One-step Reverse Transcription-polymerase Chain Research Articles

Bead-based suspension array for simultaneous differential detection of five major swine viruses.

A novel multiplex detection array based on Luminex xMAP technology was developed and validated for simultaneous detection of five major viruses causing swine reproductive diseases. By combining one-step asymmetric multiplex reverse transcription polymerase chain reaction (RT-PCR) with xMAP bead-based hybridization and flow cytometry analysis, the resulting multiplex assay was capable of detecting single and mixed infections of PRRSV, PCV-2, PRV, CSFV, and PPV in a single reaction. The assay accurately detected and differentiated 23 viral strains used in this study. The low detection limit was determined as 2.2-22 copies/μL (corresponding to 0.5-6.8 fg/μL DNA template) on plasmid constructs containing viral fragments. The intra-assay and inter-assay variances (CV%) were low that ranged from 2.5 to 5.4 % and 4.1 to 7.6 %, respectively. The assay was applied to test field samples and detected single and mixed viral infections. The detection rate was higher than that of uniplex conventional PCR and RT-PCR methods. The detection of PRRSV by the bead-based multiplex assay was comparable with a commercially available real time RT-PCR kit. The test procedure on purified DNA or RNA samples could be completed within 2 h. In conclusion, the bead-based suspension array presented here proved to be a high-throughput practical tool that provided highly specific and sensitive identification of single and multiple infections of five major viruses in pigs and boar semen.

Some epidemiological features of BCoVs infection in Al-Qadisiyah Province by using real time-qPCR technique

This study was carried out to evaluate some epidemiological features of Bovine Coronavirus infection by using one-step real-time fluorogenic quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay based on SYBR Green I dye in detection. Coronaviruses detected by the same nucleocapsid (N) gene primers under 98% similarity with HECV-4408 (human enteric Coronavirus) in children according to NCBI with product size 124bp. 285 fecal samples have been examined by routine methods against pathogenic bacteria in the intestines (E.coli, Salmonella Spp.) and Cryptosporidium parvum, the samples positive for the parasite submitted to molecular testing because they may be mixed with coronavirus infections. 100 samples were screened for the presence of BCoVs antigens by using an immunochromatographic rapid test as a field fast test. Where 44% of samples showed positivity to BCoVs, out of 50 samples submitted to quantitative reverse transcription (RT-qPCR) assay. Out of 50 – 31 samples had been positive. We found that distribution of BCoVs was significantly higher in rural areas 33.3%-87.5% as compare to cities 71.4%-75%, the infection in males reach to75% vas 53.5% in females, high infection rate 62.9% in < 1- 4 months age as compared with > 1 month age 62.9%. The results of infection rate showed high percentage during February 77.7% while the percentage on (January, December, March, and April) was (66.6%, 66.1%, 54.5%, and 50%) respectively.

One-step multiplex quantitative RT-PCR for the simultaneous detection of viroids and phytoplasmas of pome fruit trees

A one-step multiplex real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan chemistry was developed for the simultaneous detection of Pear blister canker viroid and Apple scar skin viroid along with universal detection of phytoplasmas, in pome trees. Total nucleic acids (TNAs) extraction was performed according to a modified CTAB protocol. Primers and TaqMan MGB probes for specific detection of the two viroids were designed in this study, whereas for phytoplasma detection published universal primers and probe were used, with the difference that the later was modified to carry a MGB quencher. The pathogens were detected simultaneously in 10-fold serial dilutions of TNAs from infected plant material into TNAs of healthy plant up to dilutions 10−5 for viroids and 10−4 for phytoplasmas. The multiplex real-time assay was at least 10 times more sensitive than conventional protocols for viroid and phytoplasma detection. Simultaneous detection of the three targets was achieved in composite samples at least up to a ratio of 1:100 triple-infected to healthy tissue, demonstrating that the developed assay has the potential to be used for rapid and massive screening of viroids and phytoplasmas of pome fruit trees in the frame of certification schemes and surveys.

Detection of Citrus psorosis virus Using an Improved One-Step RT-PCR

We report an improvement of a one-step reverse transcription polymerase chain reaction (RT-PCR) assay for the detection of Citrus psorosis virus (CPsV; genus Ophiovirus) in citrus trees. Two different sample preparation procedures were compared. The data showed that when using total RNA extracted by the Qiagen procedure more virus isolates could be detected compared with the Trizol procedure. Three pairs of primers reported in literature and selected within the coat protein (CP) region of the virus were used for a reliable detection of CPsV. Only one primer pair has been able to detect all CPsV isolates collected from different citrus regions of Morocco. In addition, this report showed that one-step RT-PCR was more sensitive and more consistent than ELISA test. Notably, 15 out of 22 samples tested positive by one-step RT-PCR could not be detected by Mab Ps29, thus providing a degree of differentiation among isolates. The detection protocol described in this study could be used in citrus certification programs and to test trees in nurseries and commercial orchards for CPsV infection.

Overexpression of MAGE-A9 predicts unfavorable outcome in breast cancer

Melanoma-associated antigens (MAGEs) are a group of well-characterized members of the cancer/testis antigen (CTA) family, which is one of the largest groups of human tumor-associated antigens. MAGE-A9 is a particular member in the context of the MAGE-A gene family and was defined as presenting prognostic relevance in certain type of human cancer. However, the expression of MAGE-A9 in invasive ductal breast cancer (IDC) and the relationship with the clinical attributes of IDC, especially prognostic characteristic, remain poorly understood. In this present study, one-step quantitative reverse transcription polymerase chain reaction (18 fresh-frozen IDC tissues and corresponding non-cancerous tissues) and immunohistochemistry by tissue microarrays (82 IDC tissue samples and 70 matched tumor-adjacent non-cancerous tissue samples) were performed to characterize expression of the MAGE-A9 gene in IDC. Kaplan–Meier survival and Cox regression analyses were performed to evaluate the prognosis of IDC. The results of qPCR and IHC analysis showed that the expression of MAGE-A9 in IDC was significantly higher than that in corresponding non-cancerous tissue. Moreover, the expression level of MAGE-A9 protein in IDC was significantly related to histological grade (p=0.011) and distant metastasis (p=0.019). Multivariate analysis with the Cox regression model showed that MAGE-A9 protein expression (p=0.009), histological grade (p=0.014), lymph node metastasis (p=0.012) and distant metastasis (p=0.011) were independent prognostic factors for overall survival of IDC patients. The data suggest that MAGE-A9 expression is correlated with malignant attributes of IDC and it may serve as a novel prognostic factor and an ideal candidate for targeted therapy in IDC treatment.

Elimination of mixed ‘Odontoglossum ringspot’ and ‘Cymbidium mosaic’ viruses from Phalaenopsis hybrid ‘V3’ through shoot-tip culture and protocorm-like body selection

Phalaenopsis is one of the most popular orchid plants in the global market. Several viruses have been reported to negatively impact its growth, yield and quality. A mixed infection of Odontoglossum ringspot virus and Cymbidium mosaic virus was detected in Phalaenopsis hybrid “V3” (Phal. Yukimai × Phal. Taisuco Kochdian) plants in Taiwan. In the present communication, we report a relatively simple protocol for elimination of these two viruses using shoot-tip culture, and early isolation and selection of virus free protocorm-like body (PLB) through subcultures. The indexing of viruses in the field grown plants, PLBs and tissue culture plants was carried out by the Indirect enzyme-linked immunosorbent assay (ELISA), and one-step multiplex reverse transcription polymerase chain reaction (RT-PCR). The induction of PLBs in shoot-tips was achieved on 1/2× Murashige and Skoog's basal medium supplemented with 1% sucrose and 0.9% Bacto-agar. PLBs could be maintained, proliferated and converted to plantlets on 1 g/L Hyponex medium supplemented with 1% sucrose, 6% potato pulp, 0.5 g/L tryptone, 0.25% activated charcoal and 0.6% Bacto-agar. The regenerated plantlets from virus-free PLBs acclimatized easily in a greenhouse and showed 100% survival rate. All the tissue culture-raised Phalaenopsis plants in the greenhouse tested negative for the two viruses. Our study demonstrates that some PLB lines selected at the first subculture as virus-free were found to be infected with virus at second subculture, however, re-occurrence of virus was never found in PLB lines at third subculture onwards. Hence, at least 3 subcultures are necessary to authenticate that the cultures are free of viruses. Simple culture media without plant growth regulators used in the present study minimizes the chances of somaclonal variations and ensures genetic uniformity of cultured plantlets, a highly desirable trait in the orchid industry. The method developed in the present study has potential of virus elimination, mass propagation of genetically uniform and virus-free Phalaenopsis plants.

Detection of immune response activation by exogenous nucleic acids by a multiplex RT-PCR method

Transfection of mammalian cells or in vivo administration of nucleic acids can induce inflammatory cytokines and/or interferon response, which could significantly influence the ex vivo or in vivo applications of gene-targeting strategies based on nucleic acids. Further induction of the interferon and inflammatory related stress responses may result in off-target effects and toxicity. This work describes an original one-step multiplex reverse transcription polymerase chain reaction procedure, which allows testing the induction of interferon and proinflamatory related responses by nucleic acids in the cell system of choice. The developed procedure has been tested on mammalian cells transfected with ssRNA, dsRNA, enzymatically synthesized siRNA and synthetic oligodesoxyribonucleotides containing unmethylated cytosine-guanosine motifs. This procedure is a rapid and convenient screening assay that could be used routinely in both the clinical and the research laboratory to validate the stimulation of the immune system on mammalian cells by nucleic acids.

Expression change and significance of homebox gene-A10 in rat cryptorchidism

To explore the effects of HOXA10 gene expression in undescended and descended testis. Twenty-four male Sprague Dawley rats were surgically prepared for unilateral cryptorchidism model. Their undescended and descended testes were removed at days 7 (infancy period, group B7) and 60 (sexual maturity period, group B60) post-operation. And contralateral descended testis served as controls (group A7, group A60). The expression of HOXA10 with histologic changes in experimental cryptorchidism were detected with one-step real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) and immunohistochemistry. Compared with the control group, the levels of HOXA10 gene for groups B7 and B60 decreased markedly to 0.78 ± 0.11 (P < 0.01) and 0.56 ± 0.03 (P < 0.01) respectively.However the levels of HOXA10 gene and protein in group B60 were significantly lower than those in group B7 (P < 0.01). There is a lower expression of HOXA10 in undescended testes than in normally developed counterparts. And the expression of HOXA10 decreases with the elapsing time of cryptorchidism.

Comparison of primer sets and one-step reverse transcription polymerase chain reaction kits for the detection of bluetongue viral RNA

Bluetongue virus is the etiological agent of bluetongue, one of the most important insect-transmitted animal diseases in the world. To establish a feasible diagnostic procedure for detecting the viral RNA, seven commercially available one-step RT-PCR kits in combination with three primer sets were evaluated. Results of this study showed remarkable differences in analytical sensitivity between the examined RT-PCR kits. In addition, it was found that a World Organization for Animal Health-recommended primer set may not be effective in detecting most BTV RNA.

Application of a SYBR®Green one step real-time RT-PCR assay to detect type 1 porcine reproductive and respiratory syndrome virus.

ABSTRACTThe emergence in Japan of field isolates of type 1 porcine reproductive and respiratory syndrome virus (PRRSV) suggests problems with control. We therefore developed a one-step real-time reverse transcription polymerase chain reaction (qRT-PCR) with improved sensitivity that detects as little as 1 × 10−2 TCID50/ml of viral RNA. We tested serum samples collected in January and September 2008, October 2009 and January 2011 from a farm with an outbreak and found infected pigs between January and September 2008, but not in January 2011. Further, between 2008 and 2011, we did not detect infection in pigs at 8 nearby farms or in 2,052 serum samples collected from pigs from 74 farms in 12 prefectures. This assay should help prevent future outbreaks.

Development and Validation of One-Step SYBR Green Real-Time RT-PCR for the Rapid Detection of Newly Emerged Duck Tembusu Virus

Duck Tembusu virus (DTMUV) is a single-stranded positive-sense RNA virus that causes disease to emerge in duck flocks and results in huge economic losses to the duck industry. However, no vaccines and control measures are available in China to date. Development of reliable and fast detection methods is necessary to prevent and control this disease. Therefore, a one-step SYBR Green real-time reverse transcription polymerase chain reaction (RT-PCR) method is established here for DTMUV detection. The results show that the method can specifically detect DTMUV without cross-reactions with selected avian pathogens. The sensitivity of the assay was 1000 times greater than that of a conventional RT-PCR and able to test as few as 20 copies from RNA standard samples. The coefficients of variations of inter- and intra-assay values ranged from 0.09% to 0.36% and 0.1% to 0.23%, respectively. Testing 168 field samples and 96 experimentally infected samples by conventional RT-PCR and the one-step SYBR Green real-time RT-PCR, the positive rates were 35.1% and 73.8% from field samples and 30.2% and 64.6% from infected samples. The one-step SYBR Green real-time RT-PCR developed in this study was shown to be a sensitive, specific, high-throughput, cost-effective, and simple diagnostic tool for the rapid detection and epidemiological surveillance of the emerging DTMUV infection.

Evaluation of virus isolation, one-step real-time reverse transcription polymerase chain reaction assay, and two rapid influenza diagnostic tests for detecting canine Influenza A virus H3N8 shedding in dogs

Sustained transmission of canine Influenza A virus (CIV) H3N8 among U.S. dogs underscores the threat influenza continues to pose to canine health. Because rapid and accurate detection of infection is critical to the diagnosis and control of CIV, the 2 main objectives of the current study were to estimate and compare the sensitivities of CIV testing methods on canine swab samples and to evaluate the performance of Flu Detect™ (Synbiotics Corp., Kansas City, MO) for detecting CIV nasal shedding in high-risk shelter dogs. To address the first objective, nasal and pharyngeal swab samples were collected from 124 shelter and household dogs seen by Colorado State University Veterinary Teaching Hospital clinicians for canine infectious respiratory disease between April 2006 and March 2007 and tested for CIV shedding using virus isolation, the rapid influenza diagnostic test Directigen Flu A+B™ (BD Diagnostic Systems, Sparks, MD), and real-time reverse transcription polymerase chain reaction (RT-PCR). For the second objective, 1,372 dogs with unknown respiratory health status were sampled from 6 U.S. shelters from December 2009 to November 2010. Samples were tested for presence of CIV using real-time RT-PCR and Flu Detect. Using a stochastic latent class modeling approach, the median sensitivities of virus isolation, rapid influenza diagnostic test, and real-time RT-PCR were 72%, 65%, and 95%, respectively. The Flu Detect test performed poorly for detecting CIV nasal shedding compared to real-time RT-PCR. In conclusion, the real-time RT-PCR has the highest sensitivity for detecting virus nasal shedding and can be used as a rapid diagnostic test for CIV.

Detection of Potato virus Y from the stylets of a single aphid by one‐step reverse transcription polymerase chain reaction

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Detection of Viable Cronobacter spp. (Enterobacter sakazakii) by One‐Step RT‐PCR in Dry Aquatic Product

Cronobacter are opportunistic food-borne pathogens associated with meningitis, sepsis, and necrotizing enterocolitis. Little attempt has focused on detection of viable cell of Cronobacter spp. in dry aquatic products, which were frequently used for raw materials of infant foods due to high nutrition. In this paper, one-step reverse transcription polymerase chain reaction (RT-PCR) was developed for detection of viable Cronobacter spp. in dry aquatic products. Specificity test indicated that clearly expected amplicon in size 469 bp was amplified from RNA of Cronobacter, but not from RNA of negative controls and DNA of Cronobacter strains. The sensitivity was 10(4) CFU/mL of Cronobacter strain in artificially fish meal samples and 10(1) CFU/mL of Cronobacter after 10-h enrichment. In a total of 81 dry aquatic products, 9.8%, 8.6%, and 9.8% of samples were found to be positive for Cronobacter by one-step RT-PCR, U.S. Food and Drug Administration method, and Druggan-Forsythe-Iversen medium, respectively. The results clearly indicated that one-step RT-PCR could avoid the interference of residual DNA of Cronobacter in food samples and be used to specifically detect viable Cronobacter spp. for large-scale monitoring of food samples. The use of rapid and specific detection of food borne pathogens in food samples was most of importance for control and precaution of food borne diseases. In this study, one-step RT-PCR was developed for detection of Cronobacter spp. in aquatic products. A comparison of different methods for detection of Cronobacter indicated that the newly developed method could be widely used to specifically detect Cronobacter spp. in food samples.

Amplification of all 11 RNA segments of group A rotaviruses based on reverse transcription polymerase chain reaction

Group A rotaviruses (RVA) are a major cause of acute infantile gastroenteritis. The viral genome comprises 11 double-stranded RNA segments and the respective gene segments are classified into more than eight genotypes, according to the nucleotide sequence similarities. So far, it has been difficult to amplify full-length sequences of long RNA segments of rotaviruses by one-time only RT-PCR (especially in the genes for the viral proteins VP1, VP2, VP3 and VP4). In this study, a set of universal primers to amplify all 11 segments of RVA was designed by aligning the nucleotide sequences of the typical rotavirus strains. Using these primers and a high-fidelity and rapid DNA polymerase in a one-step reverse transcription polymerase chain reaction, almost the entire length of all 11 segments of the seven rotavirus strains Wa, DS-1, Hochi, 69M, WI61, M37 and SA11-S1 were accurately and rapidly amplified. In addition, all 11 segments of rotavirus obtained from a fecal specimen were successfully amplified. In conclusion, the method described here will be useful as an RVA detection system and protocol for complete analysis of the 11 genome sequences.

Effects of metoclopramide on mRNA levels of steroid 5α-reductase isozymes in prostate of adult rats

The rising incidence of prostate cancer and benign prostatic hypertrophy in the Western world is a cause of increasing public health concern. The most active androgen in the prostate is 5α-dihydrotestosterone obtained from testosterone (T) by the enzyme 5α-reductase (5α-R), expressed in the prostate as two isozymes, 5α-R1 and 5α-R2. These isozymes are involved in the growth and development of normal prostate and in the onset and progression of prostate disease. Besides androgens, prolactin (PRL) may also play a role, although it is not clear whether its effects on the prostate are in synergism with or independent of those of androgens. We previously demonstrated that sulpiride, an inductor of hyperprolactinemia, increased mRNA levels of 5α-R isozymes in prostate of adult rat. We hypothesized a possible interrelationship between PRL levels and 5α-R, although the effects of sulpiride per se cannot be ruled out. In the present study, one-step quantitative reverse transcription polymerase chain reaction coupled with laser-induced fluorescence capillary electrophoresis was used to quantify mRNA levels of both 5α-R isozymes in prostate of adult rat after administration of metoclopramide (MTC), another inductor of PRL secretion. With the administration regimens studied, MTC produced an increase in prostate weight and mRNA levels of 5α-R1 and 5α-R2 in adult rats. Given our finding that MTC per se or MTC-induced hyperprolactinemia modifies prostate disease-related parameters in animals with reduced plasma T levels, further investigation is warranted into the possibility that MTC use by aging males may increase their risk of prostate disease.

Rapid and sensitive detection of mud crab Scylla serrata reovirus by a reverse transcription loop-mediated isothermal amplification assay

Scylla serrata reovirus (SsRV) is one of the most prevalent viral pathogens of the mud crab (S. serrata). This pathogen is widespread in east China and causes severe economic losses to the nation's mud crab industry. Early detection of this pathogen is necessary for disease control and reduction of economic loss. In the present study, a reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for the rapid and sensitive detection of SsRV was developed and evaluated. The LAMP reaction mix was optimized, as were the reaction temperature (62°C) and the duration of the assay (60min). The sensitivity of the RT-LAMP assay was determined to be 0.8fg SsRV dsRNA, which was 1000-fold higher than that of a one-step reverse transcription polymerase chain reaction (RT-PCR). The RT-LAMP assay also had higher sensitivity than a one-step RT-PCR, as it identified nine more positive cases from 55 mud crabs suspected of having SsRV. No cross-reactivity was found with the DNA/RNA of other tested viruses and SsRV-negative animals. Importantly, the assay can be completed within 60min and is faster than conventional RT-PCR. In summary, the RT-LAMP assay is a simple, cost-effective, sensitive, and specific tool for the rapid detection of SsRV infection.

Molecular detection and identification of Dasheen mosaic virus infecting Amorphophallus paeoniifolius

Occurrence of various types of viral symptoms viz. mosaic, mottling, puckering, stunting and filiformy/shoestring was noticed on Elephant foot yam in India. Immunosorbent electron microscopy of infected leaf samples with Potyvirus group–specific antiserum revealed the association of flexuous Potyvirus particles. Infected leaf samples were collected from different locations in Kerala, Orissa and Andhra Pradesh; and total RNA was extracted from infected leaves. One-step reverse transcription polymerase chain reaction assay was carried out using Potyvirus group–specific primers and an amplified product of 327 and 719 bp were obtained. Sequence analysis of nucleic acid and deduced amino acid sequences with the already available Potyvirus sequences in Genbank showed 91% and 97% similarity with Dasheen mosaic virus (DsMV) isolate DeSLK2 (accession Number AJ305434) at nucleic acid and amino acid level respectively. Comparison of 3′UTR region using universal primers MJ1 and M4T also confirmed that the virus under study is DsMV and is closely related to DeSLK2 isolate. This is the first molecular level detection of the virus infecting Amorphophallus paeoniifolius in India.

Development of one-step SYBR Green real-time RT-PCR for quantifying bovine viral diarrhea virus type-1 and its comparison with conventional RT-PCR

BackgroundBovine viral diarrhea virus (BVDV) is a worldwide pathogen in cattle and acts as a surrogate model for hepatitis C virus (HCV). One-step real-time fluorogenic quantitative reverse transcription polymerase chain reaction (RT-PCR) assay based on SYBR Green I dye has not been established for BVDV detection. This study aims to develop a quantitative one-step RT-PCR assay to detect BVDV type-1 in cell culture.ResultsOne-step quantitative SYBR Green I RT-PCR was developed by amplifying cDNA template from viral RNA and using in vitro transcribed BVDV RNA to establish a standard curve. The assay had a detection limit as low as 100 copies/ml of BVDV RNA, a reaction efficiency of 103.2%, a correlation coefficient (R2) of 0.995, and a maximum intra-assay CV of 2.63%. It was 10-fold more sensitive than conventional RT-PCR and can quantitatively detect BVDV RNA levels from 10-fold serial dilutions of titrated viruses containing a titer from 10-1 to 10-5 TCID50, without non-specific amplification. Melting curve analysis showed no primer-dimers and non-specific products.ConclusionsThe one-step SYBR Green I RT-PCR is specific, sensitive and reproducible for the quantification of BVDV in cell culture. This one-step SYBR Green I RT-PCR strategy may be further optimized as a reliable assay for diagnosing and monitoring BVDV infection in animals. It may also be applied to evaluate candidate agents against HCV using BVDV cell culture model.

Avian Influenza Survey in Migrating Waterfowl in Sonora, Mexico

A two-year survey was carried out on the occurrence of avian influenza in migrating birds in two estuaries of the Mexican state of Sonora, which is located within the Pacific flyway. Cloacal and oropharyngeal swabs were collected from 1262 birds, including 20 aquatic bird species from the Moroncarit and Tobari estuaries in Sonora, Mexico. Samples were tested for type A influenza (M), H5 Eurasian and North American subtypes (H5EA and H5NA respectively) and the H7 North American subtype (H7NA). Gene detection was determined by one-step real-time reverse transcription polymerase chain reaction (RRT-PCR). The results revealed that neither the highly pathogenic avian influenza virus H5 of Eurasian lineage nor H7NA were detected. The overall prevalence of avian influenza type A (M-positive) in the sampled birds was 3.6% with the vast majority in dabbling ducks (Anas species). Samples from two birds, one from a Redhead (Aythya americana) and another from a Northern Shoveler (Anas clypeata), were positive for the low-pathogenic H5 avian influenza virus of North American lineage. These findings represented documented evidence of the occurrence of avian influenza in wintering birds in the Mexican wetlands. This type of study contributes to the understanding of how viruses spread to new regions of North America and highlights the importance of surveillance for the early detection and control of potentially pathogenic strains, which could affect animal and human health.