The detection of recombinant, tuber necrosing isolates of Potato virus Y (PVY(NTN)) using a three-primer PCR based in the coat protein gene

One-Enzyme RTX-PCR for the Detection of RNA Viruses from Multiple Virus Genera and Crop Plants

Reverse transcription PCR (RT-PCR) is a popular method for detecting RNA viruses in plants. RT-PCR is usually performed in a classical two-step procedure: in the first step, cDNA is synthesized by reverse transcriptase (RT), followed by PCR amplification by a thermostable polymerase in a separate tube in the second step. However, one-step kits containing multiple enzymes optimized for RT and PCR amplification in a single tube can also be used. Here, we describe an RT-PCR single-enzyme assay based on an RTX DNA polymerase that has both RT and polymerase activities. The expression plasmid pET_RTX_(exo-) was transferred to various E. coli genotypes that either compensated for codon bias (Rosetta-gami 2) or contained additional chaperones to promote solubility (BL21 (DE3) with plasmids pKJE8 or pTf2). The RTX enzyme was then purified and used for the RT-PCR assay. Several purified plant viruses (TMV, PVX, and PVY) were used to determine the efficiency of the assay compared to a commercial one-step RT-PCR kit. The RT-PCR assay with the RTX enzyme was validated for the detection of viruses from different genera using both total RNA and crude sap from infected plants. The detection endpoint of RTX-PCR for purified TMV was estimated to be approximately 0.01 pg of the whole virus per 25 µL reaction, corresponding to 6 virus particles/µL. Interestingly, the endpoint for detection of TMV from crude sap was also 0.01 pg per reaction in simulated crude plant extracts. The longest RNA fragment that could be amplified in a one-tube arrangement was 2379 bp long. The longest DNA fragment that could be amplified during a 10s extension was 6899 bp long. In total, we were able to detect 13 viruses from 11 genera using RTX-PCR. For each virus, two to three specific fragments were amplified. The RT-PCR assay using the RTX enzyme described here is a very robust, inexpensive, rapid, easy to perform, and sensitive single-enzyme assay for the detection of plant viruses.

Visual detection of Maize chlorotic mottle virus using unmodified gold nanoparticles

Visual detection of Maize chlorotic mottle virus was investigated using unmodified gold nanoparticles (AuNPs).

An Improved Multiplex IC-RT-PCR Assay Distinguishes Nine Strains of Potato virus Y

A multiplex reverse-transcription polymerase chain reaction (RT-PCR) assay was previously developed to identify a group of Potato virus Y (PVY) isolates with unusual recombinant structures (e.g., PVY^NTN-NW and SYR-III) and to differentiate them from other PVY strains. In the present study, the efficiency of this multiplex RT-PCR assay was validated and extended considerably to include five additional strains and strain groups not tested before. To make the multiplex RT-PCR assay more applicable and suitable for routine virus testing and typing, it was modified by replacing the conventional RNA extraction step with the immunocapture (IC) procedure. The results obtained using well-characterized reference isolates revealed, for the first time, that this multiplex RT-PCR assay is an accurate and robust method to identify and differentiate the nine PVY strains reported to date, including PVY^O (both PVY^O and PVY^O-O5), PVY^N, PVY^NA-N, PVY^NTN, PVY^Z, PVY^E, PVY-NE11, PVY^N-Wi, and PVY^N:O, which is not possible by any of the previously reported RT-PCR procedures. This would make the IC-RT-PCR procedure presented here a method of choice to identify PVY strains and assess the strain composition of PVY in a given area. The IC-RT-PCR protocol was successfully applied to typing PVY isolates in potato leaf tissue collected in the field.

Assessment of SNaPshot and single step RT-qPCR methods for discriminating Potato virus Y (PVY) subgroups

Potato virus Y (PVY) is the most important virus infecting potato (Solanum tuberosum), causing potato tuber necrotic ringspot disease (PTNRD), with a great impact on seed potato production. Numerous PVY strain groups with different pathogenicity and economical impact are distributed worldwide. Tools for accurate and reliable detection and discrimination of PVY strain groups are therefore essential for successful disease management. Two state of the art characterization tools based on detecting molecular markers - RT-qPCR (Kogovsek et al., 2008) and SNaPshot (Rolland et al., 2008) - were assessed for their ability to assign PVY accurately to the correct group. The results were validated by bioassay, ELISA and in silico sequence analysis. The spectrum of PVY strain groups distinguished by SNaPshot is broader than that by RT-qPCR. However, the latter was more reliable in discriminating the PVY(NTN) group members, known for their ability to induce PTNRD on selected potato cultivars. The difference in discrimination precision was due to different molecular markers being targeted by RT-qPCR and SNaPshot. Both tools use genotypic markers for detecting PVY(NTN) strain groups. Future development, however, should be focused on identifying the genomic determinants of the tuber necrosis property. Until then, the RT-qPCR and SNaPshot methods remain the most powerful diagnostic tools for detecting the PVY subgroup isolates found in Europe.

The simultaneous differentiation of Potato virus Y strains including the newly described strain PVY(NTN-NW) by multiplex PCR assay

New recombinant strain and genotype of PVY, designated as PVY(NTN-NW) and SYR-III, respectively, shared properties with PVY(NTN) and PVY(N)W has been reported recently. PVY(NTN-NW) predominated in potato fields in Syria and was able to induce potato tuber necrotic ringspot disease (PTNRD). Due to the rapid spread of the recombinant strains of PVY which might be the case of PVY(NTN-NW), a specific and reliable detection method is an essential step to control this strain and minimize its spread. The shared properties of PVY(NTN-NW) and SYR-III with PVY(NTN) and PVY(N)W, however, complicate their identification involving multiple detection methods. Therefore, a multiplex polymerase chain reaction (PCR), that relies on a combination of previously published and newly designed primers was developed for the detection and identification of PVY(NTN-NW) and SYR-III in single or mixed infections with the main PVY strains, PVY(O), PVY(N), PVY(NTN) and PVY(N)W. In addition, the present PCR assay was able to detect the recombination points in the P1 region enabling the differentiation of the variable genotypes of the recombinant strains PVY(NTN-NW), PVY(NTN) and PVY(N)W. The reliability of this PCR assay was confirmed using a significant number of well characterized PVY isolates collected from Syria and Japan including those of PVY(NTN-NW), SYR-III, PVY(O), NA-PVY(N), PVY(N)W and PVY(NTN).

Regulation of phosphoenolpyruvate carboxylase in PVY(NTN)-infected tobacco plants

The effect of viral infection on the regulation of phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) in Nicotiana tabacum L. leaves was studied. PEPC activity was 3 times higher in infected plant leaves compared to healthy plants. Activity of plant PEPC can be regulated, e.g., by de novo synthesis or reversible phosphorylation. The reason for the increase of PEPC activity as a consequence of PVY(NTN) infection was studied. The amount of PEPC determined by Western blot analysis or by relative estimation of PEPC mRNA by real-time PCR did not differ in control and PVY(NTN)-infected plants. Changes in posttranslational modification of PEPC by phosphorylation were evaluated by comparing activity of the native and the dephosphorylated enzyme. The infected plants were characterized by a higher decrease of the enzyme activity after its dephosphorylation, which indicated a higher phosphorylation level. Immunochemical detection of phosphoproteins by Western blot analysis showed a more intensive band corresponding to PEPC from the infected material. This strengthens the hypothesis of an infection-related phosphorylation, which could be part of the plant's response to pathogen attack. The physiological implications of the increase in PEPC activity during PVY(NTN) infection are discussed.

Rapid detection of Potato Y potyvirus in potato farms of Kermanshah using RT-PCR amplification of the P1-protease gene and its cloning

In this study, the RT-PCR method was used to detect the Y virus in potato tubers and leaves. Samples suspicious of virus infection with symptoms of virus infection were gathered from farms in Kermanshah and placed in plastic bags and kept at -80 degrees C temperature in order to maintain the RNA of the virus until extraction. The extraction and purification of RNA were carried out using Tri-Reagent kit. One of the virus genes is the P1 protease gene which codes a proteinase enzyme. This enzyme plays a role in breaking the initial polyprotein. For amplification of this gene three primer, including primer-1, primer-2 and primer-3, were designed and used. Using primer 1 and reverse transcriptase enzyme, cDNA was synthesized and then PCR was performed using the primers 1, 2 and 3. The PCR products were examined by agarose gel electrophoresis (1%). Consequently, two pieces of DNA (400 and 800 bp) were yielded which were identical to the genome DNA sequencing. Thus, the proposed technique is a convenient method for quick and accurate detection of viruses and, therefore, the application of this method for detecting Potato Y virus in potato farms is recommended.

A multiple single nucleotide polymorphisms interrogation assay for reliable Potato virus Y group and variant characterization

The complex Potato virus Y classification, including groups (PVYN and PVYO) and variants (PVYNTN and PVYN-W), is based mainly on biological properties of isolates. Published PVY detection tools targeting markers not associated with biological properties could fail to assign correctly isolates in the current classification. To improve PVY detection tools, a single nucleotide polymorphism (SNaPshot) detection assay was developed. The technique was adapted to target the T/C9259, A/C2271, G/C8573 and A/G2213 PVY polymorphic nucleotides. The "TAGA", "CCCG", "CACA" and "CAGA" four-digit codes associated with tested samples allowed identification of PVYN, PVYO, PVYN-W and PVYNTN isolates, respectively. The PVY SNaPshot procedure is efficient and reliable for PVY detection and characterization in samples containing as few as 10(2) viral RNA copies. Moreover, PVY group assignment is possible for fractions containing only 10 copies of a PVY RNA genome. Finally, the SNaPshot assay allows PVY(N)/PVYO dual characterization for mixed samples containing PVYN/PVYO quantity ratios in the range of 0.1-10. This innovative SNaPshot tool improved clearly PVY diagnostic assays described previously by targeting simultaneously major functional markers and sequence unlinked to biological properties used separately in PVY detection tools available currently.

Rapid identification of potato virus Y strains by one-step triplex RT-PCR

A one-step triplex RT-PCR method was characterised that allows rapid, strain-specific detection of potato virus Y (PVY) occurring on potato: PVY(N), PVY(O), PVY(NTN) (recombinant isolates), PVY(N)Wi and PVY(C). Three specific primer pairs were designed on aligned PVY sequences available from genomic data banks. The specificity of the selected primers was first examined by simplex RT-PCR with a large number of PVY reference isolates. Two fragments of 0.44 and 1.11kb were amplified for PVY(N) and non-recombinant PVY(NTN) isolates, two fragments of 0.53 and 0.66kb for PVY(O) isolates, a single fragment of 0.44kb for recombinant PVY(NTN) isolates, a 0.66kb fragment for PVY(C) isolates and a 0.53kb fragment for PVY(N)Wi isolate. The primers were then combined in a one-step triplex RT-PCR reaction, optimised stepwise and validated with the reference isolates. The great similarity between the genomes of PVY(N) and non-recombinant PVY(NTN) prevented their differentiation using this method. No fragments were amplified with samples infected by non-related potato viruses, as well as with samples from healthy tobacco and potato plants. The one-step triplex RT-PCR described here fastens specific detection of PVY strains that are otherwise only distinguishable by combined serological and biological assays.

Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers

Potato virus Y (PVY) is one of the most important viruses of potato world-wide, several strain groups are recognized. In the past two decades, novel PVY variants have appeared causing necrotic symptoms on potato tubers. Implicated are two groups of recombinant strains: PVY(N)W and PVY(NTN), and NA-PVY(NTN). While the first two are recombinants between PVY-N- and O-strains the latter is a recombinant between an N-strain and an unknown PVY strain or other Potyvirus. Available biological and molecular data on PVY suggest that classification of PVY strains has to be revised. Some drawbacks have been found with recently published primers used in RT-PCR based differentiation of PVY strains as some defined isolates could not be identified correctly. Consequently we developed new primers using both recently available sequences and newly generated complete sequences of PVY strains. The reliability of these newly developed primers and procedures was successfully demonstrated on nearly 100 biologically and serologically characterised PVY isolates.

Emergence of a resistance-breaking isolate of Rice yellow mottle virus during serial inoculations is due to a single substitution in the genome-linked viral protein VPg

The recessive gene rymv-1, responsible for the high resistance of Oryza sativa 'Gigante' to Rice yellow mottle virus (genus Sobemovirus), was overcome by the variant CI4*, which emerged after serial inoculations of the non-resistance-breaking (nRB) isolate CI4. By comparison of the full-length sequences of CI4 and CI4*, a non-synonymous mutation was identified at position 1729, localized in the putative VPg domain, and an assay was developed based on this single-nucleotide polymorphism. The mutation G1729T was detected as early as the first passage in resistant plants and was found in all subsequent passages. Neither reversion nor any additional mutation was observed. The substitution G1729T, introduced by mutagenesis into the VPg of an nRB infectious clone, was sufficient to induce symptoms in uninoculated leaves of O. sativa 'Gigante'. This is the first evidence that VPg is a virulence factor in plants with recessive resistance against viruses outside the family Potyviridae.

NL-3 K Strain Is a Stable and Naturally Occurring Interspecific Recombinant Derived from Bean common mosaic necrosis virus and Bean common mosaic virus

ABSTRACT A strain of Bean common mosaic necrosis virus (BCMNV) from Idaho was identified by enzyme-linked immunosorbent assay using monoclonal antibodies and determined to be similar to the NL-3 D strain (of Drifjhout) by reaction of differential bean cultivars. However, this BCMNV strain (designated NL-3 K) caused earlier and more severe symptoms on bean plants representing host groups 0, 4, and 5. The nucleotide sequence encoding the predicted polyprotein of NL-3 K was 9,893 nucleotides (nt) in length, yielding a peptide with a molecular size of 362.1 kDa compared with a 9,626-nt, 350.9-kDa polyprotein for NL-3 D. Sequence analysis of the putative P1 protein suggests that the NL-3 K strain is a recombinant between NL-3 D and the Russian strain (RU1) of Bean common mosaic virus. The P1 protein of NL-3 K consisted of 415 amino acids compared with 317 for NL-3 D. The first 114 predicted amino acids of the NL-3 K P1 region were 98% identical with RU1. The remaining 301 amino acids of the protein shared only 34% identity with RU1 but were 98% identical with NL-3 D. Primers were designed that flanked the recombination point in the P1 coding sequence of NL-3 K. An amplicon of the expected size was produced by reverse-transcriptase polymerase chain reaction of total nucleic acid extracts of bean plants inoculated with NL-3 K, but not from those with NL-3 D or RU1. The increased symptom severity on selected common bean lines induced by NL-3 K suggests that the P1 gene may play a significant role in pathogenicity and virulence.

Specific detection of the PVY(N)-W variant of Potato virus Y

PVY(N)-W is one of the variant populations of Potato virus Y (PVY). This variant is of concern in seed potato production and requires a specific diagnosis since it induces more or less symptomless infections and is not detectable easily in field inspections. Moreover, this variant is serologically indistinguishable from the common strain PVY(O). This study describes a simple and specific molecular detection test for the PVY(N)-W variant using a PCR protocol based on the recombinant point within the HC-Pro/P3 region of PVY(N) variants (PVY(NTN), PVY(N)-W). To avoid both detection of recombinant PVY(NTN) and PVY(N)-W isolates, a forward PVY(N)-like primer located in the HC-Pro region coupled to a reverse PVY(O)-like primer located in the NIa region was designed to amplify a specific PCR product of 4114 nt from PVY(N)-W isolates. This technique was assessed on 41 PVY reference and field isolates. Only isolates referenced as PVY(N)-W were amplified and gave the expected PCR product of 4114 nt, whereas no band was obtained from PVY(N), PVY(NTN) or PVY(O) isolates. In conclusion, this PVY(N)-W diagnosis tool is rapid, easy-to-use and suitable for large-scale testing in laboratories of seed potato certification.

A single nucleotide polymorphism-based technique for specific characterization of YO and YN isolates of Potato virus Y (PVY)

One of the most important properties used to classify Potato virus Y (PVY) isolates is their ability to induce (PVY(N)) or not (PVY(O)) veinal necrosis symptoms on the indicator host plant Nicotiana tabacum cv. Xanthi. As an alternative to biological assays, several serological and molecular detection tools have been developed for PVY detection and characterization and these have evolved as our knowledge of PVY has improved. However, the assays that have been previously published are all based on the use of neutral markers (antigenic determinants, sequence data, recombination sites or restriction enzyme cleavage sites), which are unlinked to the biological property being characterized (e.g. veinal necrosis). Using the recently identified molecular determinants of the tobacco leaf necrosis symptom induced by PVY(N) isolates, a one-step fluorescent [TaqMan] RT-PCR assay, based on a single nucleotide polymorphism (SNP) linked to the necrosis property of PVY isolates, has been designed. This assay reliably detects and distinguishes PVY(N) and PVY(O) isolates. The method is simple (leaf soak extraction process, gel-free, no post-PCR manipulations), rapid (96 tests in less than 3h from plants sampling to diagnostic results), sensitive (threshold in a range of 10(4)-10(5) PVY copies), reliable (correctly assigns 42 PVY isolates in their respective group) and allows co-detection of mixed samples containing close to equivalent PVY(N) and PVY(O) quantities. All these characteristics suggest that the newly developed SNP assay could be used to reliably classify PVY isolates, as a substitute for biological assays performed on N. tabacum cv. Xanthi.

In vitro recombinants of two nearly identical potyviral isolates express novel virulence and symptom phenotypes in plants

Six novel chimeric viruses were constructed by sequentially exchanging segments of the viral genomes between the infectious cDNA clone (pPVA-B11) of Potato virus A (isolate PVA-B11) and pUFL, an almost identical infectious cDNA of PVA (isolate U) made in this study. The infectious in vitro transcripts of pUFL and pPVA-B11 caused similar severe mosaic and leaf malformation phenotypes in systemically infected leaves of Nicotiana benthamiana. In contrast, one chimera induced a unique phenotype of yellow vein chlorosis without leaf malformation with viral titres that were equivalent to those of the parental viruses. Furthermore, as opposed to the viral cDNAs from which it was assembled, one chimera showed no detectable infectivity of N. benthamiana plants. Thus, recombination of nearly identical, phenotypically similar virus genomes can give rise to new viral strains with novel virulence and symptom phenotypes, which has not previously been demonstrated with potyviruses. One chimera failed to cause systemic infection in potato plants, but, nevertheless, avirulence could not be attributed to a single genomic region. These data suggest that different parts of the potyviral genome function coordinately. The results provide novel insights into the evolution of the genus Potyvirus.

Specific differentiation of recombinant PVY(N:O) and PVY(NTN) isolates by multiplex RT-PCR

The recombinant isolates of tobacco veinal necrotic strain of Potato virus Y (PVYN) and potato tuber necrotic group (PVY(NTN)) contain segments of the PVYO and the PVY(N) genome. Three major recombinant junctions (RJ) are present in the genome of the recombinant PVY(NTN) at sites HC/Pro-P3, 6K2-NIa, and the C-terminal region of CP gene and one RJ at HC/Pro-P3 site in some recombinant PVYN isolates (termed PVY(N:O)). Protocols for specific differentiation of the recombinant PVY(NTN) and PVY(N:O) from the non-recombinant PVYN are described. Specific primer pairs were designed to target the three RJs so that sense and antisense primers completely matched the nucleotide sequences at either side of the RJ. In a uniplex reverse transcription-polymerase chain reaction (RT-PCR), the first primer pair amplified a fragment of 641bp from the recombinant PVY(NTN) and PVY(N:O). The second and third primer pairs exclusively amplified fragments of 448 and 290bp, respectively from the recombinant PVY(NTN). In a multiplex (triplex) RT-PCR, when all three primer pairs were used simultaneously, the three fragments (641, 448 and 290bp) were amplified exclusively from the recombinant PVY(NTN), while only one fragment (641bp) was amplified from the PVY(N:O) isolates, clearly differentiating the two recombinant isolates. No amplification was observed from the non-recombinant PVY, including PVYO and North American (NA)-PVY(N/NTN). For further improvement of the multiplex RT-PCR, effects of cDNA preparation using specific antisense primers, random primers or oligo(dT) plus random primers were investigated. The cDNA prepared by random primer plus oligo(dT) increased the overall band intensity.