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a simple method for the purification of poplar mosaic virus and onion yellow dwarf virus by low centrifugal forces.a simple method for the purification of poplar mosaic virus and onion yellow dwarf virus by low centrifugal forces is described. the method yields a high concentration of purified virus, avoiding virus aggregation or fragmentation.1979462788
nucleotide sequences of the 3' terminal region of onion yellow dwarf virus isolates from allium plants in japan.the 2032 nucleotide sequence of the 3' terminal region of onion yellow dwarf virus (oydv) isolated from allium wakegi, bearing the genes for viral coat protein (cp) and a truncated rna-dependent rna polymerase, has been determined. respective homologies of the nucleotide sequence in the corresponding region and the deduced amino acid sequence of cp with the equivalents of leek yellow stripe virus (lysv) from garlic were 68.0 and 59.3%. variation in the nucleotide sequence is concentrated in the ...19979354273
nucleotide sequence analysis of virus isolates indicates the presence of three potyvirus species in allium plants.cdnas of potyviruses from allium plants cultivated in different parts of the world were cloned by rt-pcr with a common primer for amplifying the 3' terminal genomic rnas of onion yellow dwarf virus (oydv), leek yellow stripe virus (lysv) and, probably, of closely related potyviruses. their nucleotide sequences bearing the viral coat protein (cp) gene and the 3' non-coding sequence were determined and compared. the degree of their sequence similarities clearly differentiated the respective viruse ...19989505969
coat protein gene sequences of garlic and onion isolates of the onion yellow dwarf potyvirus (oydv).partial genomic sequences from an unknown garlic potyvirus and from an onion isolate of the onion yellow dwarf potyvirus (oydv) were obtained. comparison of the deduced amino acid sequences showed a similarity of 88% between the respective viral coat proteins. the garlic potyvirus coat protein was expressed in e. coli cells, purified, and subjected to western blot analysis using antibodies raised against different garlic-infecting viruses. the expression protein was consistently recognised by an ...19969526536
a universal pcr primer to detect members of the potyviridae and its use to examine the taxonomic status of several members of the family.a universal primer (sprimer: 5'-ggx aay aay agy ggx caz cc-3', x = a, g, c or t; y = t or c; z = a or g), designed from the consensus sequences that code for the conserved sequence gnnsgqp in the nib region of members of the family potyviridae, was used to amplify by rt-pcr the 3'-terminal genome regions from infected plant samples representing 21 different viruses in the family. sequencing of some of the fragments (c. 1.7 kb) showed that the type strain (attc pv-107) of oat necrotic mottle viru ...200111402861
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 allexi ...200111722009
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 z ...200211890533
sequence analysis demonstrates that onion yellow dwarf virus isolates from china contain a p3 region much larger than other potyviruses.the complete sequence of an isolate of onion yellow dwarf virus (oydv) from yuhang, zhejiang province, china, was determined. it was 10538 nts in length and was predicted to encode a polyprotein 3403 amino acids (aa) long with a calculated m(r) of 385.1 kda. the predicted p3 protein (530 aa) was larger than that of any of the potyviruses sequenced to date (344-378 aa). the additional sequence occurs at the n-terminus of the protein, does not represent a duplication from elsewhere in the oydv gen ...200312756621
characterisation of the welsh onion isolate of shallot yellow stripe virus from china.the host range and nucleotide sequence of shallot yellow stripe virus (sysv) from welsh onion in shandong province, china is described. of the plants tested, only shallot and welsh onion became infected but most shallot plants were symptomless. the complete sequence of one isolate (10429 nt) and the 3'-terminal 3540 nts of a second isolate were determined. they had c. 90% nt identity to one another and to published (partial) sequences of sysv. sysv was most closely related to onion yellow dwarf ...200515968472
identification and sequence analysis of potyviruses infecting crops in vietnam.fifty-two virus isolates from 13 distinct potyvirus species infecting crops in vietnam were identified and the 3' region of each genome was sequenced. the viruses were: bean common mosaic virus (bcmv), potato virus y (pvy), sugarcane mosaic virus (scmv), sorghum mosaic virus (srmv), chilli veinal mottle virus (chivmv), zucchini yellow mosaic virus (zymv), leek yellow stripe virus (lymv), shallot yellow stripe virus (sysv), onion yellow dwarf virus (oydv), turnip mosaic virus (tumv), dasheen mosa ...200817906829
further evidence that shallot yellow stripe virus (sysv) is a distinct potyvirus and reidentification of welsh onion yellow stripe virus as a sysv strain.abstract an antiserum to shallot yellow stripe virus (sysv) was raised and used in combination with a range of other antisera to potyviruses of allium spp. in electron microscopic decoration experiments. the serological results corroborated an earlier finding that the type isolates of sysv and welsh onion yellow stripe virus (woysv) are closely related to each other and only distantly related to onion yellow dwarf (oydv) and leek yellow stripe (lysv) viruses, the two other major potyviruses infe ...199918944789
n-terminal of papaya ringspot virus type-w (prsv-w) helper component proteinase (hc-pro) is essential for prsv systemic infection in zucchini.the papaya ringspot virus (prsv) is one of the limiting factors affecting papaya and cucurbits production worldwide. prsv belongs to the potyvirus genus which consists of 30% of known plant viruses. two serological closely related strains, namely type-p and -w, have been reported. prsv type-p infects both papaya and cucurbits, while type-w infects only cucurbits. the genome of prsv thailand isolate consists of a (+) rna molecule of 10323 nucleotides, which is first translated into a single polyp ...200919322647
a new isolate of iris severe mosaic virus causing yellow mosaic in iris ensata thunb.severe mosaic disease was observed on iris ensata thunb. in spring 2008, in hangzhou, china and it was found to be widely distributed in that region. detection of viruses by electron microscopy resulted in the occurrence of a potyvirus in most symptomatic seedlings. sequencing 1745 nucleotides of the 3'-terminal region of the genome of the typical viral isolate revealed that it was a new isolate of iris severe mosaic potyvirus (ismv), tentatively named ismv-phz .this strain shared high nucleotid ...201020352710
interaction between potyvirus p3 and ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) of host plants.the p3 protein encoded by shallot yellow stripe virus onion isolate (sysv-o) interacted in the yeast two-hybrid (y2h) system and in co-immunoprecipitation (co-ip) assays with the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) protein that is encoded by the rbcl gene of its onion host. dissection analysis by y2h showed that the main part of sysv p3 (amino acids 1-390) and onion rbcl (amino acids 1-137) were responsible for the interaction. the p3 proteins encoded b ...201121400205
molecular characterization of indian isolate of peanut mottle virus and immunodiagnosis using bacterial expressed core capsid protein.peanut mottle virus (pemov), a seed borne potyvirus was recorded in india in 1978, however the virus was not characterized at molecular level. in the present study, an isolate of pemov infecting peanut in southern india was characterized based on host reactions and coat protein (cp) gene sequence, which revealed that the indian isolate was very close to a peanut isolate reported from israel and distinct from pea isolate reported from usa. the core region of cp gene that contained majority of the ...201425674600
the global trade in fresh produce and the vagility of plant viruses: a case study in garlic.as cuisine becomes globalized, large volumes of fresh produce are traded internationally. the potential exists for pathogens infecting fresh produce to hitchhike to new locations and perhaps to establish there. it is difficult to identify them using traditional methods if pathogens are novel, scarce, and/or unexpected. in an attempt to overcome this limitation, we used high-throughput sequencing technology as a means of detecting all rna viruses infecting garlic (allium sativum l.) bulbs importe ...201425133543
simultaneous detection of four garlic viruses by multiplex reverse transcription pcr and their distribution in indian garlic accessions.indian garlic is infected with onion yellow dwarf virus (oydv), shallot latent virus (slv), garlic common latent virus (garclv) and allexiviruses. identity and distribution of garlic viruses in various garlic accessions from different geographical regions of india were investigated. oydv and allexiviruses were observed in all the garlic accessions, while slv and garclv were observed only in a few accessions. a multiplex reverse transcription (rt)-pcr method was developed for the simultaneous det ...201424598229
viruses occurring in onion crop in amasya province, the major onion producing region in turkey.amasya is the greatest onion producing area in turkey. onion fields from amasya region were surveyed for virus diseases in 2009-2011 and tested for the presence of the most important onion viruses such as onion yellow dwarf virus (oydv), iris yellow spot virus (iysv), leek yellow stripe virus (lysv), shallot latent virus (slv) and garlic common latent virus (gclv). the presence of virus diseases and their identification was ascertained through symptom observation in the fields, sap transmission ...201324426263
simultaneous detection of mixed infection of onion yellow dwarf virus and an allexivirus in rt-pcr for ensuring virus free onion bulbs.reduced seed production in onion is associated with onion yellow dwarf virus (oydv), a filamentous potyvirus. onion is also infected with other filamentous virus particles suspected to be allexivirus. rt-pcr was used to detect mixed infection of both the viruses in leaves and bulbs. a duplex rt-pcr was developed, which simultaneously detected the presence of these two viruses in winter (rabi) onion bulb. in summer (kharif) onion bulbs only allexivirus was detected. the absence of oydv in summer ...201023637480
use of tissue culture techniques for producing virus-free plant in garlic and their identification through real-time pcr.this study was performed for comparison of meristem culture technique with shoot tip culture technique for obtaining virus-free plant, comparison of micropropagation success of two different nutrient media, and determination of effectiveness of real-time pcr assay for the detection of viruses. two different garlic species (allium sativum and allium tuncelianum) and two different nutrient media were used in this experiment. results showed that medium 2 was more successful compared to medium 1 for ...201323935432
variability in the p1 gene helps to refine phylogenetic relationships among leek yellow stripe virus isolates from garlic.nucleotide sequences from the p1 gene and the 5' untranslated region of leek yellow stripe virus (lysv), collected from several locations, were used to refine the phylogenetic relationships among the isolates. multiple alignments revealed three distinct regions of insertions and deletions to classify lysvs. in our phylogenetic analyses, the lysv isolates separated into two major groups (n-type and s-type). s-type viruses had two large deletions compared to n-type viruses. considering that the ou ...201221964945
ultra-sensitive detection of two garlic potyviruses using a real-time fluorescent (taqman) rt-pcr assay.a method for the detection of onion yellow dwarf virus (oydv) and leek yellow stripe virus (lysv), the two most prevalent garlic potyviruses, has been developed that combines ic-rt-pcr/rt-pcr with the use of taqman probes. comparisons with elisa results obtained with identical oydv and lysv infected samples showed sensitivity in detecting these viruses increased up to 10(6)-fold. oydv and lysv were detected using different fluorochromes in the probe, thus allowing unequivocal diagnosis for each ...200415158064
the first complete genome sequence of iris severe mosaic virus.the first complete genome sequence of ismv was determined by deep sequencing of a small rna library constructed from ismv-infected samples and rapid amplification of cdna ends (race) pcr. the ismv genome consists of 10,403 nucleotides excluding the poly(a) tail and contains a large open reading frame encoding a polyprotein of 3316 amino acids. putative proteolytic cleavage sites were identified by blast analysis. the ismv polyprotein showed highest amino acid sequence identity to that encoded by ...201626729478
striking differences in the biological and molecular properties of onion and garlic isolates of onion yellow dwarf virus.complete nucleotide (nt) and deduced amino acid sequences of two onion yellow dwarf virus (oydv) isolates showing mild and severe symptoms in onion but being unable to infect garlic were determined. the genomes consisted of 10,459 and 10,461 nt (without the 3' poly(a) tail) and were 92.2 % identical. comparison of their whole genomes, polyproteins and p1, hc-pro, p3, ci, vpg and nia-pro regions with those of garlic isolates previously identified as oydv gave percentage values below that proposed ...201323397330
molecular variability and genetic structure of the population of onion yellow dwarf virus infecting garlic in iran.onion yellow dwarf virus (oydv) is one of the most important viral diseases of garlic crops worldwide. this study surveyed the occurrence of oydv in 26 garlic ecotypes collected from different regions in iran during 2008-2009. using an electron microscope, we detected filamentous particles with about 700-800 nm in length and 12 nm in width in five samples. these features are typical of the genus potyvirus. the coat protein (cp) gene from 26 samples was pcr amplified, cloned, sequenced, and compa ...201020652628
the complete nucleotide sequence of attenuated onion yellow dwarf virus: a natural potyvirus deletion mutant lacking the n-terminal 92 amino acids of hc-pro.the complete nucleotide sequence of a severe isolate of onion yellow dwarf virus contains 10,459 nucleotides encoding 3,403 amino acids, while that of an attenuated isolate contains 10,183 nucleotides encoding 3,311 amino acids. the sequence coding for the n-terminal 92 amino acids of hc-pro was missing in the attenuated isolate. interestingly, garlic plants growing in commercial gardens were co-infected with isolates of both types. this is the first report of a natural potyvirus deletion mutant ...200616463124
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