Multiplex Reverse transcription-PCR Assay Research Articles

Development and Clinical Application of a Molecular Assay for Four Common Porcine Enteroviruses

Porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and porcine rotavirus-A (PoRVA) are the four main pathogens that cause viral diarrhea in pigs, and they often occur in mixed infections, which are difficult to distinguish only according to clinical symptoms. Here, we developed a multiplex TaqMan-probe-based real-time RT-PCR method for the simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA for the first time. The specific primers and probes were designed for the M protein gene of PEDV, N protein gene of TGEV, N protein gene of PDCoV, and VP7 protein gene of PoRVA, and corresponding recombinant plasmids were constructed. The method showed extreme specificity, high sensitivity, and excellent repeatability; the limit of detection (LOD) can reach as low as 2.18 × 102 copies/μL in multiplex real-time RT-PCR assay. A total of 97 clinical samples were used to compare the results of the conventional reverse transcription PCR (RT-PCR) and this multiplex real-time RT-PCR for PEDV, TGEV, PDCoV, and PoRVA detection, and the results were 100% consistent. Subsequently, five randomly selected clinical samples that tested positive were sent for DNA sequencing verification, and the sequencing results showed consistency with the detection results of the conventional RT-PCR and our developed method in this study. In summary, this study developed a multiplex real-time RT-PCR method for simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA, and the results of this study can provide technical means for the differential diagnosis and epidemiological investigation of these four porcine viral diarrheic diseases.

Detection of Newcastle disease virus and H5-subtype Influenza virus in swiftlet houses by Multiplex reverse transcription PCR assay

The purpose of this study was to investigate the presence of Avian paramyxovirus 1 (APMV-1), also known as Newcastle disease virus (NDV), and Avian influenza type A, especially H5 subtype (AIV-H5) in swiftlet houses and swiftlet nest by multiplex RT-PCR (mRT-PCR). The assay used two specific primer pairs designed to detect the conserved sequence of the F gene of NDV and the HA gene of the AIV-H5, with product sizes of 282 bp and 420 bp, respectively. The mRT-PCR was established with detection limit of 25 copies/reaction for each target virus. The thermal cycle was optimized as follows: cDNA synthesis at 45ºC for 20 min, an initial denaturation at 95ºC for 5 min, followed by 35 cycles of amplification encompassing denaturation at 95ºC for 30 sec, annealing at 58ºC for 30 sec, and extension at 72ºC for 45 sec, ending by a final extension step at 72ºC for 7 min. Eighty-eight field samples including feces and swabs of the nest surface were examined and all samples were confirmed to be negative for these two viruses. The results of this study indicated that the swiftlet nests and the environment of swiftlet houses were not contaminated with NDV or AIV-H5 viruses. Moreover, the established mRT-PCR protocol had good specificity, detection limit, and can apply for routine veterinary diagnosis.

Precise and comprehensive determination of multiple body fluids by applying statistical cutoff values to a multiplex reverse transcription-PCR and capillary electrophoresis procedure for forensic purposes

Body fluid identification from crime scene evidence is an essential procedure in forensic investigations. Among various procedures, multiplex reverse transcription PCR assays have a clear advantage over conventional methods because different types of body fluids can be analyzed simultaneously. For more precise, comprehensive, and objective identification of forensically relevant body fluids, 15 target genes for blood, saliva, semen, vaginal fluid, and nasal secretion were selected; their primers were re-designed and multiplex PCR conditions were optimized to prioritize specificity for those body fluids. Multiple amplicons were separated and determined by the SeqStudio Genetic Analyzer with an all-in-one and easy-to-use cartridge. Then, the cutoff value was set for each marker to eliminate the detection of slight amplification in non-targeted body fluids. As a result, the targeted body fluid specificities of the developed procedure were drastically improved. Although successful determination of the target gene depends on sample condition and marker sensitivity, our procedure was applicable for the precise determination of body fluids in mixed body fluid stains, aged samples, and various mock casework samples. Therefore, it could be a powerful and convenient tool for the precise identification of multiple body fluids in forensic laboratories.

POCT Detection of 14 Respiratory Viruses Using Multiplex RT-PCR

Over the past 6 years, acute respiratory infections have constituted an average of more than 70,000 cases in South Korea. It results in a high mortality rate in infants and the elderly with weak immunity. There are several types of respiratory viruses that invade the human respiratory tract and cause infectious disease. Reverse transcription PCR (RT-PCR) is mainly used for respiratory virus detection owing to its high sensitivity and reproducibility. In response, a multiplex real-time RT-PCR (rRT-PCR) assay was developed for the detection of influenza A and B viruses, parainfluenza viruses 1–4 (PIV1-4), human metapneumovirus, adenovirus, human rhinovirus, respiratory syncytial virus (RSV), and SARS-CoV-2. Detection ability of RT-PCR assay was confirmed by applying it to a portable device capable of point-of-care testing (POCT). Amplicons were synthesized using primer pairs and probe sets designed for each target virus, and a standard curve was constructed to confirm the limit of detection. An experiment using nasopharyngeal swab samples was conducted to understand the field applicability of the rRT-PCR assay. Detection was confirmed in most samples. This study demonstrated that rapid and accurate detection results can be obtained using the multiplex rRT-PCR based POC test, and that it is possible to detect 14 types of respiratory viruses that are generally difficult to distinguish at the same time, enabling timely treatment. Furthermore, we expect that the portable PCR device can significantly reduce the processing procedure of clinical samples before testing, which is the main disadvantage of common RT-PCR tests and can help reduce costs.

Detection and differentiation of dengue virus serotypes by one-step multiplex reverse transcription PCR assays

Detection and differentiation of dengue virus serotypes by one-step multiplex reverse transcription PCR assays

Molecular epidemiological study of adenovirus causing acute respiratory infection in children in Hebei Province

Objective To analyze the molecular epidemiology of adenovirus (ADV) causing acute respiratory diseases and to investigate the mixed infection of ADV and other respiratory pathogens in Hebei Province. Methods Sputum samples were collected from inpatient children with acute respiratory diseases at Children′s Hospital of Hebei Province between June 2017 and May 2018. Multiplex reverse transcription PCR assay was used to detecte 13 kinds of respiratory pathogens. Nested PCR was performed to amplify ADV hexon gene and the amplified products were then sequenced. Results A total of 353 ADV-positive specimens were detected in 8 839 specimens with a positive rate of 3.99%. Significant difference in the positive rate of ADV was not observed between male and female patients (χ2=0.000 3, P=0.99), but found among different age groups (χ2=115.69, P<0.001). All isolated ADV strains belonged to 11 serotypes, which were type 1 (16.15%, 57/353), type 2 (35.98%, 127/353), type 3 (21.25%, 75/353), type 4 (1.13%, 4/353), type 5 (11.33%, 40/353), type 6 (3.97%, 14/353), type 7 (8.22%, 29/353), type 31 (0.28%, 1/353), type 41 (0.28%, 1/353), type 55 (0.28%, 1/353) and type 57 (1.13%, 4/353). Among the 353 ADV-positive specimens, 259 were mixed infections mainly caused by ADV and human rhinovirus (35.52%). ADV and respiratory syncytial virus co-infections accounted for 12.74% and 33.20% of the mixed infections involved three or more pathogens. ADV could be detected throughout the year, especially in September and April to May. The predominant serotypes were types 1, 2 and 3. The average ages of the two groups of ADV infection alone and ADV mixed infection were (27.56±24.67) months and (21.33 ±20.28) months, respectively, and the difference between them was statistically significant (P=0.037). The incidence of ADV 2 infection alone was 25.77% (25/97), which was lower than that of ADV 2-involved mixed infection [39.84% (102/256), χ2=6.05, P=0.014]. However, the rate of ADV 7 infection alone was significantly higher than that of ADV 7-involved mixed infection [16.49% 16/97) vs 5.08% (13/256), χ2=6.05, P<0.001]. Conclusion ADV 1, ADV 2 and ADV 3 were the predominant serotypes circulating in Hebei Province from June 2017 to May 2018, especially in September and April to May. The younger the patients were, the higher the incidence would be. ADV 2 was prone to cause mixed infections with other respiratory pathogens, while ADV 7 was less common in mixed infections. Younger patients were more susceptible to mixed infections. The most common co-infection was caused by ADV and human rhinovirus. Key words: Adenovirus; Children; Molecular epidemiology; Mixed infection

A multiplex reverse transcription PCR assay for simultaneous detection of six main RNA viruses in tomato plants

Tomato virus diseases occur all around the world, causing serious yield losses. To detect these viruses quickly and provide a basis for disease control, a multiplex reverse transcription polymerase chain reaction system was established for simultaneous detection of Tobacco mosaic virus (TMV), Cucumber mosaic virus (CMV), Tomato spotted wilt virus (TSWV), Tomato chlorosis virus (ToCV), Potato virus Y (PVY) and Potato virus X (PVX) in tomato plants, with 6 pairs of specific primers being designed based on the coat protein (CP) genes of these viruses. Transcriptional elongation factor-1α (EF-1α) from tomato was added to the multiplex RT-PCR reaction system to prevent false negatives. The concentration of the primers, annealing temperature, annealing time, extension time and amplification cycles were optimized. Expected fragments of 159 bp (ToCV), 262 bp (PVY), 362 bp (EF-1α), 430 bp (TMV), 500 bp (TSWV), 600 bp (CMV) and 705 bp (PVX) were amplified by this multiplex RT-PCR system, and their origin was confirmed by DNA sequencing. This method will have a wide application in virus detection of field samples.

Development of a multiplex reverse transcription-PCR assay for simultaneous detection of pepper viruses

The aim of the present study was to establish a fourplex RT-PCR method for examining the infecting peppers to improve the efficiency of pepper virus detection, which includes Tobacco mosaic virus (TMV), Cucumber mosaic virus (CMV), Broad bean wilt virus- 2 (BBWV-2) and Potato virus Y (PVY). According to the genome sequences of TMV, CMV, BBWV-2 and PVY published by GenBank, four specific pairs of primers were designed to verify the specificity and sensitivity of detection system by simplex and multiplex RT-PCR method. In addition, using set multiplex RT-PCR method pepper plant samples of two geographic locations in China were tested and verified by simplex RT-PCR. The anticipated amplicon sizes of four primer pairs targeting TMV, CMV, BBWV-2 and PVY in both simplex and multiplex RT-PCR were 237 bp, 323 bp, 480 bp and 1057 bp, respectively, and established fourplex RT-PCR system was able to check out all sorts of viruses accurately from the pepper leaves of two geographic locations in China, which was 37.21%, 81.4%, 23.26%, and 2.33% respectively, and two or more mixed infections viruses sample accounted for 48.83% of the pepper samples. The research results show a detection technique of multiplex RT-PCR method for major peppers' viruses, which is a rapid, sensitive and reliable method and examines CMV, TMV, PVY and BBWV-2.

Potential Point-of-Care Testing for Dengue Virus in the Field.

The four serotypes of dengue virus (DENV) cause one of the most important and rapidly emerging mosquito-borne viral diseases in humans. Of the currently available diagnostic tests for dengue, the reverse transcription-PCR (RT-PCR) assay is the most sensitive and specific, and so it is commonly used as the gold standard. However, the requirement of a sophisticated and expensive thermal cycler makes it very difficult to use as a point-of-care diagnostic test in resource-limited regions where dengue is endemic. Tsai et al. (J Clin Microbiol 56:e01865-17, 2018, https://doi.org/10.1128/JCM.01865-17) report the analytical and clinical performances of a reverse transcription-insulated isothermal PCR (RT-iiPCR) assay with a portable nucleic acid analyzer for rapid detection of the four DENV serotypes; its reproducibility and complete agreement on clinical samples with the multiplex RT-PCR assay developed by the Centers for Disease Control and Prevention suggest that the dengue RT-iiPCR is a potential point-of-care test. Compared with other DENV RNA detection methods, the unique isothermal PCR design of RT-iiPCR, together with further improvements, would represent a promising new type of field-deployable diagnostic test for dengue.

Clinical evaluation of a new single-tube multiplex reverse transcription PCR assay for simultaneous detection of 11 respiratory viruses, Mycoplasma pneumoniae and Chlamydia in hospitalized children with acute respiratory infections

Respiratory Pathogen 13 Detection Kit (13× kit) is able to simultaneously detect 11 respiratory viruses, Mycoplasma pneumoniae (MP) and Chlamydia in a single reaction. Using 572 Nasopharyngeal aspirates collected from hospitalized children, the clinical performance of 13× kit for detecting 11 respiratory viruses was evaluated in comparison with a routinely used 2-tube multiplex reverse transcription PCR assay (2-tube assay) at provincial Centers for Disease Control and Prevention in China. The clinical performance of 13× kit for detecting MP and Chlamydia was evaluated by commercial real-time quantitative PCR (qPCR) kits or sequencing. For tested viruses, the assay concordance was 95.98% and the kappa coefficient was 0.89. All the MP and Chlamydia positive samples detected by 13× kit were confirmed as true positives. The utilization of the 13× kit in clinical settings will be helpful for doctors to assess clinical outcome according to virus type or multiple infections, and to limit the use of antibiotics.

180-Nucleotide Duplication in the G Gene of Human metapneumovirus A2b Subgroup Strains Circulating in Yokohama City, Japan, since 2014.

Human metapneumovirus (HMPV), a member of the family Paramyxoviridae, was first isolated in 2001. Seroepidemiological studies have shown that HMPV has been a major etiological agent of acute respiratory infections in humans for more than 50 years. Molecular epidemiological, genetic, and antigenetic evolutionary studies of HMPV will strengthen our understanding of the epidemic behavior of the virus and provide valuable insight for the control of HMPV and the development of vaccines and antiviral drugs against HMPV infection. In this study, the nucleotide sequence of and genetic variations in the G gene were analyzed in HMPV strains prevalent in Yokohama City, in the Kanto area, Japan, between January 2013 and June 2016. As a part of the National Epidemiological Surveillance of Infectious Diseases, Japan, 1308 clinical specimens (throat swabs, nasal swabs, nasal secretions, and nasal aspirate fluids) collected at 24 hospitals or clinics in Yokohama City were screened for 15 major respiratory viruses with a multiplex reverse transcription–PCR assay. HMPV was detected in 91 specimens, accounting for 7.0% of the total specimens, and the nucleotide sequences of the G genes of 84 HMPV strains were determined. Among these 84 strains, 6, 43, 10, and 25 strains were classified into subgroups A2a, A2b, B1, and B2, respectively. Approximately half the HMPV A2b subgroup strains detected since 2014 had a 180-nucleotide duplication (180nt-dup) in the G gene and clustered on a phylogenic tree with four classical 180nt-dup-lacking HMPV A2b strains prevalent between 2014 and 2015. The 180nt-dup causes a 60-amino-acid duplication (60aa-dup) in the G protein, creating 23–25 additional potential acceptor sites for O-linked sugars. Our data suggest that 180nt-dup occurred between 2011 and 2013 and that HMPV A2b strains with 180nt-dup (A2b180nt-dup HMPV) became major epidemic strains within 3 years. The detailed mechanism by which the A2b180nt-dup HMPV strains gained an advantage that allowed their efficient spread in the community and the effects of 60aa-dup on HMPV virulence must be clarified.

Investigation of viruses infecting rice in southern China using a multiplex RT-PCR assay

Rice black streaked dwarf virus (RBSDV), southern rice black streaked dwarf virus (SRBSDV), rice ragged stunt virus (RRSV) and rice gall dwarf virus (RGDV) are common pathogens that affect rice in eastern and southeastern Asia. They are transmitted by the white-backed planthopper, brown planthopper, leafhopper and small brown planthopper, respectively, and require different control strategies. Although rice plants develop characteristic symptoms when infected by each virus, infected plants may also exhibit similar symptoms, which can hinder accurate symptom-based diagnoses. Thus, a one-step multiplex reverse transcription-PCR assay was developed for the simultaneous detection of the four viruses. The amplification products in singly or co-infected plants were easily distinguished during agarose gel electrophoresis. The optimized multiplex reverse transcription-PCR method was used to analyze 582 field samples collected from southern China between 2013 and 2015. RGDV was the most common virus, detected in ∼36.1% of the samples, while RRSV, SRBSDV, and RBSDV were detected in ∼34.0%, ∼30.1%, and ∼0.5% of the samples, respectively. There were also differences in the geographical distributions of the four viruses. RRSV mostly occurred in southern Hainan, RGDV was mainly distributed in southwestern and northeastern Guangdong, SRBSDV was detected across southern China, and RBSDV was detected only in the northern parts of southern China.

A multiple RT-PCR assay for simultaneous detection and differentiation of latent viruses and apscarviroids in apple trees

Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV), and Apple stem pitting virus (ASPV) are three latent viruses frequently occurring in apple trees worldwide. In field orchards, these viruses are frequently found in a mixed infection with viroids in the genus Apscarviroid, including Apple scar skin viroid, and Apple dimple fruit viroid. Together these viruses and viroids could cause serious damage to apple fruit production worldwide. Rapid and efficient detection methods are pivotal to identify and select the virus-free propagation material for healthy apple orchard management. In this study a multiplex Reverse Transcription-PCR (RT-PCR) was developed and optimized for simultaneous detection and differentiation of the three latent viruses and apscarviroids. With newly designed specific primers for ACLSV, ASGV, APSV, and EF-1α (as an internal control), and a pair of degenerate primers for apscarviroids, optimized parameters for multiplex RT-PCR were determined. The resulting PCR products from each target virus and viroid could be easily identified because their product sizes differ by at least a 100bp. The multiplex RT-PCR method is expected to detect different variants of the viruses as the test results showed that a variety of isolates from different regions in China gave positive results. To the best of our knowledge, this multiplex RT-PCR assay is the first to simultaneously detect multiple viruses and viroids infecting apple trees in a single reaction tube. This assay, therefore, offers a useful tool for routine certification and quarantine programs.

Development of a multiplex reverse transcription-PCR assay for simultaneous detection of garlic viruses

A preliminary screening for garlic viruses in garlic plants in Hunan, China, using existing monoplex (simplex) reverse transcription-polymerase chain reaction (RT-PCR) procedures detected four viruses/virus groups. These viruses/virus groups were Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Shallot latent virus (SLV) and allexiviruses (e.g., garlic viruses A, B, C, D, E, X). Sequence analysis of the projected allexivirus amplicons revealed the allexivirus in the infected garlic plants was Garlic virus D (GarV-D), which shared 92–97% sequence identities with various isolates from the world. A multiplex RT-PCR (mRT-PCR) was therefore developed to simultaneously detect and differentiate the four viruses/virus groups. To achieve this, four primer pairs targeting allexiviruses, OYDV, LYSV and SLV were designed. The anticipated amplicon sizes are 183 bp (allexiviruses), 265 bp (OYDV), 404 bp (LYSV) and 592 bp (SLV), respectively. All primer pairs produced virus-specific fragments in both simplex and multiplex formats, thus confirming the efficacy of the newly developed mRT-PCR for detection of these viruses. The mRT-PCR further was evaluated by applying it to garlic plant samples collected in two geographic locations in Hunan. Allexiviruses, OYDV, LYSV and SLV were detected in 50.9, 40.3, 28.3 and 58.5% of leaf samples, respectively; and mixed infections with two or more viruses accounted for 54% of the garlic samples. The results obtained by mRT-PCR were confirmed by simplex RT-PCR assays. In conclusion, this newly developed mRT-PCR provides a rapid, sensitive and reliable method for the detection and identification of major garlic viruses.

Viral gastroenteritis in children in Colorado 2006-2009.

Acute gastroenteritis accounts for a significant burden of medically attended illness in children under the age of five. For this study, four multiplex reverse transcription PCR assays were used to determine the incidence of adenovirus, astrovirus, coronavirus, norovirus GI and GII, rotavirus, and sapovirus in stool samples submitted for viral electron microscopy (EM) to the Children's Hospital Colorado. Of 1105 stool samples available, viral RNA/DNA was detected in 247 (26.2%) of 941 pediatric samples (median age = 2.97 years, 54% male) with 28 (3.0%) positive for more than one virus. Adenovirus, astrovirus, norovirus GI, norovirus GII, rotavirus, and sapovirus were detected in 95 (10.0%), 33 (3.5%), 8 (0.9%), 90 (9.6%), 49 (5.2%), and 2 (0.2%) of the pediatric samples, respectively. No coronaviruses were identified. Sequencing of norovirus positive samples indicated an outbreak of norovirus strain GII.4 in 2006 with evidence of numerous circulating strains. Multiple samples from the same immunocompromised patients demonstrated symptomatic shedding of norovirus for up to 32 weeks and astrovirus for 12 weeks. RT‐PCR detected 99 of 111 (89%) adenovirus‐positive samples versus 12 (11%) by EM, and 186 of 192 (97%) sapovirus/astrovirus/norovirus‐positive samples versus 21 (11%) by EM. Noroviruses and adenoviruses are common causes of gastroenteritis in children. Immunocompromised patients can be infected with multiple viruses and shed viruses in their stools for prolonged periods. This data support the superiority of RT‐PCR compared to EM for diagnosis of viral gastroenteritis. J. Med. Virol. 87:931–939, 2015. © 2015 Wiley Periodicals, Inc.

Sensitive detection and discrimination method for studying multiple infections of five major plant viruses infecting ornamental plants in nursery environments

Tobacco mosaic virus (TMV), Hosta virus X (HVX), Cucumber mosaic virus (CMV), Tomato spotted wilt virus (TSWV) and Impatiens necrotic spot virus (INSV) are a few of the major viruses that infect ornamental and nursery plants. These viruses cause significant losses that impact growers and the ornamental industry. Often, a single ornamental plant is co-infected by more than one virus, which makes identification and discrimination of these viruses a difficult task, thus creating delays and limiting regulatory measures for effective quarantine. The aim of this study is to develop a sensitive, rapid, economic, and reliable multiplex Reverse Transcription PCR (RT-PCR) for simultaneous detection and discrimination of these five viruses. Specific PCR primers were designed using the consensus sequences of corresponding capsid protein (CP) genes of HVX and CMV, the nucleocapsid protein (NP) genes of TSWV and INSV, and the movement protein (MP) and CP genes of TMV. The primers were validated in vitro using single and multiplex RT-PCR assays. The detection limit of each primer set in multiplex RT-PCR was 100 fg (TMV), 1 fg (HVX), 10 fg (CMV), 10 pg (TSWV) and 10 pg (INSV). Forty-six infected nursery samples collected from different locations in the USA were screened for virus infections using this multiplex RT-PCR. The multiplex RT-PCR has a potential for its application in routine diagnostics, quarantine, and epidemiological studies. The developed method is reliable, sensitive, and economic for testing a wide range of ornamental and nursery plants for detection of these viruses.

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.

A Two-Tube Multiplex Reverse Transcription PCR Assay for Simultaneous Detection of Viral and Bacterial Pathogens of Infectious Diarrhea

Diarrhea caused by viral and bacterial infections is a major health problem in developing countries. The purpose of this study is to develop a two-tube multiplex PCR assay using automatic electrophoresis for simultaneous detection of 13 diarrhea-causative viruses or bacteria, with an intended application in provincial Centers for Diseases Control and Prevention, China. The assay was designed to detect rotavirus A, norovirus genogroups GI and GII, human astrovirus, enteric adenoviruses, and human bocavirus (tube 1), and Salmonella, Vibrio parahaemolyticus, diarrheagenic Escherichia coli, Campylobacter jejuni, Shigella, Yersinia, and Vibrio cholera (tube 2). The analytical specificity was examined with positive controls for each pathogen. The analytical sensitivity was evaluated by performing the assay on serial tenfold dilutions of in vitro transcribed RNA, recombinant plasmids, or bacterial culture. A total of 122 stool samples were tested by this two-tube assay and the results were compared with those obtained from reference methods. The two-tube assay achieved a sensitivity of 20–200 copies for a single virus and 102-103 CFU/mL for bacteria. The clinical performance demonstrated that the two-tube assay had comparable sensitivity and specificity to those of reference methods. In conclusion, the two-tube assay is a rapid, cost-effective, sensitive, specific, and high throughput method for the simultaneous detection of enteric bacteria and virus.

Application of multiplex nested RT- PCR assay for screening the fusion genes in acute myeloid leukemia and its clinical significance

To investigate the clinical value of multiplex nested reverse transcription PCR (RT-nPCR) in screening acute myeloid leukemia(AML)fusion genes. A novel multiplex RT-nPCR assay was developed to detect 16 AML-related fusion genes (AML1-EVI1, AML1-ETO, AML1-MDS1, AML1-MTG16, MLL-AF9, MLL-AF6, MLL-AF10, MLL-ENL, MLL-MLL, PML-RARα, PLZFRARα, NPM1-RARα, CBFB-MYH11, DEK-CAN, SET-CAN and TLS-ERG) according to 2008 WHO classification of AML. The chromosome reciprocal translocations of 356 AML cases were detected by multiplex RT-nPCR and karyotyping. The positive samples were further confirmed by split- out PCR and FISH. The fusion genes were detected in 172 patients with the positive detection rate of 48.31%(172/356), which was higher than that of karyotyping (31.46%) (χ²=70.314, P<0.01). Multiplex RT-nPCR is superior to karyotyping and FISH in identifying the rare, cryptic chromosome translocation (χ²=96.074, P<0.01). The multiplex RT-nPCR used in this study can quickly, effectively and accurately screen the fusion genes in AML patients, which can provide important evidence for assessing diagnosis and treatment, and also provide necessary information for minimal residual disease (MRD) and prognosis.

The 2009 pandemic influenza A(H1N1) coincides with changes in the epidemiology of other viral pathogens causing acute respiratory tract infections in children

BackgroundIn Germany, the outbreak of the novel pandemic 2009 influenza A(H1N1) virus A(H1N1)pdm09 caused a wave of high activity between November 2009 and January 2011. The aim of this study was to investigate the prevalence of 19 respiratory pathogens in children hospitalized for lower respiratory tract infections during the winter influenza seasons of 2009/2010 and 2010/2011 and to observe a possible impact of influenza A(H1N1)pdm09 on the epidemiology of other epidemic viruses.Materials and methods Specimens were nasopharyngeal aspirates which had been collected from children admitted to the participating hospitals in the area of Mainz, Wiesbaden, and Kiel, Germany, with acute community-acquired lower respiratory tract infections. The specimens were subjected to a previously described multiplex reverse transcription PCR assay to detect the following microorganisms: enterovirus, influenza virus types A and B, respiratory syncytial virus (RSV), parainfluenzavirus types 1–4, adenovirus, Mycoplasma pneumoniae, Chlamydophila pneumoniae, rhinovirus, human metapneumovirus (hMPV), coronavirus OC43 and 229E, influenza A(H1N1)pdm09, Bordetella pertussis, Bordetella parapertussis, and Legionella pneumophila.Results A total of 3,998 clinical specimens were collected from July 2009 to March 2011, of which 296 were positive for A(H1N1)pdm09. An epidemic of seasonal influenza A or B was not observed in the 2009/2010 season, but a minor epidemic of seasonal influenza B was observed in January/February 2011. Influenza A(H1N1)pdm09 coincided with the absence of the seasonal influenza A of former years. The RSV and hMPV epidemics of 2009/2010 erupted several weeks later than expected based on data collected in the PID-ARI-Network during the past 10 years, whereas in the 2010/2011 influenza season they occurred as expected.Conclusions The emergence of the novel influenza A(H1N1)pdm09 virus may have been influenced the epidemiology of other epidemic viruses, such as the RSV and hMPV. No epidemic of seasonal influenza was observed in the 2009/2010 influenza season.