain lipids or carbohydrates, have a positive sense, single-stranded, polyadenylated rna genome 8.4 to 9.3 kb in size, and a single type of coat protein with a size of 28 to 44 kda. the genome of definitive viral species is made up of five orfs encoding respectively, the replication-related proteins (orf 1), the putative mov ... | 1998 | 9687881 |
| nucleotide sequences of apple stem pitting virus and of the coat protein gene of a similar virus from pear associated with vein yellows disease and their relationship with potex- and carlaviruses. | the nucleotide sequence (9306 nucleotides) of cdna clones of apple stem pitting virus (aspv) obtained from a double-stranded rna template, extracted from diseased plant tissue, was determined. the genome is composed of five open reading frames (orfs) encoding putative proteins with m(r)s of 247083, 25147, 12832, 7429 and 43712, and has a poly(a) tail. using two oligonucleotides designed from the aspv sequence information a 1598 bp fragment from near the 3' terminus of the viral rna, containing t ... | 1994 | 8021584 |