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Objective:To select nucleic acid extraction reagents and amplification reagents by comparing the minimum detection limit, amplification efficiency, specificity, accuracy, and matching analysis with 6 nucleic acid extraction reagents of 6 novel coronavirus (2019-nCoV) nucleic acid detection reagents and provide scientific basis for clinical diagnosis and treatment.Methods:The national-standard material of 2019-nCoV nuclear acids was diluted as ths six fradient concentrations. Then, the diluted samples were analyzed by using the six kinds of agents/kits, Guangzhou Daan (DA), Beijing Jinhao (JH), Wuhan Mingde (MD), Sichuan Mike (MK), Jiangsu Shuoshi (SS) and Shanghai Zhijiang (ZJ). The minimum detection limit, amplification efficiency, accuracy, specificity and other properties of these kits were examined. The positive control levels 1, 2 (low and medium concentration) were extracted by using the six nucleic acid extraction reagents (numbered a-f) with six 2019-nCoV detective kits to detect target genes of 2019-nCoV genome, and compared between different nucleic acid extraction reagents and different nucleic acid detection reagents. Match between the different nucleic acid extraction reagents detection reagents, using two-way analysis of variance.Results:The minimum detection limit of Nucleocapsid (N) gene of DA, JH, MD, SS reagent was 7.0×10 2 copies/ml.The minimum detection limit of open reading frame 1ab (ORF1ab) gene of JH, MD, SS, MK reagent was 9.39 ×10 2 copies/ml.The minimum detection limit of envelope (E) gene of MK, ZJ reagent was 5.03×10 2 copies/ml. SS reagent N gene amplification efficiency was 89%, ORF1ab gene amplification efficiency was 90%, was the highest among six reagents.a, b, c, d extraction reagents and 6 nucleic acid detection reagents match well, But a extraction reagent was more suitable for use with SS,MK and ZJ reagents ( P<0.05), d extraction reagent was more suitable for MD,SS,DA,JH and MK nucleic acid detection reagents( P<0.05); e extraction reagent was more suitable for SS nucleic acid detection reagents( P<0.05), f extraction reagent was most suitable for DA, JH Nucleic acid detection reagents ( P<0.05); e and f reagents were not suitable for use with MK and ZJ. Conclusion:The 6 detection reagents have good performance, and the appropriate extraction reagents and detection reagents should be used in conjunction with the actual conditions of the laboratory.
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Objective: To compare and analyze 7 new coronavirus nucleic acid detection kits and 5 nucleic acid extraction methods. Methods: After extracting nucleic acids from 44 positive coronavirus clinical samples, 7 SARS-CoV-2 nucleic acid detection kits were used for RT-PCR amplification experiments to compare the positive rate and Ct value;33 new coronavirus positive clinical samples were selected to compare the acid extraction methods. Five different nucleic acid extraction methods were used to extract the samples, and then RT-PCR amplification experiments were performed to compare the positive rate and Ct value. Results: The brand A nucleic acid extraction kit had the highest positive rate and the lowest rate of missed detection;comparison of nucleic acid extraction methods showed that the manual column extraction method had the highest positive rate, followed by the magnetic bead extraction method, and the one-step extraction method had the highest missed detection rate. Conclusion: The detection capabilities of the SARS-CoV-2 detection kits are uneven, so evaluation work needs to be done before the selection of the kit. The manual column extraction method showed best extraction efficiency but took a long time. Because of the possible combination with the automatic nucleic acid extraction instrument, the magnetic bead extraction method had a high extraction efficacy, which might be suitable for use in the ex- traction of large batches of samples. Although the one-step extraction method was easily operable, the method had a high missed detection rate, so this method was not recommended for clinical use.
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Objective To study the detection of cytomegalovirus (CMV)-DNA in different kinds of blood and urine sample .Methods The CMV-DNA loads in 3 different kinds of blood sample from 52 patients and 3 different kinds of urine sample from 85 patients were detected by real-time fluorescence quantitative polymer-ase chain reaction(FQ-PCR) .The differences in CMV-DNA detection rate and virus loads were compared a-mong different kinds of blood and urine samples .Results The CMV-DNA detection rates in serum ,whole blood ,plasma and peripheral blood mononuclear cell (PBMC) from 52 patients were 48 .08％ ,71 .15％ ,57 .69％ and 69 .23％ respectively .The CMV-DNA detection rates of whole blood and PBMC were higher ,the difference was statistically significant (P<0 .05) .The quantitative results of PBMC was higher .The CMV-DNA detec-tion rates of mixed urine ,urine supernatant and urine sediment from 85 patients were 72 .94％ ,62 .35％ and 84 .71％ respectively ,the CMV-DNA detection rate of urine sediment was higher ,while the quantitative re-sults of mixed urine was higher .Conclusion The CMV-DNA detection results of blood and urine have large difference ,therefore using the same kind of sample for conducting detection has an important clinical signifi-cance in the clinical diagnosis ,treatment and monitoring of CM V infection .
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Objective@#To explore the differences among three methods of nucleic acid extraction and three kinds of real-time fluorescence quantitative PCR instrument.@*Methods@#Twenty-five respiratory virus nucleic acid and 25 enterovirus nucleic acid positive samples were with selected at random and nucleic acids were extracted by using three methods (method A, B, and C). The results among different methods were analyzed by randomized block design. 25 respiratory viral nucleic acid positive specimens and enterovirus nucleic acid positive samples were detected by using three kinds of real-time fluorescence quantitative PCR instrument (instrument A, B, and C). The results among different instruments were analyzed by randomized block design.@*Results@#There was a significant difference among three methods of nucleic acid extraction in results(χ2=42.9162, P<0.001), in which method A and C had not significant difference(Z=0.837, P=0.3816>0.05), while method A vs. B, B vs. C were significantly different(Z=7.025, P<0.001; Z=7.9, P<0.001). There was also a significant difference among three kinds of real-time fluorescence quantitative PCR instrument in results(χ2=23.773, P<0.001), in which instrument B and C had no significant difference(Z=0.75, P=0.4533>0.05), while instrument A vs. B, A vs. C were significantly different(Z=5.70, P<0.001; Z=6.45, P<0.001).@*Conclusions@#There is difference among different methods and instruments in the test results under the same condition, which call for options in practical work according to need.
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BACKGROUND: Real-time reverse transcription PCR (rRT-PCR) of sputum samples is commonly used to diagnose Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Owing to the difficulty of extracting RNA from sputum containing mucus, sputum homogenization is desirable prior to nucleic acid isolation. We determined optimal homogenization methods for isolating viral nucleic acids from sputum. METHODS: We evaluated the following three sputum-homogenization methods: proteinase K and DNase I (PK-DNase) treatment, phosphate-buffered saline (PBS) treatment, and N-acetyl-L-cysteine and sodium citrate (NALC) treatment. Sputum samples were spiked with inactivated MERS-CoV culture isolates. RNA was extracted from pretreated, spiked samples using the easyMAG system (bioMérieux, France). Extracted RNAs were then subjected to rRT-PCR for MERS-CoV diagnosis (DiaPlex Q MERS-coronavirus, SolGent, Korea). RESULTS: While analyzing 15 spiked sputum samples prepared in technical duplicate, false-negative results were obtained with five (16.7%) and four samples (13.3%), respectively, by using the PBS and NALC methods. The range of threshold cycle (Ct) values observed when detecting upE in sputum samples was 31.1-35.4 with the PK-DNase method, 34.7-39.0 with the PBS method, and 33.9-38.6 with the NALC method. Compared with the control, which were prepared by adding a one-tenth volume of 1:1,000 diluted viral culture to PBS solution, the ranges of Ct values obtained by the PBS and NALC methods differed significantly from the mean control Ct of 33.2 (both P<0.0001). CONCLUSIONS: The PK-DNase method is suitable for homogenizing sputum samples prior to RNA extraction.
Subject(s)
Humans , Acetylcysteine/chemistry , Citrates/chemistry , Coronavirus Infections/diagnosis , Deoxyribonuclease I/metabolism , Endopeptidase K/metabolism , Middle East Respiratory Syndrome Coronavirus/genetics , RNA, Viral/analysis , Real-Time Polymerase Chain Reaction , Sputum/virologyABSTRACT
BACKGROUND: Availability of an international standard will improve the standardization of quantitative PCR (qPCR) for cytomegalovirus (CMV) and Epstein-Barr virus (EBV); however, nucleic acid extraction methods may affect qPCR results. This study was designed to determine whether routine measurement of DNA concentration and purity is required in qPCR for CMV and EBV. In addition, the performance of the automated QIASymphony DSP DNA Mini kit (Qiagen, USA) and the manual QIAamp DNA Blood Mini kit (Qiagen) in extracting DNA from whole blood samples was compared. METHODS: The concentration and purity of 300 extracted DNA samples were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, USA). A total of 72 and 54 whole blood samples were tested by artus CMV and EBV qPCR (Qiagen), respectively. RESULTS: No correlation was found between DNA concentration and EBV DNA load or between DNA purity and the PCR inhibition measured by ΔCq (the difference between internal control Cq of the sample and that of the negative control). Quantification of CMV and EBV DNA using the two extraction methods showed highly similar results (rho=0.946 and 0.887, respectively). Of the 29 specimens that yielded CMV DNA by both methods, however, 8 specimens (27.6%) yielded higher CMV DNA loads with QIASymphony. CONCLUSIONS: Routine measurement of DNA concentration and purity is not necessary for qPCR of CMV and EBV. The automated QIASymphony outperformed the manual QIAamp Blood Mini kit in extracting CMV and EBV DNA from whole blood samples.
Subject(s)
Cytomegalovirus , DNA , Herpesvirus 4, Human , Polymerase Chain ReactionABSTRACT
A real-time polymerase chain reaction ( PCR ) micro total analysis system (μ-TAS ) integrated nucleic acid extraction, PCR amplification and real-time-fluorescent PCR detection on a same microfluidic chip was prepared for the fully automated and on-chip analysis of nucleic acid. The proposed method had the advantage such as low sample consumption, fast analysis and simple operation and so on. Micromachining technology was used to fabricate the anodic molds of integrated nucleic acid extraction microfluidic chip. A polydimethylsiloxane (PDMS) substrate with 3D channels was manufactured by a combination of molds and an injection molding method. The glass substrate and the chip were bonded together using a plasma treatment. The μ-TAS included a microfluidic control device whose micro fluidic velocity ( 0-10 mL/min ) could be adjusted, a TEC platform which the precision of temperature control was 0. 1℃ and a CCD detection module. The DNA of human blood was extracted by using a silica gel membrane method on the microfluidic chip. The processes of DNA extraction and detection were preset in the μ-TAS. Human blood lysate ( 20 μL ) were driven to the extraction chamber and was then washed. The fluidic drive speed was 2 mL/min. DNA and PCR reagents were mixed and then were driven into the PCR chamber. The fluidic drive speed was 1 mL/min. The GAPDH gene in extracted genome DNA was amplified by PCR and detected. The amplified product was verified by melting analysis. The results of nucleic acid extraction method on the chip were compared to those obtained using a standard manual centrifuge extraction method. The amplification curves were obvious. Ct values of the chip method were 25 . 3 and 26 . 9 . The denaturation temperature of all the melting was 89 . 9 ℃. The results validated that the chip-based method and device realized the extraction of nucleic acid, amplification and detection automatically.
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OBJECTIVE: Adequate isolation of nucleic acids from peripheral blood, fine-needle aspiration cells in stained slides, and fresh and formalin-fixed/paraffin-embedded tissues is crucial to ensure the success of molecular endocrinology techniques, especially when samples are stored for long periods, or when no other samples can be collected from patients who are lost to follow-up. Here, we evaluate several procedures to improve current methodologies for DNA (salting-out) and RNA isolation. MATERIALS AND METHODS: We used proteinase K treatment, heat shock, and other adaptations to increase the amount and quality of the material retrieved from the samples. RESULTS: We successfully isolated DNA and RNA from the samples described above, and this material was suitable for PCR, methylation profiling, real-time PCR and DNA sequencing. CONCLUSION: The techniques herein applied to isolate nucleic acids allowed further reliable molecular analyses. Arq Bras Endocrinol Metab. 2012;56(9):618-26.
OBJETIVO: O isolamento adequado de ácidos nucleicos a partir de sangue periférico, lâmina corada de punção aspirativa por agulha fina, tecido fixado em formalina e emblocado em parafina e tecido fresco é fundamental para assegurar o sucesso de técnicas aplicadas em endocrinologia molecular, principalmente quando lidamos com amostras estocadas por longos períodos ou quando há impossibilidade de nova coleta de amostra de pacientes que perderam o seguimento. Neste trabalho, objetivamos otimizar as metodologias clássicas para a extração de DNA (salting-out) e RNA. MATERIAIS E MÉTODOS: Utilizamos proteinase K, choque térmico, dentre outras modificações, com o objetivo de aumentar a quantidade e a qualidade do material recuperado a partir das amostras descritas acima. RESULTADOS: Isolamos com sucesso DNA e RNA de tais amostras e o material obtido foi adequado para a realização de PCR, perfil de metilação, PCR em tempo real e sequenciamento de DNA. CONCLUSÃO: As técnicas aplicadas neste estudo para isolar ácidos nucleicos permitiram a realização posterior de análises moleculares consistentes e confiáveis. Arq Bras Endocrinol Metab. 2012;56(9):618-26.
Subject(s)
Humans , DNA , RNA , Biopsy, Fine-Needle , DNA , Electrophoresis, Agar Gel , Paraffin Embedding , Polymerase Chain Reaction , RNA , Staining and Labeling , Tissue Fixation , Thyroid Gland/pathology , Thyroid Neoplasms/genetics , Thyroid Neoplasms/pathologyABSTRACT
PURPOSE: The extraction of nucleic acid is initially a limiting step for successful molecular-based diagnostic workup. This study aims to compare the effectiveness of three automated DNA extraction systems for clinical laboratory use. MATERIALS AND METHODS: Venous blood samples from 22 healthy volunteers were analyzed using QIAamp(R) Blood Mini Kit (Qiagen), MagNA Pure LC Nucleic Acid Isolation Kit I (Roche), and Magtration-Magnazorb DNA common kit-200N (PSS). The concentration of extracted DNAs was measured by NanoDrop ND-1000 (PeqLab). Also, extracted DNAs were confirmed by applying in direct agarose gel electrophoresis and were amplified by polymerase chain reaction (PCR) for human beta-globin gene. RESULTS: The corrected concentrations of extracted DNAs were 25.42 +/- 8.82 ng/microLiter (13.49-52.85 ng/microLiter) by QIAamp(R) Blood Mini Kit (Qiagen), and 22.65 +/- 14.49 ng/microLiter (19.18-93.39 ng/microLiter) by MagNA Pure LC Nucleic Acid Isolation Kit I, and 22.35 +/- 6.47 ng/microLiter (12.57-35.08 ng/microLiter) by Magtration-Magnazorb DNA common kit-200N (PSS). No statistically significant difference was noticed among the three commercial kits (p > 0.05). Only the mean value of DNA purity through PSS was slightly lower than others. All the extracted DNAs were successfully identified in direct agarose gel electrophoresis. And all the product of beta-globin gene PCR showed a reproducible pattern of bands. CONCLUSION: The effectiveness of the three automated extraction systems is of an equivalent level and good enough to produce reasonable results. Each laboratory could select the automated system according to its clinical and laboratory conditions.