Immunocapture RT-PCR Research Articles

Detection and Partial Molecular Characterization of Two Plum pox virus Isolates from Plum and Wild Apricot in Southeast Kazakhstan.

Plum pox virus (PPV) was detected in wild apricot and cultivated plum maintained in a germ plasm collection in Kazakhstan. Both isolates were typed as D strain, with no evidence of recombination. The virus was detected by triple-antibody sandwich enzyme-linked immunosorbent assay (ELISA) utilizing the universal PPV-specific monoclonal antibody (MAb) 5B as the secondary antibody, and by reverse-transcription polymerase chain reaction (RT-PCR) assay using primers that amplified a 243-bp fragment in the C-terminus of the coat protein (CP) coding region. Immunocapture (IC) RT-PCR was used to detect PPV in nine wild apricot accessions, including eight ELISA-negative and one ELISA-positive. The plum and apricot isolates reacted positively in Western blot assay with the universal MAb 5B, and negatively with the strain-M-specific MAb-AL. Restriction fragment length polymorphism analysis applied to the amplified 243-bp fragment showed that restriction sites for AluI and RsaI were present in the were present in the plum and apricot samples. An amplified 836-bp cDNA fragment derived from the P3-6K1 coding region of both isolates had restriction profiles typical for strain D. Nucleotide identities of 99 to 100% were observed for the 243-bp fragments of the Kazakhstan isolates when compared with the corresponding regions of strain D, and 94 to 95% identity with strain M. Nucleotide sequence analysis of the entire CP coding region of the plum and apricotisolates resulted in the identification of a unique deletion of six nucleotides (two deduced proline amino acid residues) in the N-terminal region in the plum isolate. This is the first deletion of this nature observed among PPV isolates. The DAG motif was present in both isolates. Several nucleotide substitutions in the CP coding region were common to the plum and apricot isolates and appear to be unique to the Kazakstan isolates. This suggests a close relationship between the isolates.

Citrus tristeza closterovirus

<i>Citrus tristeza closterovirus</i>

Genomic variability of Citrus tristeza virus (CTV) isolates introduced into Morocco

Genomic variability of the coat protein gene of Citrus tristeza virus isolates obtained from old Meyer lemon introductions in Morocco and more recent budwood introductions from Spain were studied. The coat protein gene of the virus was amplified directly from infected tissue by immunocapture RT-PCR and analysed by single stranded conformation polymorphism (SSCP) and sequencing. Each isolate consisted of several related genomic variants, typical of a quasi-species. Although SSCP analysis has only limited typing ability it could be used in an initial screening to discriminate between isolates of different origin and to analyse the genomic structure of each isolate. Sequence analysis showed that the isolates of Spanish origin were closely related to mild isolates characterised in Florida and in Portugal. The Meyer lemon isolate on the other hand was related to severe strains of Meyer lemon characterised in Florida some years ago and to other severe strains from Brasil. A knowledge of the coat protein gene sequence is useful to trace the origin of the isolates.

Beet necrotic yellow vein benyvirus

Beet necrotic yellow vein benyvirus

IDENTIFICATION AND PARTIAL CHARACTERIZATION OF PRUNUS NECROTIC RINGSPOT VIRUS ON STONE FRUITS IN JORDAN

Prunus necrotic ringspot virus (PNRSV, Genus Ilarvirus, Family Bromoviridae) was isolated from stone fruit trees showing virus-like symptoms grown in Jordan. Identification of this virus was based on host range, properties in crude sap, transmissibility, and serological tests. PNRSV-J has a limited range of experimental hosts. The dilution end-point of infectivity was 10-2, the thermal inactivation point was 57°C, and purified virus had an in vitro longevity of 16 h at 25°C. PNRSV-J was detected by double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA). PNRSV-J was purified from cucumber leaves harvested 6-8 days after inoculation. The modified purification method gave an adequate virus yield for antibody production. Antiserum produced by immunizing a rabbit had a titer of 1024 in direct antigen coating (DAC)-ELISA, with high specificity to PNRSV. An immunocapture-reverse transcription- polymerase chain reaction (IC-RT-PCR) protocol was useful for the detection of PNRSV in herbaceous and woody plant tissues. Nucleotide sequence and phylogenetic analysis of RT-PCR products derived from RNA3 of PNRSV-J confirmed its identity as an isolate of PNRSV and revealed that it is a member of Group I (PV32) isolates.

Immunomagnetic capture rt-PCR for detection of norovirus from foods implicated in a foodborne outbreak.

In February 2001, an outbreak of acute gastroenteritis due to Norovirus (NV) occurred among employees of 11 companies in Aichi Prefecture. The illness was strongly associated with eating a delivered box-lunch. The use of magnetic beads coated with the antibody to the baculovirus-expressed recombinant capsid proteins of the Chiba virus (rCV) facilitated capture of NV from the food items implicated in the outbreak. Following immunomagnetic capture, NV bound to the beads was detected by reverse transcriptionpolymerase chain reaction (RT-PCR). Of the nine food items tested, two were positive for a genogroup 1 NV. Sequence analysis of RT-PCR products indicated that the nucleotide sequences of NV strains from foods were almost identical to those of NV strains detected in stool samples of ill patients. As the immunocapture RTPCR method is simple and easy to perform, this technique should be useful for the detection of NV from outbreak-implicated foods.

Comparison of Detection Methods for a Novel Tobamovirus Isolated from Florida Hibiscus.

A novel tobamovirus recently was isolated from hibiscus in Florida. Serological and molecular methods, including enzyme-linked immunosorbent assay (ELISA), dot-blot immunoassay (DBIA), tissue-blot immunoassay (TBIA), and immunocapture reverse-transcription poly-merase chain reaction (IC-RT-PCR) were compared to evaluate their usefulness for diagnosis of this virus. Each method was tested with partially purified virus preparations and tissue samples from infected hibiscus and Chenopodium quinoa plants. Indirect ELISA was more sensitive than double-antibody sandwich (DAS)-ELISA with all samples tested. The Florida hibiscus virus was detectable in hibiscus leaves and bark up to 1:12,800 and 1:6,400 dilutions, respectively, by indirect ELISA and up to 1:3,200 and 1:400 dilutions by DAS-ELISA. End-point dilutions of partially purified virus preparations from indirect and DAS-ELISA were 4 and 31 ng/ml, respectively. Florida hibiscus virus was detected by DBIA in sap from hibiscus bark and leaves at dilutions up to 1:400 and 1:800, respectively, showing that DBIA was less sensitive than either ELISA method. The virus also was detected reliably by TBIA from leaves and bark of hibiscus plants. The most sensitive method was IC-RT-PCR, which could detect as little as 500 pg/ml of virus in partially purified preparations and was 16- and 32-fold more sensitive than DAS-ELISA with hibiscus bark and leaf extracts, respectively. Over 600 hibiscus samples were tested by various combinations of these methods to validate their usefulness.

Natural Spread of Plum Pox Virus in Ankara, Turkey

AbstractPlum pox virus (PPV) has a limited distribution in Turkey, so is not a serious problem for stone fruit production. However, it is widespread in apricot, plum and peach trees in the Ankara region where its natural spread was studied between 1995 and 2002 in 10 home gardens planted with apricot, plum and peach trees. The presence of the virus was determined by visual observation of symptoms in leaves and fruits and by double antibody sandwich enzyme‐linked immunosorbent assay (DAS‐ELISA); strains were identified by double antibody sandwich indirect enzyme‐linked immunosorbent assay (DASI‐ELISA) and immunocapture reverse transcription‐polymerase chain reaction (IC‐RT‐PCR) tests. Within 8 years, PPV incidence in the gardens near to, and 0.5 km from an infection source was 85.7–100 and 25–29.4%, respectively. This difference in incidence was attributed to the distance from the infection source. All PPV isolates were identified as PPV‐M. It was found that sharka disease was introduced to the healthy gardens by mealy plum aphids (Hyalopterus pruni), the only vector of PPV found in Ankara. This is the first report of PPV spread in Turkey.

First Report of Raspberry bushy dwarf virus on Red Raspberry and Grapevine in Slovenia.

In 2002, severe vein yellowing and partial or complete yellowing of leaves was observed on some shoots of red raspberry (Rubus idaeus) cvs. Golden Bliss and Autumn Bliss. Sap of infected plants of cv. Golden Bliss was inoculated onto Chenopodium quinoa and Nicotiana benthamiana. Faint chlorotic spots were observed on inoculated leaves of C. quinoa approximately 14 days after inoculation but no systemic symptoms appeared. No symptoms were observed on N. benthamiana. Raspberry bushy dwarf virus (RBDV) was detected in the original raspberry plant using double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) with polyclonal antiserum (Loewe Biochemica, Sauerlach, Germany). Systemic infections of inoculated C. quinoa and N. benthaminana were confirmed using DAS-ELISA. In 2001 and 2002, unusual virus symptoms were observed on grapevine grafts (Vitis vinifera) of cv. Laški Rizling. Symptoms appeared as curved line patterns and yellowing of the leaves. No nepoviruses were found in symptomatic plants, but RBDV was confirmed using DAS-ELISA. RBDV infection was later confirmed in grapevine cv. Štajerska Belina with similar symptoms. RBDV was transmitted mechanically from grapevine to C. quinoa where it was detected by immunocapture-reverse transcription-polymerase chain reaction (IC-RT-PCR). IC-RT-PCR was used to amplify a part of the coat protein gene of the virus from raspberry and grapevine, and the amplification products were sequenced (1). The obtained sequence shared at least 93% nucleotide sequence identity with other known RBDV sequences, which confirmed the serological results. To our knowledge, this is the first report of the natural occurrence of RBDV in grapevine and also of RBDV infection of red raspberry in Slovenia. Reference: (1) H. I. Kokko et al. Biotechniques 20:842, 1996.

First Report of Banana mild mosaic virus Isolated from Plantains (Musa AAB) in Colombia

Plantains (Musa AAB) are important sources of food and income for millions of people in Colombia and other developing countries. Colombia is the largest producer of plantains (2) and the third largest exporter of bananas in the world. In 2001, plants of 'Dominico-Hartón' plantain showing mild chlorotic streak symptoms were observed in northwestern Colombia. Electron microscopy of symptomatic tissue extracts revealed the presence of filamentous virus-like particles approximately 800 nm long. Immunocapture reverse-transcription polymerase chain reaction was performed to test for the presence of Banana mild mosaic virus (BanMMV) as described by J. E. Thomas (unpublished, Queensland Department of Primary Industries, Australia) and Sharman et al. (3). For polymerase chain reaction (PCR), the upstream primer No. 193 (5'-CAC TTA GGT TTG TGT GAT GT-3') (designed in this study by using the computer Program DNAMAN Version 4.13) and the downstream primer Poty1 (5'-GGA TCC CGG GTT TTT TTT TTT TTT TTT V-3') (1,3; J. E. Thomas, unpublished, Queensland Department of Primary Industries, Australia) were used. Amplification products of the expected size (approximately 900 bp) were obtained and sequenced after cloning in a pCR2.1 plasmid vector. Analyses of nucleic acid sequences using the international sequence databases and the BLAST program yielded nucleotide and amino acid sequence similarities of 80 to 83% and 90 to 92%, respectively, with an Australian isolate of BanMMV (GenBank Accession No. AF314662). The coat protein (CP) gene of the Colombian BanMMV isolate consists of 717 nucleotides. When the CP of the Colombian BanMMV isolates (GenBank Accession Nos. AY319331, AY319332, and AY319333) was compared with the CP of the Australian isolate, a highly variable region was observed in the N-terminus region. To our knowledge, this is the first report of BanMMV isolated from plantains in Colombia and the presence of molecular variability in the CP of BanMMV isolates. BanMMV has been found in Colombia associated with Banana streak virus and Cucumber mosaic virus in plantain.

First Report of Potato mop-top virus on Potato from the United States.

Potato mop-top virus (PMTV) is a tripartite pomovirus vectored by the powdery scab plasmodiophoromycete Spongospora subterranea pv. subterranea (1). PMTV occurs on potato (Solanum tuberosum) in Europe, the Andes, Asia, and Canada. Internal necrotic arc and fleck tuber symptoms ("spraing") may reduce commercial acceptance of some cultivars (3). PMTV symptoms were discovered in 'Shepody' tubers at the Aroostook Research Farm, Presque Isle, ME in May 2002 and subsequently in 'Russet Burbank' tubers in commercial storage from the 2001 Maine crop. Symptomatic tubers exhibited single or multiple concentric necrotic arcs that were partial or complete, but exhibited no distinct external symptoms. The presence of PMTV in eight 'Shepody' tubers was indicated by positive enzyme-linked immunosorbent assay (ELISA; Adgen, Ltd., Auchincruive, Ayr, Scotland) and confirmed by reverse transcription polymerase chain reaction (RT-PCR). 'Russet Burbank' potatoes were visually diagnosed, and the corresponding halves of 128 symptomatic tubers were forwarded to the University of Maine and APHIS (Beltsville, MD). Of these, ELISA readings in Maine were strongly positive (>3 × background) for 88, ambiguous (1.5-3 × background) for 13, and negative for 27. Subsamples from these three categories were positive by PCR in 17 of 17, 9 of 9, and 12 of 14 cases, respectively. A similar rating, positive or ambiguous, in ELISA testing was identical for all but one case at Beltsville. Confirmation of PMTV required PCR testing, resulting in a characteristic PCR product of 401 bp that was generated from the coat protein coding region on RNA 2 (2) using the primer pair PMTV 1 5'-GCAGCCGTCGAGAATAGATA-3' (RNA nucleotides 316-335) and PMTV 4 5'-GCGAGTTGATGTGCC ACATT-3' (complementary to RNA 2 nucleotides 716-697). An immunocapture RT-PCR using this primer set and the coating antibody from the Adgen ELISA kit was also successful in detecting PMTV. In separate reactions, a second product of 646 bp was generated from the triple gene block on RNA 3 (4) using the primer pair PMTV 5 5'-GGTGAACACGAGGACAAGGT-3' (RNA 3 nucleotides 1417-1436) and PMTV 7 5'-AACAGTCCGGTCTTGTGAAC-3' (complementary to RNA 3 nucleotides 2063-2044). The sequence of these products was 98 to 100% identical to PMTV published sequences. The discovery of this virus will result in adjustments to U.S. and Canadian seed potato certification standards and symptom characterization for common North American cultivars.

Development of recombinant coat protein antibody based IC-RT-PCR for detection and discrimination of sugarcane streak mosaic virus isolates from Southern India.

Sugarcane streak mosaic virus (SCSMV), causes mosaic disease of sugarcane and is thought to belong to a new undescribed genus in the family Potyviridae. The coat protein (CP) gene from the Andhra Pradesh (AP) isolate of SCSMV (SCSMV-AP) was cloned and expressed in Escherichia coli. The recombinant coat protein was used to raise high quality antiserum. The CP antiserum was used to develop an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) based assay for the detection and discrimination of SCSMV isolates in South India. The sequence of the cloned PCR products encoding 3'untranslated region (UTR) and CP regions of the virus isolates from three different locations in South India viz. Tanuku (Coastal Andhra Pradesh), Coimbatore (Tamil Nadu) and Hospet (Karnataka) was compared with that of SCSMV-AP. The analysis showed that they share 89.4, 89.5 and 90% identity respectively at the nucleotide level. This suggests that the isolates causing mosaic disease of sugarcane in South India are indeed strains of SCSMV. In addition, the sensitivity of the IC-RT-PCR was compared with direct antigen coating-enzyme linked immunosorbent assay (DAC-ELISA) and dot-blot immunobinding assays and was found to be more sensitive and hence could be used to detect the presence of virus in sugarcane breeding, germplasm centres and in quarantine programs.

Incidence of Viruses and Virus like Diseases of Sweetpotato in Uganda.

Sweetpotato plants were surveyed for viruslike diseases and viruses in the four major agroecological zones of Uganda. Testing of 1,260 sweetpotato plants, of which 634 had virus-like symptoms, showed that virus disease incidence ranged from 2.7% (Soroti district, short grassland-savannah zone) to 20% (Mukono district, tall grass-forest mosaic zone). Sweet potato chlorotic stunt virus (SPCSV), Sweet potato feathery mottle virus (SPFMV), Sweet potato mild mottle virus (SPMMV), and sweet potato chlorotic fleck virus (SPCFV) were serologically detected and positive results confirmed by immunocapture reverse transcriptase polymerase chain reaction (IC-RT-PCR) and subsequent sequence analyses of the amplified fragments, except SPCFV, which lacked sequence information. SPCSV and SPFMV were detected in all the 14 districts surveyed, whereas SPMMV and SPCFV were detected in 13 and 8 districts, respectively. Logistic regression analysis revealed that SPCSV and SPFMV, SPFMV and SPMMV, and SPFMV and SPCFV more frequently occurred together than any other virus combinations or as single virus infections. Co-infections of SPCSV with SPFMV and/or SPMMV were associated with more severe and persistent symptoms than infections with each of the viruses alone. Several plants (11%) displaying viruslike symptoms did not react with the virus antisera used, suggesting that more viruses or viruslike agents are infecting sweetpotatoes in Uganda.

Biological and molecular characterization of various isolates of Potato virus Y-N (PVY-N) strain group

Fourteen Potato virus Y (PVY) isolates were characterized. They represented PVYN strain only. However, application of serological and molecular genetic methods led to a more complicated characterization. For example, five isolates induced necrotic symptoms on tobacco plants typical of PVY&lt;sup&gt;N&lt;/sup&gt;, despite reacting as PVY&lt;sup&gt;O&lt;/sup&gt; serologically. Moreover, the PVY isolates were not identical according to molecular genetic properties. Typical PVY&lt;sup&gt;NTN&lt;/sup&gt; PCR products were observed for 11 isolates, but four of them (Hr220-5, Hr387-7, Nord 242 and Syn1Scot) did not produce potato tuber necrotic symptoms in infected cultivars. An immunocapture RT-PCR probing was developed using a set of 24 primer pairs derived from eight regions of the PVY genome. Using this method, five out of seven PVY&lt;sup&gt;NTN&lt;/sup&gt; isolates including the Czech standard PVY&lt;sup&gt;NTN&lt;/sup&gt; from the potato cv. Nicola were found to be identical. However, two PVY&lt;sup&gt;NTN&lt;/sup&gt; isolates and all the other probed PVY samples showed unique patterns, suggesting specific differences at the nucleotide level. This method enabled specific identification of individual isolates variability even within different PVY strains.

Improved PCR Detection of Blackcurrant reversion virus in Ribes and Further Evidence that It Is the Causal Agent of Reversion Disease

Within 5 years of mechanically inoculating blackcurrant cultivars with partially purified preparations of particles of Blackcurrant reversion virus (BRV), infected plants developed leaf and flower bud symptoms typical of reversion disease, demonstrating that BRV is the causal agent of this disease. To improve the erratic immunocapture reverse transcriptase-polymerase chain reaction (RT-PCR) detection of BRV in Ribes plants, various stepwise changes were made to the original protocol. Significant improvement in the reliability and sensitivity of BRV detection was made by extracting RNA from trapped BRV particles using Triton-X 100, the design of new primers with higher annealing temperatures, and the use of 'Ready-to-go' RT-PCR beads. These features, combined with other minor changes to the protocol, improved BRV detection in reverted blackcurrant plants from <50% to >90% but the reliability of BRV detection in red currant was always very much less and was possible only using nested PCR that was developed for this purpose.

Analysis of complement-bound HCV complexes using a novel immuno-capture RT-PCR method.

Recently, more and more evidence has supported the hypothesis that liver cell injury was immune-mediated in patients with hepatitis C virus (HCV) infection, and that circulating immune complexes (CICs) might play a role in the pathogenesis of chronic hepatitis C (HC). In the present study, we have combined immuno-capture and reverse transcriptase-polymerase chain reaction (RT-PCR), and developed a quick method of high specificity for the detection of complement-bound HCV-CIC. We found that there were higher frequencies of HCV-C1q CIC than that of HCV-factor B, and there was a deviation of complement from immunoglobulin (Ig) in HCV-CIC. These findings suggest that immuno-capture RT-PCR (iRT-PCR) for the detection of HCV-bound CIC is a valuable method for the analysis of the composition of the immune complexes, and for the understanding of host immune response and immune pathogenesis in HCV-infected individuals.

Characterization and detection ofCucumber green mottle mosaic virus in Greece

The host range specificity of Greek isolates ofCucumber green mottle mosaic virus (CGMMV) was determined and the ability of the virus to retain its infectivity in naturally contaminated soil, after storage at 4°C for at least 10 months, was established. An immunocapture RT-PCR protocol was developed for the detection of the virus and proved to be 105 times more sensitive than DAS-ELISA and 102 times more sensitive than F(ab’)2-ELISA using F(ab’)2 fragments that were prepared from an antiserum, which was raised against a local virus isolate. In order to clarify dissimilarities that were revelaed between the coat protein (CP) genes of the Greek isolates after restriction mapping of their respective PCR products, the CP genes of three isolates were sequenced and found to be very similar but not identical to the CP gene of CGMMV-SH.

Expression of Cardamom mosaic virus coat protein in Escherichia coli and its assembly into filamentous aggregates

Cardamom mosaic virus (CdMV), a member of the genus Macluravirus of Potyviridae, causes a mosaic disease in cardamom. A polyclonal antiserum was raised against the purified virus and IgG was prepared. Electron microscopic studies on the purified virus showed flexuous filamentous particles of ∼800 nm in length, typical of members of Potyviridae. The coat protein (CP) encoding sequence of the virus was expressed in Escherichia coli and the protein purified by affinity chromatography under denaturing conditions. The viral nature of the expressed CP was confirmed by positive reaction with anti CdMV IgG in a Western blot. The expressed CP aggregated irreversibly upon renaturation at concentrations above 0.07 mg/ml. The expression of the CP led to the formation of filamentous aggregates in E. coli as observed by immuno-gold electron microscopy. The filamentous aggregates were of 100–150 nm in length. Immuno-capture RT-PCR confirmed the absence of coat protein mRNA in the filamentous aggregates. Deletion mutations, which were expected to inhibit virus assembly, were introduced in the core region of the coat protein. However, these mutations did not improve the solubility of the CP in non-denaturing buffers.

33. Detection and serotyping of foot-and-mouth disease virus by immunocapture RT-PCR

33. Detection and serotyping of foot-and-mouth disease virus by immunocapture RT-PCR

First Report of Tomato spotted wilt virus and Impatiens necrotic spot virus in Slovenia.

In July 2000, concentric necrotic rings and patterns were observed on greenhouse-grown pepper (Capsicum anuum L. 'Blondi'). Symptoms were present only on lower leaves, not on young leaves or fruits. Typical tospovirus particles using electron microscopy were observed in leaf-dip preparations of symptomatic leaves. Impatiens necrotic spot virus (INSV) was detected in symptomatic but not in asymptomatic tissues using double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) with polyclonal antiserum (Loewe Biochemica, Sauerlach, Germany). Nicotiana benthamiana, N. rustica, and Petunia sp. were mechanically inoculated with sap of symptomatic leaves. Local and systemic symptoms were observed only on N. benthamiana. Tomato spotted wilt virus (TSWV) infections were later confirmed in some pepper and tomato plants with distinct systemic symptoms and in greenhouse-grown chrysanthemums, calla lilies, cyclamen and spatiphylum using DAS-ELISA with polyclonal antiserum. Severe systemic symptoms were observed only on some chrysanthemum cultivars, where the infection rate of TSWV was between 80 and 100%. Such TSWV-infected plants were not marketable. Symptomless infections by the same virus were also found. At one location, calla lilies were heavily infected by TSWV, but only local symptoms on leaves were observed. INSV was also confirmed using DAS-ELISA on different chrysanthemum cultivars. Mixed infections of TSWV and INSV were detected using DAS-ELISA on calla lilies with local necrotic rings and patterns on leaves and on Impatiens walerana with systemic necrosis. A limited number of weeds from the vicinity of greenhouses containing symptomatic plants were tested for the presence of TSWV using DAS-ELISA, and only Artemisia vulgaris was infected. Both viruses, TSWV from chrysanthemum and INSV from pepper, were isolated on test plants, and their identity was confirmed using DAS-ELISA. For further verification of TSWV and INSV infection, immunocapture reverse-transcription polymerase chain reaction was performed using general tospovirus primers (1). Amplification products of the expected size were detected and sequenced. Comparison of nucleic acid sequences of amplification products with viral sequence databases confirmed the identities of both viruses. To our knowledge, this is the first report of TSWV and INSV infection in ornamental and vegetable plants in Slovenia. Reference: (1) R. J. Weekes et al. Acta Hortic. 431:159, 1996.