Multiplex Reverse Transcriptase-polymerase Chain Reaction Assay Research Articles

Detection of dengue virus serotypes by single-tube multiplex RT-PCR and multiplex real-time PCR assay

BackgroundAll four dengue serotypes cause infection, with one of them predominantly reported from a particular geographical region. Coinfection by more than one serotype is reported from hyperendemic regions. These coinfections are clinically more severe than infection with a single serotype. This study was carried out to detect the predominant dengue serotype and presence of coinfections. MethodsAcute-phase serum samples of patients suffering from dengue infection were collected. They were screened for the presence of IgM, IgG and NS1Ag by a rapid test. Conventional multiplex reverse transcriptase polymerase chain reaction (RT-PCR) and multiplex real-time RT-PCR assays were carried out for detection and serotyping of the dengue virus. ResultsA total of 196 samples were positive by the rapid card test. Of these, 139 were NS1Ag positive, 40 were positive only for IgM, 5 were positive only for IgG and 12 samples were positive for different combinations of antigen and antibodies. All four serotypes were detected in these samples by PCR. DENV-3 was found to be most common circulating serotype. A total of 22 cases were found to have coinfection with more than one dengue serotypes. Samples having only antibodies and no antigen on rapid card test were also positive for virus by PCR. ConclusionPrevalence of dengue co-infections is increasing. Moreover, it is important to screen for dengue virus in those samples also which do not show NS1Ag on rapid tests and have either one or both the antibodies. Real-time multiplex RT-PCR is found to be more sensitive in detecting coinfection than conventional multiplex RT-PCR.

English

Watermelon plants can be naturally infected by several viruses in single or mixed infections, of which the diagnosis is difficult and require specific techniques. This study aims to detect and to verify the presence of Cucumber mosaic virus (CMV), Papaya ringspot virus type W (PRSV-W), Watermelon mosaic virus (WMV), Zucchini lethal chlorosis virus (ZLCV), Zucchini yellow mosaic virus (ZYMV), and the main cucurbit viruses in Brazil using multiplex reverse transcriptase polymerase chain reaction (RT-PCR) assay. Oligonucleotides were designed towards the conserved regions of the virus genomes. In the duplex-PCR, it was possible to detect all the virus combinations, except ZLCV with ZYMV. The amplified product sizes were 644 bp (CMV), 535 bp (WMV-2), 398 bp (PRSV-W), 244 bp (ZLCV), and 214 bp (ZYMV). To test the efficacy of the methodology, we analyzed plants with virus symptoms from four municipalities in the state of Tocantins, located at Brazilian Cerrado. Mixed infections were detected in 80% of samples in all the municipalities. The multiplex RT-PCR assay can be used to detect and differentiate watermelon viruses that affect crops in the state of Tocantins.   Key words: Cucumovirus, multiplex RT-PCR, Orthotospovirus, potyvirus, watermelon.

Respiratory Syncytial Virus Outbreak in the Basic Military Training Camp of the Republic of Korea Air Force

Objectives:An outbreak of acute febrile illness occurred in the Republic of Korea Air Force boot camp from May to July 2011. An epidemiological investigation of the causative agent, which was of a highly infective nature, was conducted.Methods:Throat swabs were carried out and a multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) assay was performed to identify possible causative factors.Results:The mean age of patients who had febrile illness during the study period was 20.24 years. The multiplex RT-PCR assay identified respiratory syncytial virus (RSV) as the causative agent. The main symptoms were sore throat (76.0%), sputum (72.8%), cough (72.1%), tonsillar hypertrophy (67.9%), and rhinorrhea (55.9%). The mean temperature was 38.75°C and the attack rate among the recruits was 15.7% (588 out of 3750 recruits), while the mean duration of fever was 2.3 days. The prognosis was generally favorable with supportive care but recurrent fever occurred in 10.1% of the patients within a month.Conclusions:This is the first epidemiological study of an RSV outbreak that developed in a healthy young adult group. In the event of an outbreak of an acute febrile illness of a highly infective nature in facilities used by a young adult group, RSV should be considered among the possible causative agents.

Diagnostic Utility of a Multiplex RT-PCR Assay in Detecting Fusion Transcripts From Recurrent Genetic Abnormalities of Acute Leukemia by WHO 2008 Classification

Fusion transcripts (FT) from chromosomal rearrangements are key culprits in acute leukemia, with genotype-phenotype correlations including prognostic implications. Here, we report our experience of a commercially available platform utilizing multiplex reverse-transcriptase polymerase chain reaction (RT-PCR), HemaVision, in 309 consecutive patients with acute leukemia. A total of 108 patients (35%) were diagnosed as having acute leukemia with recurrent genetic abnormalities by the World Health Organization 2008 classification. The multiplex RT-PCR platform, detected 12 different FT in 92 (85.2%; 92/108), with a 99% concordance rate with conventional cytogenetics/fluorescence in situ hybridization. Additional information obtained from the multiplex RT-PCR assay included transcript heterogeneity and novel splice variants of FT. In addition, the RT-PCR assay targeting specific FT could be used for monitoring minimal residual disease. HemaVision is a robust diagnostic platform in detecting FT in routine clinical laboratories both at initial diagnosis and for disease monitoring.

T-DNA integration site analysis in transformed barley ( Hordeum vulgare L.) by Tail-PCR

A multiplex reverse transcriptase polymerase chain reaction (MRT-PCR) assay was developed and applied to the detection of Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV) associated with field and hatchery outbreaks of white tail disease (WTD) in M. rosenbergii. Primers targeted regions of the capsid protein genes of the two viruses and produced amplicons of 1136 and 447 bp, for MrNV and XSV, respectively, with sensitivity to the level of 1 fg of total RNA for both the viruses. Assays could be completed within 7 to 9 h after samples were received. This is of great importance for epidemiological analysis and screening of large numbers of samples. MRT-PCR assay on samples collected from different hatcheries and farms of Nellore, India revealed the presence of both the viruses in all. Experimental infections produced typical clinical signs of white muscle in juveniles and mortality up to 20%. MrNV could be detected up to 1 month in surviving prawns, both by histology and RT-PCR. Sequence analysis of capsid protein gene amplicons of XSV revealed minor variations. By contrast, sequence analysis of MrNV amplicons showed no variation in amino acid sequence of the capsid protein gene.

One-Step Multiplex Reverse-Transcriptase PCR for Detecting Pandemic (H1N1) 2009 Influenza Virus

Pandemic (H1N1) 2009 influenza has spread throughout the world since April 2009 and has caused many human deaths since its first report in humans. Pandemic (H1N1) 2009 influenza virus was first identified in a Canadian pig herd in April 2009 and has been reported in more than ten countries, including Korea. We developed a one-step multiplex reverse transcriptase polymerase chain reaction (RT-PCR) assay based on the matrix gene that discriminates pandemic (H1N1) 2009 influenza virus from endemic swine influenza viruses. The sensitivity of this assay was 100 copies of in vitro-transcribed target RNA and 0.01 tissue culture infective dose (TCID(50)/ml) of virus and was as high as those of conventional influenza A virus common matrix reverse transcriptase PCR assays and real-time reverse transcriptase PCR assays (1 to 200 copies) developed for detecting pandemic (H1N1) 2009 influenza viruses from human and pig samples. This one-step multiplex RT-PCR assay would be a good tool in monitoring pandemic (H1N1) 2009 influenza virus among pig herds on a regular basis.

Establishment of a multiplex RT-PCR assay to detect different lineages of swine H1 and H3 influenza A viruses

Classical swine H1N1, emerging European avian-like H1N1 and human-like H3N2 lineages are co-circulating in the swine population in China. The reverse transcriptase polymerase chain reaction (RT-PCR) assay is an effective method for use in influenza surveillance. In this study, a multiplex RT-PCR method was developed for simultaneous identification of hemagglutinin (HA) genes derived from the three lineages of swine influenza viruses. Three primer sets were designed and aimed specifically at HA genes of these viral lineages. The specificity of the assay showed that the established methods could efficiently differentiate the HA genes of classical swine H1N1, European avian-like H1N1, and human-like H3N2 viruses while other viruses such as classical swine fever virus, porcine reproductive and respiratory syndrome virus, pseudorabies virus, and porcine circovirus type 2, could not be detected. The assay showed a sensitivity of 1 x 10(2.5) 50% egg infectious dose for each virus lineage. The comparison of the results with those obtained from the analysis of 300 swine tracheal swab samples by means of virus isolation showed a high level of agreement. This multiplex RT-PCR method provides a rapid and specific swine influenza diagnostic tool that also has the potential for investigating the epidemiology of different lineages of swine influenza virus prevalent currently in China.

The development of a mRNA multiplex RT-PCR assay for the definitive identification of body fluids

With current methodology, DNA profiling can identify an individual from a sample of biological material but it does not reveal what body fluid or tissue source the DNA profile originated from. We have developed a multiplex PCR system using messenger RNA (mRNA) that can identify blood, saliva, semen and menstrual blood in individual stains or in mixtures of body fluids. Messenger RNA transcripts specific to each type of body fluid have been identified and a multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) system developed to identify these body fluids along with three housekeeping genes. This multiplex can detect semen and seminal fluid (semen without spermatozoa present). Furthermore, we have targeted the co-isolation of RNA and DNA from the same sample and, with the RT-PCR multiplex, we can determine the type of body fluid present as well as generate a DNA profile(s) from the same stain.

Enrichment of cerebrospinal fluid samples on cell culture for enhancement of sensitivity of mumps and enterovirus detection by multiplex RT-PCR

It has been demonstrated that the detection of enteroviruses and mumps virus nucleic acid in cerebrospinal fluid (CSF) specimens improves the management of the patients with aseptic meningitis. To determine the effect of overnight enrichment of mumps and enteroviruses in CSF samples on cell culture for increasing the sensitivity of viral detection, we developed a multiplex reverse transcriptase-polymerase chain reaction (RT-PCR). CSFs were collected from 100 patients younger than 7 years. The samples were tested for the presence of enteroviruses and mumps virus by multiplex RT-PCR method. Negative samples in Multiplex RT-PCR were enriched for viral template RNAs by overnight culture of CSF samples on cells and followed by the optimized Multiplex RT-PCR. Overall, 35% of the CSF samples were positive for enteroviruses, whereas only 1% of CSF samples were positive for both viruses. After enriching in cell culture, 34% of the negative samples showed a positive polymerase chain reaction band for enteroviruses, and a 3% increase was observed for both viruses. The results showed that enrichment of viral template RNAs in cell culture can increase the sensitivity of the multiplex RT-PCR assay and provide a rapid and sensitive method for detection of viral infections.

Multiplex RT-PCR detection and sequence comparison of viruses MrNV and XSV associated with white tail disease in Macrobrachium rosenbergii

A multiplex reverse transcriptase polymerase chain reaction (MRT-PCR) assay was developed and applied to the detection of Macrobrachium rosenbergii nodavirus ( MrNV) and extra small virus (XSV) associated with field and hatchery outbreaks of white tail disease (WTD) in M. rosenbergii. Primers targeted regions of the capsid protein genes of the two viruses and produced amplicons of 1136 and 447 bp, for MrNV and XSV, respectively, with sensitivity to the level of 1 fg of total RNA for both the viruses. Assays could be completed within 7 to 9 h after samples were received. This is of great importance for epidemiological analysis and screening of large numbers of samples. MRT-PCR assay on samples collected from different hatcheries and farms of Nellore, India revealed the presence of both the viruses in all. Experimental infections produced typical clinical signs of white muscle in juveniles and mortality up to 20%. MrNV could be detected up to 1 month in surviving prawns, both by histology and RT-PCR. Sequence analysis of capsid protein gene amplicons of XSV revealed minor variations. By contrast, sequence analysis of MrNV amplicons showed no variation in amino acid sequence of the capsid protein gene.

Immunobead multiplex RT-PCR detection of carcinoembryonic genes expressing cells in the blood of colorectal cancer patients

Circulating cell detection using reverse transcriptase-polymerase chain reaction (RT-PCR) techniques has been studied as a new prognostic factor in colorectal cancer patients. With the view of enhancing detection sensitivity, we developed a new multiplex RT-PCR assay for circulating cell detection based on the expression of carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5; formerly CEA) and CEACAM7 (formerly CGM2). Between November 2002 and December 2003, 45 stage III-IV, 39 stage I-II colorectal cancer patients, 32 non-colorectal cancer patients and 41 healthy individuals were included. Positive selection using HEA-125 immunobeads was applied to blood samples before mRNA extraction, cDNA synthesis and a multiplex CEACAM5/CEACAM7 RT-PCR assay. For both CEACAM5 and CEACAM7, the limit of detection was found to be as low as 1 expressing cell in 10(6) nucleated blood cells. The multiplex RT-PCR assay was negative for the 41 healthy individuals and the 32 non-colorectal cancer patients. The test was positive in 53/84 (63%) of the colorectal cancer patients for CEACAM5 and/or CEACAM7, whereas 32/84 (38%) were positive for both markers. Colorectal cancer patients were positive for one of the two markers in 80% of cases (36/45) for stage III-IV patients (CEACAM5 73%, CEACAM7 51%) and in 44% of cases (17/39) for stage I-II patients. This multiplex RT-PCR assay with two markers proved to be more sensitive than use of a single marker in detecting circulating tumour cells. The discrepant expression of CEACAM5 and CEACAM7 may label circulating tumour cells that have different levels of differentiation and subsequent aggressive behaviour.

A novel method for the detection, quantitation, and breakpoint cluster region determination of t(15;17) fusion transcripts using a one-step real-time multiplex RT-PCR.

Individuals with acute promyelocytic leukemia (APL) usually express 1 of 3 primary hybrid transcripts associated with a t(15;17). The 3 fusion transcripts are the result of heterogeneous breakpoint cluster regions (bcr) within the promyelocytic leukemia (PML) gene and are denoted bcr1 (long), bcr2 (variant), and bcr3 (short) forms. Many researchers have shown that real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) of the involved transcript is a valuable tool for monitoring APL and its treatment. In addition, some research suggests that identification of a specific breakpoint region may be used to predict an individual's likelihood of relapse and possibly their response to all-trans retinoic acid treatment. We describe the first reported 1-step multiplex RT-PCR assay capable of t(15;17) fusion transcript real-time relative quantitation and simultaneous transcript form identification in 2 reactions. This assay uses a novel dual-probe technique to achieve what has required a laborious procedure of 2 or more reactions followed by postamplification analysis. We found a correlation of 100% in detection and breakpoint determination of the long, short, and variant forms with a breakpoint 5' to nucleotide 1709 compared with results from traditional methods.

Multiplex RT-PCR assay for the detection of major fusion transcripts in Taiwanese children with B-lineage acute lymphoblastic leukemia.

The classification of B-lineage acute lymphoblastic leukemia (ALL) by specific chromosomal translocations may have prognostic implications. Reverse transcriptase-polymerase chain reaction (RT-PCR) assay is a useful tool for the detection of fusion transcript resulting from specific chromosomal translocation of the leukemic cells. In general, fusion transcripts are determined individually, a process which is labor intensive in order to detect all major fusion transcripts. We use a multiplex RT-PCR assay to detect both the CML- and ALL-type BCR-ABL transcripts of the t(9;22), all described variants of the E2A-PBX1 transcripts of t(1;19), the MLL-AF4 transcripts of t(4;11), and all described variants of TEL-AML1 (also termed ETV6-CBFA2) of the cryptic t(12;21) in 165 leukemic samples at diagnosis. The study yielded a completely concordant result with those obtained by the individual RT-PCR assay. In this cohort of Taiwan children, the relative frequencies of the four translocations of B-lineage ALL were as following: 6% with ALL-type t(9;22)/BCR-ABL, 7% t(1;19)/E2A-PBX1, 3% t(4;11)/MLL-AF4, and 18% t(12;21)/TEL-AML1, comparable to those in the Western countries. Multiplex RT-PCR assay is an efficient, sensitive, accurate, and cost-effective diagnostic tool, which will likely improve our ability in accurately and rapidly risk-stratifying children with ALL.

API2-MALT1 Fusion Transcripts Involved in Mucosa-Associated Lymphoid Tissue Lymphoma : Multiplex RT-PCR Detection Using Formalin-Fixed Paraffin-Embedded Specimens

Malignant lymphoma of mucosa-associated lymphoid tissue (MALT) type is a distinct clinicopathological disease entity in the category of extranodal marginal zone B-cell lymphoma. Recently, we and others have shown that the API2 gene on chromosome 11 and the MALT1 gene on chromosome 18 are fused as a result of t(11;18)(q21;q21) in MALT lymphomas. Here we report a detection assay that can be used for formalin-fixed, paraffin-embedded specimens. It consists of a multiplex one-tube reverse transcriptase-polymerase chain reaction (RT-PCR) followed by three parallel multiplex nested polymerase chain reactions. Eight variants of the fusion transcripts have been reported to date. When these variants were used as positive controls, all were successfully detected. The subsequent direct sequencing confirmed the results. Using this rapid and simple method, we could detect API2-MALT1 fusion transcripts in 5 of 15 (33%) archival cases of MALT lymphoma for a frequency comparable with those of RT-PCR assays using frozen materials. The lung was the preferential anatomical site of origin of MALT lymphomas harboring API2-MALT1 fusion. No fusion transcript was detected in any of 20 high-grade B-cell lymphomas. Our multiplex RT-PCR assay, which can be used for routinely-processed paraffin samples, should serve as a useful molecular tool for clarifying the clinicopathological significance of API2-MALT1 fusion in MALT lymphoma.

A multiplex RT-PCR assay for the detection of chimeric transcripts encoded by the risk-stratifying translocations of pediatric acute lymphoblastic leukemia.

Modern therapy for pediatric acute lymphoblastic leukemia (ALL) is based on the principle of risk stratification. One of the most important laboratory features used to accurately risk stratify patients is the presence of specific chromosomal translocation within the leukemic blasts. In this paper, we describe a multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) assay for the accurate, sensitive, and rapid identification of chimeric transcripts encoded by the major risk-stratifying translocations of pediatric ALL. This assay will identify both the CML- and ALL-type BCR-ABL transcripts encoded by the t(9;22), all described variants of the E2A-PBX1 transcripts encoded by the t(1;19), the MLL-AF4 transcripts encoded by the t(4;11), and all variants of TEL-AML1 encoded by the t(12;21). In addition, we have developed a reverse dot-blot detection system as an alternative to traditional post-PCR Southern blot analysis. Application of this combined assay to the analysis of 70 leukemic samples and five cell lines resulted in a complete concordance between this multiplex assay and individual PCR reactions. The characteristics of the multiplex assay suggest that its application to routine clinical screening will significantly improve the ability of clinical laboratories to accurate risk stratify pediatric ALL patients.

Simultaneous detection of circulating prostate specific antigen (PSA)-expressing and prostate specific membrane antigen (PSM)-expressing cells by a multiplex reverse transcriptase polymerase chain reaction (RT-PCR) assay

It has yet to be determined whether the detection of prostate specific antigen (PSA)-expressing or prostate specific membrane antigen (PSM)-expressing cells in the circulation of prostate cancer patients is a more accurate predictor of clinical outcome. A method of evaluating both markers simultaneously would aid in the determination of the clinical relevance of reverse transcriptase polymerase chain reaction (RT-PCR) as a staging tool for prostate cancer. We describe the development of a multiplex RT-PCR assay that simultaneously detects the presence of both PSA-expressing cells and PSM-expressing cells, as well as a ubiquitously expressed internal control all within a single reaction. Both PSA cDNA and PSM cDNA were concurrently amplified by multiplex PCR using LNCaP mRNA as the starting template. When used as part of a nested PCR system, the multiplex RT-PCR assay identified one prostate cancer cell when placed in a background of one million cultured B lymphocytes. The multiplex assay was then applied to mRNA isolated from metastatic prostate cancer patients and from healthy male and female volunteers. While all were positive for the internal control G3PDH, three of seven prostate cancer patients were positive for both PSA and PSM expression and two more were positive for either PSA or PSM. None of the male or female volunteers were positive for either PSA or PSM. Multiplex RT-PCR allows for the amplification of both PSA and PSM cDNA within a single RT-PCR reaction, and this approach should allow a consistent comparison of the clinical utility of both PSA and PSM markers as staging tools and predictors of response to therapy.