scholarly journals Comparative evaluation of cost effective extraction free molecular technique for detection of SARS-CoV-2 with reference to standard VTM based RT-qPCR method

2021 ◽  
Author(s):  
Megh Singh Dhakad ◽  
Sanjib Gogoi ◽  
Ansu Kumari ◽  
Aashish Kumar Singh ◽  
Manoj B. Jais ◽  
...  
Keyword(s):  
Detection Method ◽  
Cost Effective ◽  
Molecular Technique ◽  
Rt Pcr ◽  
Index Method ◽  
Resource Limited ◽  
Qpcr Method ◽  
Kappa Value ◽  
The Cost ◽  
Higher Sensitivity

Background and Objectives: The entire globe is undergoing an unprecedented challenge of COVID-19. Considering the need of rapid and accurate diagnostic tests for SARS-CoV-2, this study was planned to evaluate the cost effective extraction free RT-PCR technique in comparison to the standard VTM based RT-qPCR method. Materials and Methods: Paired swabs from nasopharynx and oropharynx were collected for SARS-CoV-2 testing, from 211 adult patients (≥18 years) in VTM and plain sterile tubes (dry swabs). These samples were processed and RT-qPCR was carried out as per standard protocols. Results: 54.5% of the patients were females and 45.5% were males with sex ratio 1:1.19 (M: F). 38.86% were symptomatic, of which fever (86.59%), cough (79.23%) and breathlessness (46.34%) were the most common symptoms. The positivity by VTM based method and index method was 31.27% and 13.27% respectively. Of the 27 inconclusive results from index method, 37.04% were positive, 48.15% were negative by VTM based method. However, in 40 inconclusive results by VTM based method, 90% were negative and rest remained inconclusive by index method. The sensitivity and specificity of the index method were 39.39% and 85.71% respectively. The overall agreement between VTM based method and index method was 49.59% with estimated Kappa value of 0.19. Conclusion: VTM based method showed higher sensitivity compared to the index method. The higher positivity by VTM based method, suggests that VTM based method could plausibly be a better detection method of SARS-CoV-2. Still, the index method might add value in a resource limited setups for detection of SARS-CoV-2.  

scholarly journals Genomic approaches and their contributions to understanding the European Neolithisation

2016 ◽  
Vol 43 ◽  
pp. 253-264
Author(s):  
Cristina Gamba
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
Significant Contribution ◽  
Cost Effective ◽  
Petrous Bone ◽  
Molecular Technique ◽  
Complete Genomes ◽  
Technical Advances ◽  
High Throughput Dna Sequencing ◽  
The Cost

The contribution of ancient DNA to the understanding of past events has been increasing exponentially in recent years. This is mainly due to the synergy of technical advances, such as the molecular technique of high-throughput DNA sequencing, which has allowed for the reconstruction of complete genomes as old as 750 000 years. Another step toward the cost-effective characterisation of ancient genomes is the sampling of petrous bone, which has allowed sequencing of the first ancient African genome. Here I review the significant contribution of ancient genomics to our understanding of the European Neolithisation process.

scholarly journals Cost-Effective Pooling of DNA from Nasopharyngeal Swab Samples for Large-Scale Detection of Bacteria by Real-Time PCR

2014 ◽  
Vol 53 (3) ◽  
pp. 1002-1004 ◽  
Author(s):  
Sophie Edouard ◽  
Elsa Prudent ◽  
Philippe Gautret ◽  
Ziad A. Memish ◽  
Didier Raoult
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Large Scale ◽  
High Sensitivity ◽  
High Specificity ◽  
Cost Effective ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Scale Detection ◽  
The Cost

We investigated the potential of pooling DNA from nasopharyngeal specimens to reduce the cost of real-time PCR (RT-PCR) for bacterial detection. Lyophilization is required to reconcentrate DNA. This strategy yields a high specificity (86%) and a high sensitivity (96%). We estimate that compared to individual testing, 37% fewer RT-PCR tests are needed.

scholarly journals Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection

2020 ◽  
Author(s):  
Xiaoshuai Ren ◽  
Yan Liu ◽  
Hongtao Chen ◽  
Wei Liu ◽  
Zhaowang Guo ◽  
...  
Keyword(s):  
Basic Research ◽  
Rt Pcr ◽  
Pharyngeal Swab ◽  
Positive Stool ◽  
Kappa Value ◽  
Global Threat ◽  
Basic Research Project ◽  
Efficient Screening ◽  
Higher Sensitivity ◽  
Good Agreement

SummaryBackgroundCoronavirus Disease 2019 (COVID-19) caused by Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat to public health. Aiming to construct an efficient screening pattern, we comprehensively evaluated the performances of RT-PCR and chest CT in diagnosing COVID-19.MethodsThe records including demographics, RT-PCR, and CT from 87 confirmed COVID-19 cases and 481 exclusion cases were collected. The diagnostic accuracy of the pharyngeal swab RT-PCR, CT, combination with the second pharyngeal swab RT-PCR or with CT were evaluated individually. Besides, all the stool RT-PCR results were plotted by time to explore the value of stool RT-PCR.FindingsCombination of RT-PCR and CT has the higher sensitivity (91.9%,79/86) than RT-PCR alone (78.2%,68/87) or CT alone (66.7%, 54 of 81) or combination of two RT-PCR tests (86.2%,75/87). There was good agreement between RT-PCR and CT (kappa-value, 0.430). In 34 COVID-19 cases with inconsistent results, 94.1% (n=32) are mild infection, 62.5% of which (20/32) showed positive RT-PCR. 46.7% (35/75) COVID-19 patients had at least one positive stool during the course. Two cases had positive stool earlier than the pharyngeal swabs. Importantly, one patient had consecutive positive stool but negative pharyngeal swabs.InterpretationCombination of RT-PCR and CT with the highest sensitivity is an optimal pattern to screen COVID-19. RT-PCR is superior to CT in diagnosing mild infections. Stool RT-PCR should be considered as an item for improving discovery rate and hospital discharge. This study shed light for optimizing scheme of screening and monitoring of SARS-CoV-2 infection.FundingThis work was supported by the National Natural Science Foundation of China (No. 81502104), National Program on Key Basic Research Project (No. 2018YFC0910600),the Nature Science Foundation of Guangdong Province, China (Grant No: 2017A030313771 and 2020A151501001) and the Young Teachers Nurturing Program of Sun Yat-Sen University (Grant No:17ykpy62)

scholarly journals A Comparative Study of LAMP and PCR in Relation to Time and Cost

2022 ◽  
Vol 12 (2) ◽  
pp. 72-75
Author(s):  
Tanzila Rawnuck ◽  
Md Selim Reza ◽  
Mohammad Jahidur Rahman Khan ◽  
Rashida Akter Khanam ◽  
Saif Ullah Munshi
Keyword(s):  
Low Cost ◽  
Cost Effective ◽  
Molecular Techniques ◽  
Molecular Technique ◽  
Serum Samples ◽  
Setup Cost ◽  
Time Duration ◽  
Time Operation ◽  
The Cost ◽  
Short Time

Background: The Loop-mediated isothermal amplification (LAMP) represents a very sensitive, easy to use, and less time consuming diagnostic method. Aims: The aim was to establish a simple, cost-effective, molecular technique. Materials and methods: An analytical study was conducted using two hundred acute serum samples using two different molecular techniques; qPCR and LAMP to standardize a costeffective and less time-consuming technique. Results: The cost of in-house LAMP reagents was one-ninth of the cost of commercial qPCR. Consume cost was 23 times less than qPCR besides, lab setup cost was 92 times less than qPCR. More importantly, LAMP requires 5-6 times less time duration than qPCR. Conclusion: Due to its simple short-time operation with low cost, it would be a prevalent molecular technique globally, particularly in Bangladesh. J Shaheed Suhrawardy Med Coll 2020; 12(2): 72-75

scholarly journals A Simple and Cost-Effective Freeze-Thaw Based Method for Plasmodium DNA Extraction from Dried Blood Spot

2019 ◽  
Author(s):  
Supriya SHARMA ◽  
Riti MANN ◽  
Sandeep KUMAR ◽  
Neelima MISHRA ◽  
Bina SRIVASTAVA ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Dna Isolation ◽  
Cost Effective ◽  
Detection Sensitivity ◽  
Freezing And Thawing ◽  
Freeze Thaw ◽  
Resource Limited ◽  
Cost Effective Method ◽  
The Cost ◽  
Processing Steps

Background: Available DNA isolation methods for Plasmodium involve numerous processing steps, adding to the cost and conferring risk of contamination. Here we devise a simple and cost-effective method for direct extraction of Plasmodium DNA from dried filter paper spot (DBS), appropriate for resource-limited setups. Methods: The protocol involves simple freezing and thawing of DBS, neither involves any purification step nor any chemical reagent. The method was assessed in terms of DNA quantity, PCR detection sensitivity, time requirement, cost effectiveness, labor intensiveness and degree of shearing. The reliability of this method was confirmed by comparing it with other in use methods for Plasmodium DNA isolation. Results: Pure DNA was obtained with this method, as exemplified by the absorbance ratio (260nm /280nm) of 1.2. The protocol produced digestible, PCR-grade genomic DNA, also found to be suitable for sequencing. DNA isolated remained stable and retained its integrity after storage for one month at 4 0C. Conclusion: Our process substantiated as efficient, reproducible, simple, fast, and inexpensive. Development of this optimized freeze-thaw based DNA extraction method for malaria parasite may provide a valuable tool for molecular analysis in resource-limited setups. This is the first report of DNA extraction from DBS of Plasmodium utilizing freeze-thaw.

scholarly journals Detection of Mycobacteria in Clinical Samples by the Newly Developed PaxView TB/NTM MPCR-ULFA Kit

2020 ◽  
pp. 11-17
Author(s):  
Jong-Hee Choo ◽  
Chang-Ki Kim ◽  
Young-Kil Park
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Gel Electrophoresis ◽  
Body Fluid ◽  
Cost Effective ◽  
Diagnostic Tools ◽  
Clinical Samples ◽  
Resource Limited ◽  
Kappa Value ◽  
Bronchial Washing

Aims: To evaluate sensitivity and specificity of the newly developed PaxView TB/NTM MPCR-ULFA Kit.  Study Design: Compared with the licensed AdvanSure TB/NTM real-time PCR. Place and Duration of Study: SCL and PaxGenBio in Gyeonggi-do, Korea, between August 2018 and May 2019. Methodology: In this study, 350 specimens including sputum, bronchial washing, body fluid, tissue, urine, and cerebrospinal fluid were examined to evaluate the performance of the PaxView TB/NTM MPCR-ULFA Kit compared to results of the currently licensed AdvanSure TB/NTM real-time PCR (LG Chem, Korea). Results: Compared to the AdvanSure TB/NTM real-time PCR, the PaxView TB/NTM MPCR-ULFA Kit test was found to possess a 100% sensitivity. In other words, all 140 MTB and 61 non-tuberculous mycobacteria (NTM) specimens that tested positive with the AdvanSure TB/NTM real-time PCR also tested positive with the PaxView TB/NTM MPCR-ULFA Kit. However, the specificity of the later kit found to be 97.9% (146/149; 95% CI 95.6–100.0), meaning that out of 149 MTB/NTM specimens that tested negative with the AdvanSure TB/NTM real-time PCR, 146 were identified as MTB/NTM-negative according to the PaxView TB/NTM MPCR-ULFA Kit. Nonetheless, the overall agreement between the two diagnostic tools was 99.1% (347/350; 95% CI 98.1– 100.0) and the kappa value was 0.982 (350; 95% CI 0.968 – 0.995), meaning that the two diagnostic tools rendered almost identical results. Conclusion: The PaxView TB/NTM MPCR-ULFA Kit could be useful to identify MTB and NTM in resource-limited countries, as this procedure is far more cost-effective than real-time PCR and convenient than conventional gel electrophoresis approaches.

scholarly journals Rapid and Visual Detection of the Emerging Novel Duck Reovirus by Using a Specific and Sensitive Reverse Transcription Recombinase Polymerase Amplification Method

2020 ◽  
Author(s):  
Weiwei Wang ◽  
Yan Zhang ◽  
Yu Huang ◽  
Guo Chen ◽  
Mengya Shi ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Reverse Transcription ◽  
Disease Transmission ◽  
Cost Effective ◽  
Cross Reactivity ◽  
Recombinase Polymerase Amplification ◽  
Rt Pcr ◽  
Amplification Method ◽  
Resource Limited ◽  
S3 Gene

Abstract Background Duck spleen necrosis disease (DSND) caused by Novel Duck Reovirus (NDRV), is an emerging infectious disease that causes severely threaten to duck industry. Currently, the popular conventional PCR technique for detecting NDRV is time consuming. So, it is essential to develop a rapid and accurate molecular diagnosis techniques of viral pathogens for the purpose to prevent further disease transmission or outbreaks. Recombinase polymerase Amplification (RPA) is a new generation of simple, rapid and cost-effective molecular diagnosis technology, which has been applied to the molecular detection of various pathogens. Methods In our study, a simple, rapid and reliable detection method was developed target NDRV by an isothermal reverse transcription-recombinase polymerase amplification (RT-RPA). The RT-RPA primers were designed based on the S3 gene of NDRV, and a series of other waterfowl-origin pathogens were detected by RT-RPA. A total of 20 field and experimental infected samples were tested by RT-RPA and compared with the results of conventional RT-PCR and quantitative RT-PCR simultaneously. Results The RT-RPA method proved to be repeatable and could detect as little as 3.48 × 10− 6 ng/µl of the standard plasmid DNA inserted with the viral S3 gene. This was a 10 × higher sensitivity rate than that of conventional RT-PCR. The major advantage of this RT-RPA method is that it could be performed as an isothermal reaction at 37 ℃ and completed within 20 min. In addition, no cross-reactivity was detected with other waterfowl-origin viruses. Also, the amplified products could be visualized faster, without the gel electrophoresis, by adding the SYBR Green I and observing them under an ultraviolet light. Conclusions This newly developed RT-RPA method offers a simple, rapid and accurate for rapid detection of NDRV, which especially useful in on-site facilities and resource-limited areas.

A universal linker-RT PCR based quantitative method for the detection of circulating miRNAs

2014 ◽  
Vol 6 (22) ◽  
pp. 9101-9107 ◽  
Author(s):  
Qinyu Ge ◽  
Fei Tian ◽  
Youxia Zhou ◽  
Yanan Zhu ◽  
Jiafeng Lu ◽  
...  
Keyword(s):  
Quantitative Method ◽  
Circulating Mirnas ◽  
Rt Pcr ◽  
Qpcr Method ◽  
Higher Sensitivity

A higher sensitivity and reliable qPCR method based on a random pre-adenylated DNA adaptor ligation was developed and validated for the detection of circulating miRNAs.

scholarly journals MO835AFTERMATH OF FORTNIGHTLY UNIVERSAL TESTING FOR SEVERE ACUTE RESPIRATORY CORONA VIRUS-2 INFECTION IN MAINTENANCE IN HEMODIALYSIS PATIENTS

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Narayan Prasad ◽  
Manas Ranjan Patel ◽  
Dharmendra Bhadauria ◽  
Anupama Kaul ◽  
Ravi Sankar Kushwaha
Keyword(s):  
Cost Effective ◽  
Hemodialysis Patients ◽  
Maintenance Hemodialysis ◽  
Effective Strategy ◽  
Rt Pcr ◽  
Dialysis Unit ◽  
Universal Testing ◽  
Asymptomatic Patients ◽  
The Cost ◽  
Maintenance Hemodialysis Patients

Abstract Background and Aims Asymptomatic maintenance hemodialysis patients with SARS-COV-2are missed with pre-dialysis screening without testing. The possible ideal strategy of testing each patient before each shift with RT-PCR was not feasible. We aimed to study the effectiveness of fortnightly screening with RT -PCR for SARS-CoV-2 in curbing transmission. Method Between July 1, 2020, and September 30, 2020, all 273 patients receiving hemodialysis were subjected to fortnightly testing for SARS-Cov-2 in the unit to detect asymptomatic patients. The cost and effectiveness of universal testing in preventing transmission were analyzed using Susceptible-Infectious-Removed (SIR) modeling assuming R0 of 2.2. Results Of 273 MHD patients, 55 (20.1%) got infected with SARS-CoV-2 over three months. Six (10.9%) were symptomatic, and 49 (89.1%) asymptomatic at the time of testing. Six (10.9%) asymptomatic patients develop symptoms later; and 43 (78.2%) remained asymptomatic. A total of 7(6.1%) HCWs also tested positive for the virus. With an assumption of R0 2.2 and isolation of symptomatic patients only, all 273 patients could have been affected by September 30, 2020; with the isolation of both symptomatic patients and those testing positive after pre-dialysis screen, only 52 (19%) infections could have been prevented. However, at the end of the study period, 218 (80%) patients remained uninfected of SARS-CoV-2. Fortnightly universal testing is cost-effective, and SIR modeling proved effective in preventing person-to-person transmission. Conclusion Repeated universal testing in maintenance hemodialysis patients detected 89% of asymptomatic SARS-CoV-2 patients over three months and appeared to be an effective strategy to prevent person-to-person transmission in the dialysis unit.

The IBM-PC in electron microscopy

1996 ◽  
Vol 54 ◽  
pp. 612-613
Author(s):  
James F. Mancuso
Keyword(s):  
Head Start ◽  
Image Acquisition ◽  
Cost Effective ◽  
Financial Applications ◽  
Number Of Factors ◽  
Instrument Control ◽  
The Cost ◽  
Training And Support ◽  
Control Image ◽  
Ibm Pc

IBM PC compatible computers are widely used in microscopy for applications ranging from control to image acquisition and analysis. The choice of IBM-PC based systems over competing computer platforms can be based on technical merit alone or on a number of factors relating to economics, availability of peripherals, management dictum, or simple personal preference.IBM-PC got a strong “head start” by first dominating clerical, document processing and financial applications. The use of these computers spilled into the laboratory where the DOS based IBM-PC replaced mini-computers. Compared to minicomputer, the PC provided a more for cost-effective platform for applications in numerical analysis, engineering and design, instrument control, image acquisition and image processing. In addition, the sitewide use of a common PC platform could reduce the cost of training and support services relative to cases where many different computer platforms were used. This could be especially true for the microscopists who must use computers in both the laboratory and the office.

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