Simultaneous detection and identification of four cherry viruses by two step multiplex RT-PCR with an internal control of plant nad5 mRNA

Conventional and cutting-edge advances in plant virus detection: emerging trends and techniques

Plant viruses pose a significant threat to global agriculture. For a long time, conventional methods including detection based on visual symptoms, host range investigations, electron microscopy, serological assays (e.g., ELISA, Western blotting), and nucleic acid-based techniques (PCR, RT-PCR) have been used for virus identification. With increased sensitivity, speed, and specificity, new technologies like loop-mediated isothermal amplification (LAMP), high-throughput sequencing (HTS), nanotechnology-based biosensors, and CRISPR diagnostics have completely changed the way plant viruses are detected. Recent advances in detection techniques integrate artificial intelligence (AI), machine learning (ML), and the Internet of Things (IoT) for real-time monitoring. Innovations like hyperspectral imaging, deep learning, and cloud-based IoT platforms further support disease identification and surveillance. Nanotechnology-based lateral flow assays and CRISPR-Cas systems provide rapid, field-deployable solutions. Despite these advancements, challenges such as sequence limitations, multiplexing constraints, and environmental concerns remain. Future research should focus on refining portable on-site diagnostic kits, optimizing nanotechnology applications, and enhancing global surveillance systems. Interdisciplinary collaboration across molecular biology, bioinformatics, and engineering is essential to developing scalable, cost-effective solutions for plant virus detection, ensuring agricultural sustainability and ecosystem protection.

Development of simplex and quintuplex RT-PCR for simultaneous detection of soybean viruses

Five simplex and a multiplex-RT-PCR (m-RT-PCR) protocols were developed for detection and differentiation of bean pod mottle virus (BPMV), cherry leaf roll virus (CLRV), raspberry ringspot virus (RpRSV), soybean mosaic virus (SMV) and tomato ringspot virus (ToRSV) infecting soybean. The simplex RT-PCR protocols produced virus-specific amplicons of 538 bp for BPMV, 139 bp for CLRV, 298 bp for RpRSV, 403 bp for SMV, and 282 bp for ToRSV, with sensitivity down to 10-4 diluted cDNA. Further, to detect all the five viruses simultaneously in a single tube a quintuplex RT-PCR protocol was optimized with as low as 10-3 diluted cDNA and 0.05 µM primer. To validate the reliability of the simplex RT-PCR protocol, imported soybean samples were tested by ELISA as well as RT-PCR. The results revealed that the developed protocol could detect the viruses in imported soybean, and found to be efficient than ELISA in resolving ambiguity in detection of seed borne viruses. The developed simplex and quintuplex RT-PCR protocol will be quite helpful for the diagnosis of soybean germplasm co-infected with viruses during the quarantine processing for ensuring virus free long term seed conservation in the National Gene Bank as well as for quarantine certification.

Development and evaluation of one-step RT-qPCR TaqMan multiplex panels applied to six viruses occurring in lily and tulip bulbs

One-step RT-qPCR TaqMan assays have been developed for six plant viruses with considerable economic impact in the growing of tulip and lily bulbs: lily mottle virus, lily symptomless virus, lily virus X, Plantago asiatica mosaic virus, tulip breaking virus and tulip virus X. To enhance efficacy and cost-efficiency these assays were combined into multiplex panels. Four different multiplex panels were designed, each consisting of three virus assays and an adapted assay for the housekeeping gene nad5 of lilies and tulips, that acts as an internal amplification control. To eliminate false negative results due to variation in the viral genome sequences, for each target virus two assays were developed on distinct conserved genomic regions. Specificity, PCR efficiency and compatibility of primers and probes were tested using gBlock constructions. Diagnostic samples were used to evaluate the strategy. High Throughput Sequencing of a set of the diagnostic samples, further verified the presence or absence of the viruses in the RNA samples and sequence variations in the target genes. This interchangeable multiplex panel strategy may be a valuable tool for the detection of viruses in certification, surveys and virus diagnostics.

CTAB Protocol for Obtaining High-Quality Total RNA from Hibiscus rosa-sinensis and Other Related Plants of the Family Malvaceae

Malvaceae family, also known as the Mallow family, is a family of flowering plants containing Hibiscus rosa-sinensis and other plants of high medicinal value. This study focuses on the challenges associated with high-quality RNA extraction from Hibiscus rosa-sinensis and its related plants characterized by high levels of mucilage and phenolic compounds in their tissues. High mucilage and secondary metabolite content pose obstacles in obtaining high-quality RNA, negatively impacting downstream applications, such as gene expression analysis. Our research aimed to develop an efficient RNA extraction method tailored to the unique characteristics of Malvaceae family plants especially Hibiscus rosa-sinensis. Through the substitution of NaCl with KCl, a crucial component of the CTAB buffer, our methodology successfully addressed the challenges posed by high mucilage and phenolic compound levels. This modification led to a significant reduction in sample viscosity, which is because of the high mucilage in these plants. Our modified CTAB extraction method yielded significantly more RNA with higher purity than the conventional CTAB methods alone. The extracted RNA was largely intact, as indicated by 28S/18S ratios and RIN values, yielding high-quality RNA with improved purity suggested by the 260/280 and 260/230 ratios. The proposed approach not only serves as a solution to the specific challenges encountered in Hibiscus rosa-sinensis but also holds promise for broader applications across different plants within the family.

Whole genome characterization and diagnostics of prunus necrotic ringspot virus (PNRSV) infecting apricot in India

Prunus necrotic ringspot virus (PNRSV) is a pathogen that infects Prunus species worldwide, causing major economic losses. Using one and two-step RT-PCR and multiplex RT-PCR, the whole genome of the PNRSV-infecting apricot was obtained and described in this study. Computational approaches were used to investigate the participation of several regulatory motifs and domains of the Replicase1, Replicase2, MP, and CP. A single degenerated reverse and three forward oligo primers were used to amplify PNRSV's tripartite genome. The size of RNA1 was 3.332 kb, RNA2 was 2.591 kb, and RNA3 was 1.952 kb, according to the sequencing analysis. The Sequence Demarcation Tool analysis determined a percentage pair-wise identity ranging between 91 and 99% for RNA1 and 2, and 87-98% for RNA3. Interestingly, the phylogenetic analysis revealed that closely related RNA1, RNA2, and RNA3 sequences of PNRSV strains from various geographical regions of the world are classified into distinct clades or groups. This is the first report on the characterization of the whole genome of PNRSV from India, which provides the cornerstone for further studies on the molecular evolution of this virus. This study will assist in molecular diagnostics and management of the diseases caused by PNRSV.

Nearly Complete Genome Sequence of Cherry Virus A, Isolated from Prunus armeniaca in Jammu and Kashmir, India

A nearly complete genome sequence of cherry virus A (CVA), isolated from the Prunus armeniaca plant, is presented in this publication. The genome is 7,380 bases in length and is divided into two open reading frames, with a 54-nucleotide (nt) 5′ noncoding region (NCR) and a 297-nt 3′ NCR.

Development of a novel polyprobe for simultaneous detection of six viruses infecting stone and pome fruits

A biotin-labeled, non-isotopic, novel polyprobe was developed for the simultaneous detection of six viruses viz. apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), apple stem grooving virus (ASGV), cherry virus A (CVA), prunus necrotic ringspot virus (PNRSV) and plum pox virus (PPV) infecting stone and pome fruit trees through dot-blot hybridization assay. The sensitivity of the polyprobe was checked by serial dilutions of total RNA extracted from the tissues of infected trees. ACLSV was detected up to a dilution of 5^-5, whereas ApMV, ASGV, CVA, PPV and PNRSV up to 5^-4. The developed assay was validated following testing a total of 45 symptomatic leaf samples collected from different geographical regions of Jammu and Kashmir (India), and the presence of the viruses was further confirmed by RT-PCR and sequencing. The polyprobe, designed for performing molecular hybridization assay can be developed quickly and avoid the tedious transformation and cloning procedures. Apart from simultaneously detecting viruses in stone and pome fruit trees, it holds great potential for virus indexing programmes to ascertain the supply of virus-free plant materials to the growers.

Multiplex RT-PCR to simultaneously detect three viruses that infect peach

Peach is a major crop in China, and like any other stone fruit, virus and virus-like diseases can reduce the yield and quality of the fruit. Herein, we developed a multiplex RT-PCR (mRT-PCR) assay for simultaneously detecting three viruses known to infect peach: peach-associated luteovirus (PaLV), peach virus D (PeVD) and nectarine stem-pitting-associated virus (NSPaV). Plant nad5 mRNA was used as the internal control. Field samples that were co-infected with PaLV, PeVD and NSPaV were used; we identified three primer pairs to be the most specific for detecting these viruses, followed by determining the ideal concentration of each primer pair and optimizing the annealing temperature for mRT-PCR. We also assessed the detection limit using serial dilutions of RNA and cDNA. The newly developed mRT-PCR assay could simultaneously detect PaLV, PeVD and NSPaV. To validate the reliability of mRT-PCR for virus detection, mRT-PCR was used to detect viruses in the leaves of 21 peach plants collected in Liaoning Province, China. The obtained results revealed the presence of single and co-infections. To conclude, the mRT-PCR assay developed herein is sensitive, reliable and economical, and we believe that it can thus be used for large-scale surveys of PaLV, PeVD and NSPaV. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study, we developed a multiplex reverse transcriptase PCR (mRT-PCR) assay for simultaneously detecting three viruses that infect peach: peach-associated luteovirus (PaLV), peach virus D (PeVD) and nectarine stem-pitting-associated virus (NSPaV). This assay is simple, easy to perform, reliable and cost-effective, and can thus be applied for large-scale surveys of PaLV, PeVD and NSPaV.

Simultaneous detection and differentiation of three genotypes of Brassica yellows virus by multiplex reverse transcription-polymerase chain reaction

BACKGROUND

Brassica yellows virus (BrYV), proposed to be a new polerovirus species, three distinct genotypes (BrYV-A, BrYV-B and BrYV-C) have been described. This study was to develop a simple, rapid, sensitive, cost-effective method for simultaneous detection and differentiation of three genotypes of BrYV.

RESULTS

In this study, a multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for simultaneous detection and differentiation of the three genotypes of BrYV. The three genotypes of BrYV and Tunip yellows virus (TuYV) could be differentiated simultaneously using six optimized specific oligonucleotide primers, including one universal primer for detecting BrYV, three BrYV genotype-specific primers, and a pair of primers for specific detection of TuYV. Primers were designed from conserved regions of each virus and their specificity was confirmed by sequencing PCR products. The mRT-PCR products were 278 bp for BrYV-A, 674 bp for BrYV-B, 505 bp for BrYV-C, and 205 bp for TuYV. Amplification of three target genotypes was optimized by increasing the PCR annealing temperatures to 62 °C. One to three fragments specific for the virus genotypes were simultaneously amplified from infected samples and identified by their specific molecular sizes in agarose gel electrophoresis. No specific products could be amplified from cDNAs of other viruses which could infect crucifer crops. Detection limits of the plasmids for multiplex PCR were 100 fg for BrYV-A and BrYV-B, 10 pg for BrYV-C, and 1 pg for TuYV, respectively. The mRT-PCR was applied successfully for detection of three BrYV genotypes from field samples collected in China.

CONCLUSIONS

The simple, rapid, sensitive, and cost-effective mRT-PCR was developed successfully for detection and differentiation of the three genotypes of BrYV.

Doubling Throughput of a Real-Time PCR

The invention of polymerase chain reaction (PCR) in 1983 revolutionized many areas of science, due to its ability to multiply a number of copies of DNA sequences (known as amplicons). Here we report on a method to double the throughput of quantitative PCR which could be especially useful for PCR-based mass screening. We concurrently amplified two target genes using only single fluorescent dye. A FAM probe labelled olionucleotide was attached to a quencher for one amplicon while the second one was without a probe. The PCR was performed in the presence of the intercalating dye SYBR Green I. We collected the fluorescence amplitude at two points per PCR cycle, at the denaturation and extension steps. The signal at denaturation is related only to the amplicon with the FAM probe while the amplitude at the extension contained information from both amplicons. We thus detected two genes within the same well using a single fluorescent channel. Any commercial real-time PCR systems can use this method doubling the number of detected genes. The method can be used for absolute quantification of DNA using a known concentration of housekeeping gene at one fluorescent channel.

Survey of Cherry necrotic rusty mottle virus and Cherry green ring mottle virus incidence in Korea by Duplex RT-PCR

The incidence of Cherry necrotic rusty mottle virus (CNRMV) and Cherry green ring mottle virus (CGRMV) have recently been occurred in Korea, posing a problem for sweet cherry cultivation. Since infected trees have symptomless leaves or ring-like spots on the pericarp, it is difficult to identify a viral infection. In this study, the incidence of CNRMV and CGRMV in sweet cherry in Gyeongbuk province was surveyed using a newly developed duplex reverse transcriptase polymerase chain reaction (RT-PCR) method that can detect both viruses in a single reaction. CNRMV and CGRMV co-infection rates were 29.6%, 53.6%, and 17.6%, respectively, in samples collected from three different sites (Daegu, Gyeongju and Gyeongsan) in Gyeongbuk province during 2012 and 2013. This duplex RT-PCR method offers a simple, rapid, and effective way of identifying CNRMV and CGRMV simultaneously in sweet cherry trees, which can aid in the management of viral infections that could undermine yield.

Development and validation of a multiplex reverse transcription PCR assay for simultaneous detection of three papaya viruses

Papaya ringspot virus (PRSV), Papaya leaf distortion mosaic virus (PLDMV), and Papaya mosaic virus (PapMV) produce similar symptoms in papaya. Each threatens commercial production of papaya on Hainan Island, China. In this study, a multiplex reverse transcription PCR assay was developed to detect simultaneously these three viruses by screening combinations of mixed primer pairs and optimizing the multiplex RT-PCR reaction conditions. A mixture of three specific primer pairs was used to amplify three distinct fragments of 613 bp from the P3 gene of PRSV, 355 bp from the CP gene of PLDMV, and 205 bp from the CP gene of PapMV, demonstrating the assay's specificity. The sensitivity of the multiplex RT-PCR was evaluated by showing plasmids containing each of the viral target genes with 1.44 × 103, 1.79 × 103, and 1.91 × 102 copies for the three viruses could be detected successfully. The multiplex RT-PCR was applied successfully for detection of three viruses from 341 field samples collected from 18 counties of Hainan Island, China. Rates of single infections were 186/341 (54.5%), 93/341 (27.3%), and 3/341 (0.9%), for PRSV, PLDMV, and PapMV, respectively; 59/341 (17.3%) of the samples were co-infected with PRSV and PLDMV, which is the first time being reported in Hainan Island. This multiplex RT-PCR assay is a simple, rapid, sensitive, and cost-effective method for detecting multiple viruses in papaya and can be used for routine molecular diagnosis and epidemiological studies in papaya.