A primer pair for amplifying part of the genome of all potyvirids by RT-PCR

A one-step reverse transcription-polymerase chain reaction system for the simultaneous detection and identification of multiple tospovirus infections

ABSTRACT A one-step reverse transcription-polymerase chain reaction (RT-PCR) method has been developed for the simultaneous detection and identification of multiple tospoviruses that infect plants. The RT-PCR system is composed of six primers in a single tube: a universal degenerate primer and five virus species-specific primers. Amplifications resulted in an 848-bp PCR product for Watermelon silver mottle virus, 709-bp for Tomato spotted wilt virus, 589-bp for Impatiens necrotic spot virus, 511-bp for Melon yellow spot virus, and a 459-bp amplicon for Iris yellow spot virus. This system enables the simultaneous detection of at least three types of tospovirus infections, in addition to their species identities, from five possible tospoviruses studied, on the basis of their S RNA combinations. This multiplex RT-PCR system was applied to the detection of tospovirus in ornamental crops cultivated in fields and shows potential for epidemiological studies.

Development of a Molecular Tool for the Diagnosis of Leprosis, a Major Threat to Citrus Production in the Americas

Citrus leprosis virus (CiLV), a tentative member of the Rhabdoviridae family, affects citrus trees in Brazil, where it is transmitted by mites Brevipalpus spp. It also occurs in other South American countries and was recently identified in Central America. This northbound spread of CiLV is being considered a serious threat to the citrus industry of the United States. However, despite its importance, difficulties related to the biology of CiLV have hindered much of the progress regarding its accurate detection, leaving both the analyses of symptoms and electron microscopy as the only tools available. An attempt to overcome this problem was made by constructing a cDNA library from double-stranded RNA extracted from leprosis lesions of infected Citrus sinensis (sweet orange) leaves. After cloning and sequencing, specific primers were designed to amplify putative CiLV genome regions with similarity to genes encoding the movement protein and replicase of other plant viruses. RNA from infected citrus plants corresponding to different varieties and locations were amplified by reverse transcription-polymerase chain reaction (RT-PCR) using the two pairs of primers. Amplified products were purified, cloned in pGEM-T, and sequenced. The sequences confirmed the genomic regions previously associated with CiLV. The results demonstrate that RT-PCR was specific, accurate, rapid, and reliable for the detection of CiLV.

Properties of Strains of Sweet potato feathery mottle virus and Two Newly Recognized Potyviruses Infecting Sweet Potato in the United States

Some biological and molecular properties of six potyvirus isolates (LSU-1, -2, -3, and -5; 95-2; and 95-6) from sweet potato (Ipomoea batatas) were evaluated. Isolates LSU-1 and -3 and 95-2 were transmitted by Aphis gossypii and Myzus persicae while LSU-2 and -5 were not transmitted by either aphid. The partial nucleotide sequence of the nuclear inclusion b (NIb) and the coat protein (CP) genes of these six isolates were compared with the corresponding sequences of 17 Sweet potato feathery mottle virus (SPFMV) strains and 18 other potyviruses. LSU-1 and -3 had high sequence similarity to the published sequences for Sweet potato virus G (SPVG), did not react with antisera to other known sweet potato viruses, and caused distinct symptoms. We propose to designate these two isolates as SPVG. This report documents the occurrence of this virus in the United States and provides the first characterization of its biological properties. LSU-2 and -5 were distinct in symptomatology; partial Nib, CP nucleotide, and derived amino acid sequence; and serology to other viruses. We propose to call this virus (LSU isolates 2 and 5) Ipomoea vein mosaic virus. The present study revealed a high degree of sequence similarity between 95-6 and the common strain of SPFMV, and between 95-2 and the russet crack strain of SPFMV. Results from this study suggest not only that at least two strains of SPFMV occur in the United States, but that two other potyviruses also are present.

High genetic diversity in the coat protein and 3′ untranslated regions among geographical isolates ofCardamom mosaic virus from south India

A survey was conducted to study the biological and genetic diversity of Cardamom mosaic virus (CdMV) that causes the most widespread disease in the cardamom growing area in the Western Ghats of south India. Six distinct subgroups were derived based on their symptomatology and host range from the sixty isolates collected. The serological variability between the virus isolates was analysed by ELISA and Western blotting. The 3 terminal region consisting of the coat protein (CP) coding sequence and 3 untranslated region (3 UTR) was cloned and sequenced from seven isolates. Sequence comparisons revealed considerable genetic diversity among the isolates in their CP and 3 UTR, making CdMV one of the highly variable members of Potyviridae. The possible occurrence of recombination between the isolates and the movement of the virus in the cardamom tract of south India are discussed.

Coat protein sequence analysis reveals occurrence of new strains of Sweet potato feathery mottle virus in Uganda and Tanzania

The 3'-proximal part (1.8 kb) of the Sweet potato feathery mottle virus (SPFMV) genome was studied in four SPFMV isolates collected from farmers' fields in western Uganda (SPFMV-Bny), eastern Uganda (SPFMV-Sor) and Bagamoyo district, Tanzania (SPFMV-TZ1 and SPFMV-TZ2). Unlike the other three SPFMV isolates, SPFMV-Sor was not detected with the polyclonal antisera to SPFMV. It showed moderately high coat protein (CP) nucleotide (93.3-96.7%) and amino acid (93.6-96.8%) sequence identity to the isolates of the SPFMV strain group C. In contrast, identities (78.1-80.1%, and 79.9-83.1%) to isolates of the SPFMV strain groups O, RC, and the East African (EA) strain group were low. Similar to some isolates (SPFMV-CH2 and SPFMV-6) of strain group C, but different from other SPFMV isolates, SPFMV-Sor contained a deletion of 6 nucleotides in the CP-encoding region (CP amino acid positions 62-63). Phylogenetic analysis of the CP sequences indicated that SPFMV-Sor belongs to the SPFMV strain group C that has not been reported from Africa. Sequence data were obtained for the first time from Tanzanian SPFMV isolates in this study, and phylogenetic analysis indicated that they belong to the strain group EA, which is unique to East Africa.

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.

Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues

Awareness of crop biosecurity and phytosanitation has been heightened since 9/11 and the unresolved anthrax releases in October 2001. Crops are highly vulnerable to accidental or deliberate introductions of crop pathogens from outside U.S. borders. Strategic thinking about protection against deliberate or accidental release of a plant pathogen is an urgent priority. Rapid detection will be the key to success. This review summarizes recent progress in the development of rapid real-time PCR protocols and evaluates their effectiveness in a proposed nationwide network of diagnostic laboratories that will facilitate rapid diagnostics and improved communication.

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 approximately 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.

3'-Terminal sequence analysis of the RNA genome of the Indian isolate of cardamom mosaic virus: a new member of genus Macluravirus of potyviridae

Cardamom mosaic virus, a possible member of the family Potyviridae has been associated with the mosaic disease (Katte disease) of small cardamom in India. A virus isolated from the symptomatic cardamom leaves was positive in ELISA only with antiserum to the Guatemalan isolate of cardamom mosaic virus and not with a number of other potyviruses. The size of the viral RNA (8.5 kb) and the molecular weight of the coat protein (CP) (38 kDa) were determined. A 1.8-kb product containing the partial nuclear inclusion body (NIb) gene, the entire coat protein gene and the 3' untranslated region (UTR) was amplified by reverse transcription (RT) and polymerase chain reaction (PCR), cloned and sequenced. The viral origin of the clone was confirmed by Northern hybridization with viral RNA. The experimentally determined N-terminal sequence of the CP matched with the deduced amino acid sequence of the CP gene. Sequence analysis of the clone suggests that the cardamom mosaic virus is a member of the Maclurvirus genus of the family Potyviridae.

Biological and Molecular Characterization of Moroccan watermelon mosaic virus and a Potyvirus Isolate from Eastern Sudan

A potyvirus (Su-94-54) was isolated from a naturally infected snake cucumber (Cucumis melo var. flexuosus) plant with severe mosaic and leaf deformation symptoms collected in Eastern Sudan. This isolate has a host range limited to cucurbits and is serologically distantly related to Moroccan watermelon mosaic virus (MWMV) and to Papaya ringspot virus (PRSV). Coat protein sequence analysis of Su-94-54 and MWMV and comparison with other potyviruses indicate that Su-94-54 is more closely related to MWMV than to any other potyvirus. Based on the amino acid sequence identity in the core part of the coat protein with MWMV (86%), this isolate could be regarded as a distinct species. However, because of biological, cytological, and serological affinities with MWMV, we propose that this isolate be considered as a strain of MWMV, possibly an evolutionary intermediate between MWMV and PRSV, until more is known on the structure of the PRSV subgroup within the genus Potyvirus.

Development of a multiplex immunocapture PCR with colourimetric detection for viruses of banana

A multiplex, immunocapture PCR (M-IC-PCR) was developed for the simultaneous detection of three viruses from crude sap extracts of banana and plantain (Musa spp.). A reverse transcription step was required for Banana bract mosaic virus and Cucumber mosaic virus, which have ssRNA genomes. The detection of Banana bunchy top virus (ssDNA genome) was not adversely affected by inclusion in this step. All the three viruses could be detected simultaneously from a mixed infection. Identification and detection of individual viruses was achieved through the visualisation of discretely sized PCR amplicons by gel electrophoresis. Alternatively, a colourimetric microplate detection system utilising digoxigenin-labelled virus-specific probes was used. The latter assay was up to five times more sensitive than detection by gel electrophoresis and between 25 and 625 times more sensitive than ELISA for the various viruses. Careful selection of PCR primers was necessary to ensure the detection of a wide range of virus isolates and to avoid detrimental interactions between heterologous templates and primers.

Cytological and molecular evidence that the whitefly-transmitted cucumber vein yellowing virus is a tentative member of the family Potyviridae

Cucumber vein yellowing virus (CVYV) is widespread in cucurbits in the Middle East. CVYV has filamentous particles and is transmitted by Bemisia tabaci by the semi-persistent mode. It has not yet been assigned to a specific genus or family. Ultramicroscopic observations revealed numerous cylindrical cytoplasmic inclusions in melon and cucumber cells infected by CVYV isolates from Israel and Jordan. Depending on the section orientation, the inclusions appeared as pinwheels or as bundles. In addition, a 1.9 kb DNA fragment was amplified by RT-PCR from CVYV-infected plant extracts using primers designed to detect all potyvirids. Sequence comparisons with the amplified fragment indicated that CVYV is more closely related to Sweet potato mild mottle virus than to any other virus in the family Potyviridae: These results suggest that CVYV can be considered as a tentative new member of the genus Ipomovirus:, family Potyviridae:

Impacts of Molecular Diagnostic Technologies on Plant Disease Management

Detection and diagnosis of plant viruses has included serological laboratory tests since the 1960s. Relatively little work was done on serological detection of plant pathogenic bacteria and fungi prior to the development of ELISA and monoclonal antibody technologies. Most applications for laboratory-based tests were directed at virus detection with relatively little emphasis on fungal and bacterial pathogens, though there was some good work done with other groups of plant pathogens. With the advent of molecular biology and the ability to compare regions of genomic DNA representing conserved sequences, the development of laboratory tests increased at an amazing rate for all groups of plant pathogens. Comparison of ITS regions of bacteria, fungi, and nematodes has proven useful for taxonomic purposes. Sequencing of conserved genes has been used to develop PCR-based detection with varying levels of specificity for viruses, fungi, and bacteria. Combinations of ELISA and PCR technologies are used to improve sensitivity of detection and to avoid problems with inhibitors or PCR often found in plants. The application of these technologies in plant pathology has greatly improved our ability to detect plant pathogens and is increasing our understanding of, their ecology and epidemiology.

Simultaneous quantitation of two orchid viruses by the TaqMan real-time RT-PCR

Simultaneous quantitation of two orchid viruses, cymbidium mosaic potexvirus (CymMV) and odontoglossum ringspot tobamovirus (ORSV), were carried out using the TaqMan((R)) real-time RT-PCR, a novel detection technique that combines RT-PCR with the power of fluorescent detection. Four TaqMan((R)) probes were synthesized, targeting at the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes of both viruses. The reporter dye FAM (6-carboxyfluorescein) was used to label the 5' terminus of probes specific to CymMV, while TET (tetrachloro-6-carboxyfluorescein) was used for the ORSV probes. TAMRA (6-carboxy-tetramethyl-rhodamine), which was attached at the 3' terminus of each probe, was used as the universal quencher. With increasing amounts of standard RNA templates, the respective threshold cycle (C(T)) values were determined and a linear relationship was established between these C(T) values and the logarithm of initial template amounts. The amounts of starting templates in mixed-infected Oncidium flowers and leaves were estimated from the standard curves. As little as 10(4) copies or 5 fg each of CymMV and ORSV could be detected simultaneously with either the RdRp or CP gene as the target. This system offers a sensitive, high throughput and rapid method for plant virus detection.

Detection of multiple potato viruses using an oligo(dT) as a common cDNA primer in multiplex RT-PCR

A novel usage of multiplex reverse transcription polymerase chain reaction (m-RT-PCR) for simultaneous detection of multiple viruses is reported. By use of an oligo(dT), as a common primer, nearly full-length cDNAs can be synthesized. Furthermore, combining an oligo(dT) primer with a specific antisense primer can be used to simultaneously prime reverse transcription of both polyadenylated and non-polyadenylated RNAs. Four viral genera including five potato viruses [(carlavirus (PVS), polerovirus (PLRV), potexvirus (PVX), potyvirus (PVA and PVY))] and a viroid genus including a viroid genome (pospiviroid (PSTVd)) were used to develop various formats of m-RT-PCR. In artificially created viral RNA mixtures, all six RNA pathogens were detected successfully by uniplex- and m-RT-PCR. In naturally infected field grown tubers, m-RT-PCR detected infection of two to three viruses, which were present in the tubers.

RT-PCR detection and identification of three species of cucumoviruses with a genus-specific single pair of primers

Reverse transcription and polymerase chain reaction (RT-PCR) was used for detection and identification of three cucumoviruses (cucumber mosaic virus, CMV; peanut stunt virus, PSV; tomato aspermy virus, TAV) in various plants sources with a single pair of primers, designed as CPTALL-3 and CPTALL-5. The pair of cucumovirus genus-specific primers that flank the coat protein gene were designed and used to amplify a DNA fragment of approximately ranging from 938 to 966 bp. The RT-PCR with the set of primers specifically amplified the target size of DNA fragment in all the tested cucumoviruses (CMV S-IA, S-IB and S-II, PSV and TAV). No DNA product of any length was produced when brome mosaic virus or tobacco mosaic virus RNA was used as templates. The cucumoviruses examined were differentiated by PCR-restriction fragment length polymorphism with different enzymes. This indicates that the designed primers are only specific for the cucumoviruses and useful for reliable information of identification of members of the Cucumovirus genus.

Reverse-transcription polymerase chain reaction for the detection of viruses from plants and aphids

A reverse transcription polymerase chain reaction (RT-PCR) protocol used for the detection of potato viruses in dormant tubers and leaves and in an aphid vector is described. Problems in plant sample preparation from different hosts, uneven distribution or low concentration of viruses and the presence of PCR inhibitors in plant extracts are discussed and various ways to eliminate their effect are described. Using Potyviridae viruses, it has been shown that RT-PCR in various modified forms can be used to differentiate viruses at the level of family, genus, species, strains and their subtypes or serotypes. The specificity of primer pairs and PCR modifications has been used to separate closely related potato viruses A and PVY strains (PVY(O), PVY(N) and PVY(NTN)) from a known mixture.

The GPRIME package: computer programs for identifying the best regions of aligned genes to target in nucleic acid hybridisation-based diagnostic tests, and their use with plant viruses

The GPRIME (Group PRIMEr design) programs examine aligned sets of gene sequences to discover homologous regions to be targeted in diagnostic tests. The core program moves a 'window' over the aligned sequences and calculates, at each window position, a 'redundancy value', namely the number of sequences that would represent all permutations of the variable sequence positions within that window. Regions with minimal redundancy values may then be targeted in diagnostic tests based on oligonucleotide hybridisation. The likely specificity of tests targeting such regions can be assessed by searching the international databases with those regions using FASTA. The GPRIME programs, which include programs for designing primers to distinguish between two sub-sets of a group of aligned sequences, can be obtained from http://life.anu.edu.au/software.html. We have used GPRIME to design redundant primers for RT-PCR tests to detect all potexviruses and tobamoviruses, and then used these, together with a previously reported pair of primers for the Potyviridae, to screen some Australian orchid collections. Two orchid viruses previously reported from Australia were found; cymbidium mosaic potexvirus was common, but odontoglossum ringspot tobamovirus was not. In addition the recently described ceratobium mosaic potyvirus was found to be common, and three other novel potyviruses were also found.

Simultaneous TD/RT-PCR detection of cymbidium mosaic potexvirus and odontoglossum ringspot tobamovirus with a single pair of primers

Cymbidium mosaic potexvirus (CymMV) and odontoglossum ringspot tobamovirus (ORSV) are the two most prevalent and economically important orchid viruses which have attained a world-wide distribution. We have designed one pair of common primers, which were able to detect, simultaneously, both viruses by a single polymerase chain reaction (PCR). Sequence alignment and primer analyses were employed in primer design. The effect of touch-down PCR, primer annealing temperature, number of thermal cycles, MgCl2 concentration and the degree of primer degeneracy, were investigated and applied to the optimisation of PCR conditions in the detection of both viruses in order to achieve equal amplification efficiencies. This is the first successful attempt at using a single pair of PCR primers to detect two viruses belonging to different taxonomic groups simultaneously.

Separation of Slovenian isolates of PVY(NTN) from the North American isolates of PVY(N) by a 3-primer PCR

The potato tuber ringspot necrosis isolate of potato virus Y (PVY(NTN)) is a recently recognized and highly aggressive isolate of the PVY(N) group of strains. In order to screen specifically sources of resistance to PVY(NTN) a method to separate PVY(NTN) from PVY(N) is needed. To achieve this, 61 isolates from 13 imported and locally developed potato cultivars in Slovenia were studied. On the basis of the reactions in indicator plants Nicotiana tabacum cv. Samsun and Solanum brachycarpum and with a PVY(N) specific monoclonal antibody (4E7), all Slovenian isolates (Sl-NTN) were identified as PVY(N). Using two primer pairs from the P1 gene of a Hungarian isolate of PVY(NTN) by a conventional single primer pair, reverse transcription polymerase chain reaction (RT-PCR) both PVY(NTN) and PVY(N) were amplified similarly. However, specific amplification of PVY(NTN) was achieved by a nested-PCR at an annealing temperature of 63 degrees C. A simplified form of the nested-PCR, termed 3-primer PCR was developed, which is applicable for large-scale testing of samples. Using the 3-primer PCR at annealing temperature of 63 degrees C, known mixtures of PVY(NTN) and PVY(N) were correctly separated. PVY(NTN) was detected in dormant tubers and leaves from all Sl-NTN isolates. The 3-primer PCR was specific to PVY(NTN) and did not react with nine isolates of PVY(N), 13 isolates of PVY(o), one isolate of PVY(C), six commonly occurring potato viruses and a viroid.

Specific Detection of Potato Virus A in Dormant Tubers by Reverse-Transcription Polymerase Chain Reaction

A reverse-transcription polymerase chain reaction (RT-PCR) protocol was developed for the detection of potato virus A (PVA) in dormant tubers. A 255-bp amplified product was produced using a primer pair from the P1 gene of the PVA genome. The 255-bp product was detected in nucleic acids from leaves, tubers, and purified virions and was specific to PVA as determined by Southern blot tests and detection by a PVA-specific probe. When presented with seven potato virus/strain nucleic acids and a viroid, singly and in mixed infections, the primer pair did not amplify any products. Its specificity to PVA was further demonstrated by RT-PCR detection of PVA from the known mixtures of PVA and potato virus Y samples. PVA was detected in foliage nucleic acids at a dilution of 1:1024-1:4096 and tuber nucleic acids at 1:256-1:1024. It was uniformly present in various parts of the potato tuber. PVA was detected in composite tuber samples containing a ratio of infected to healthy sap of 1:29 and was readily detected in tubers of several cultivars or breeding lines, in dormant as well as in sprouting tubers stored at 20-25°C for 4 months.