scholarly journals Rapid, Reliable and Robust approach for extraction-free RT-PCR based detection of SARS-CoV-2 in clinical setting to expedite large scale screening

2021 ◽  
Author(s):  
Abhilasha Dubey ◽  
Sanjay Upadhyay ◽  
Manjeet Mehta
Keyword(s):  
Large Scale ◽  
Target Genes ◽  
Low Cost ◽  
Diagnostic Methods ◽  
Analysis Method ◽  
Rt Pcr ◽  
Qpcr Method ◽  
Quantitative Results ◽  
Pooled Samples ◽  
Large Scale Screening

Rapid, reliable and robust method for the detection of SARS-CoV-2 is an indispensable need for diagnostics. The development of diagnostic methods will aid to address further waves of the pandemic potentially with rapid surveillance of disease and to allay the fears. To meet this challenge, we have developed a rapid RT-qPCR method for the detection of 3 target genes or confirmatory genes in less than 30 minutes. The assay showed 100% sensitivity and 100% specificity when tested on 120 samples. We compared a conventional extraction based method with extraction-free method, and then further reduced the run time of extraction free method. Additionally, we have validated our rapid RT-qPCR method for the assessment of pooled samples. We hereby propose a most reliable approach for the mass screening of samples with ease of operation at a low cost. Finally we designed a single tube analysis method which provides qualitative as well as quantitative results in minimum time.

scholarly journals Massive Multiplexing Can Deliver a $1 Test for COVID-19

2020 ◽  
Author(s):  
Paul DN Hebert ◽  
Sean WJ Prosser ◽  
Natalia V Ivanova ◽  
Evgeny V Zakharov ◽  
Sujeevan Ratnasingham
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Rna Extraction ◽  
Respiratory Syndrome Virus ◽  
Major Advance ◽  
Rt Pcr ◽  
Screening Programs ◽  
Global Pandemic ◽  
Gene Coding ◽  
Large Scale Screening

ABSTRACTThe severe acute respiratory syndrome virus, SARS-CoV-2 (hereafter COVID-19), rapidly achieved global pandemic status, provoking large-scale screening programs in many nations. Their activation makes it imperative to identify methods that can deliver a diagnostic result at low cost. This paper describes an approach which employs sequence variation in the gene coding for its envelope protein as the basis for a scalable, inexpensive test for COVID-19. It achieves this by coupling a simple RNA extraction protocol with low-volume RT-PCR, followed by E-Gel screening and sequencing on high-throughput platforms to analyze 10,000 samples in a run. Slight modifications to the protocol could support screening programs for other known viruses and for viral discovery. Just as the $1,000 genome is transforming medicine, a $1 diagnostic test for viral and bacterial pathogens would represent a major advance for public health.

scholarly journals The Biology of Acute Promyelocytic Leukemia and Its Impact on Diagnosis and Treatment

Hematology ◽  
2006 ◽  
Vol 2006 (1) ◽  
pp. 156-161 ◽  
Author(s):  
Francesco Lo-Coco ◽  
Emanuele Ammatuna
Keyword(s):  
Acute Promyelocytic Leukemia ◽  
Target Genes ◽  
Low Cost ◽  
Genetic Diagnosis ◽  
Promyelocytic Leukemia ◽  
Nuclear Staining ◽  
Rt Pcr ◽  
Treatment Type ◽  
Related Phenotype ◽  
Repressor Complex

Abstract Several genetic and phenotypic characteristics of acute promyelocytic leukemia (APL) blasts provide relevant targets and the rationale for tailored treatment. These include the PML/RARα fusion and the transcription co-repressor complex recruited at the promoter of target genes by the hybrid protein, the intense and homogeneous expression of the CD33 antigen, absence of multidrug resistance–related phenotype, and a frequently mutated and constitutively activated FLT3 receptor. Such genotypic and phenotypic features are targeted by agents currently in use in front-line therapy or at relapse (i.e., retinoids, arsenic trioxide, anthracyclines and anti-CD33 monoclonal antibodies), and by novel agents that may find a place in future treatments such as histone deacetylase and FLT3 inhibitors. The unique PML/RARα aberration serves as a molecular marker for rapid diagnosis and prediction of response to ATRA-and ATO-containing therapies. Methods for prompt and low-cost detection of this genetic abnormality, such as the analysis of PML nuclear staining, are extremely useful in clinical practice and could be adopted in countries with limited resources as a surrogate for rapid genetic diagnosis. Finally, PML/RARα monitoring through sensitive RT-PCR can be regarded as an integrating part of the overall treatment strategy in this disease, whereby the treatment type and intensity are modulated in patients at different risk of relapse according to RT-PCR status during follow-up. Because recent clinical studies suggest that most APL patients receiving intensive chemotherapy may be over-treated, longitudinal and stringent RT-PCR monitoring is becoming increasingly important to test the extent to which chemotherapy can be minimized in those presenting with low-risk disease.

Transit Travel Demand Analysis Method Based on APTS Multi-Source Data

2013 ◽  
Vol 361-363 ◽  
pp. 2122-2126
Author(s):  
Jun Chen ◽  
Xiao Hua Li ◽  
Lan Ma
Keyword(s):  
Public Transportation ◽  
Large Scale ◽  
Travel Demand ◽  
Low Cost ◽  
Transportation Systems ◽  
Demand Analysis ◽  
Sample Survey ◽  
Analysis Method ◽  
Source Data ◽  
Bus Stops

Traditional transit travel information is acquired by Trip Sample Survey which has some disadvantages including high cost and short data lifecycle. This paper researched transit travel demand analysis method using Advanced Public Transportation Systems (APTS) data. The study collected APTS data of Nanning City in China and established APTS multi-source data analysis platform applying data warehouse technology. Based on key problems research, the paper presented the analysis procedure and content. Then, this study proposed the core algorithms of the method which are determinations of boarding bus stops, alighting bus stops and transfer bus stops of smart card passengers. Finally, these algorithms programs are experimented using large scale practical APTS data. The results show that this analysis method is low cost, operability and high accuracy.

scholarly journals A Weakly Supervised and Deep Learning Method for an Additive Topic Analysis of Large Corpora

2019 ◽  
Author(s):  
Yair Fogel-Dror ◽  
Shaul R. Shenhav ◽  
Tamir Sheafer
Keyword(s):  
Content Analysis ◽  
Deep Learning ◽  
Text Classification ◽  
Large Scale ◽  
Low Cost ◽  
Initial Number ◽  
Analysis Method ◽  
Training Set ◽  
Topic Analysis ◽  
Weakly Supervised

The collaborative effort of theory-driven content analysis can benefit significantly from the use of topic analysis methods, which allow researchers to add more categories while developing or testing a theory. This additive approach enables the reuse of previous efforts of analysis or even the merging of separate research projects, thereby making these methods more accessible and increasing the discipline’s ability to create and share content analysis capabilities. This paper proposes a weakly supervised topic analysis method that uses both a low-cost unsupervised method to compile a training set and supervised deep learning as an additive and accurate text classification method. We test the validity of the method, specifically its additivity, by comparing the results of the method after adding 200 categories to an initial number of 450. We show that the suggested method provides a foundation for a low-cost solution for large-scale topic analysis.

scholarly journals Fast and low-cost detection of SARS-CoV-2 peptides by tandem mass spectrometry in clinical samples

2020 ◽  
Author(s):  
Karina Helena Morais Cardozo ◽  
Adriana Lebkuchen ◽  
Guilherme Goncalves Okai ◽  
Rodrigo Andrade Schuch ◽  
Luciana Godoy Viana ◽  
...  
Keyword(s):  
Real Time ◽  
Large Scale ◽  
Low Cost ◽  
Large Population ◽  
Virus Detection ◽  
Standard Test ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Fast Processing

Abstract The current outbreak of severe acute respiratory syndrome associated with coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Real-time reverse-transcription PCR (real-time RT-PCR) is the gold standard test for virus detection but the soaring demand for this test resulted in shortage of reagents and instruments, severely limiting its applicability to large-scale screening. To be used either as an alternative, or as a complement, to real-time RT-PCR testing, we developed a high-throughput targeted proteomics assay to detect SARS-CoV-2 proteins directly from clinical respiratory tract samples. Sample preparation was fully automated by using a modified magnetic particle-based proteomics approach implemented on a robotic liquid handler, enabling a fast processing of samples. The use of turbulent flow chromatography included four times multiplexed on-line sample cleanup and UPLC separation. MS/MS detection of three peptides from SARS-CoV-2 nucleoprotein and a 15N-labeled internal global standard was achieved within 2.5 min, enabling the analysis of more than 500 samples per day. The method was validated using 562 specimens previously analyzed by real-time RT-PCR and was able to detect over 83% of positive cases. No interference was found with samples from common respiratory viruses, including other coronaviruses (NL63, OC43, HKU1, and 229E). The strategy here presented has high sample stability and low cost and should be considered as an option to large population testing.

scholarly journals A Weakly Supervised and Deep Learning Method for an Additive Topic Analysis of Large Corpora

2021 ◽  
Vol 3 (1) ◽  
pp. 29-59
Author(s):  
Yair Fogel-Dror ◽  
Shaul R. Shenhav ◽  
Tamir Sheafer
Keyword(s):  
Content Analysis ◽  
Deep Learning ◽  
Text Classification ◽  
Large Scale ◽  
Low Cost ◽  
Initial Number ◽  
Analysis Method ◽  
Training Set ◽  
Topic Analysis ◽  
Weakly Supervised

Abstract The collaborative effort of theory-driven content analysis can benefit significantly from the use of topic analysis methods, which allow researchers to add more categories while developing or testing a theory. This additive approach enables the reuse of previous efforts of analysis or even the merging of separate research projects, thereby making these methods more accessible and increasing the discipline’s ability to create and share content analysis capabilities. This paper proposes a weakly supervised topic analysis method that uses both a low-cost unsupervised method to compile a training set and supervised deep learning as an additive and accurate text classification method. We test the validity of the method, specifically its additivity, by comparing the results of the method after adding 200 categories to an initial number of 450. We show that the suggested method provides a foundation for a low-cost solution for large-scale topic analysis.

scholarly journals Low-Cost Technology for the Prevention of Cervical Cancer in Cameroon

2020 ◽  
Vol 6 (Supplement_1) ◽  
pp. 8-8
Author(s):  
Nkegoum Blaise ◽  
Mboumtou Liliane
Keyword(s):  
Cervical Cancer ◽  
Predictive Value ◽  
Large Scale ◽  
Low Cost ◽  
Screening Method ◽  
Previous History ◽  
Pap Smears ◽  
Cervical Lesions ◽  
History Of ◽  
Large Scale Screening

PURPOSE Our aim was to assess the accuracy of visual inspection with acetic acid (VIA) as a screening method for cervical lesions. METHODS VIA and cytologic smears were carried out on the cervices of nonpregnant women age 30 to 60 years with no previous history of cervical cancer. Cervices with acetowhite lesions or positive Pap smears, as well as 1 in 10 negative cervices (control), were biopsied. RESULTS Of patients, 10,020 women were enrolled and 9,626 (96.1%) were screened. With screening, 9,534 patients (99.0%) had adequate cytology smears, 1,148 (11.9%) underwent colposcopy, and 3,486 biopsies were obtained, of which 1,056 were controls. Sensitivity of VIA was 70.4% versus 47.7%, specificity was 77.6% versus 94.2%, positive predictive value was 44.0% versus 67.2%, and negative predictive value was 91.3% versus 87.8% for Papanicolau test, respectively. CONCLUSION VIA has acceptable test qualities and is now well implemented as a large-scale screening method in Cameroon.

scholarly journals Point-of-Care Diagnostic Tests for Detecting SARS-CoV-2 Antibodies: A Systematic Review and Meta-Analysis of Real-World Data

2020 ◽  
Vol 9 (5) ◽  
pp. 1515 ◽  
Author(s):  
Matteo Riccò ◽  
Pietro Ferraro ◽  
Giovanni Gualerzi ◽  
Silvia Ranzieri ◽  
Brandon Michael Henry ◽  
...  
Keyword(s):  
Systematic Review ◽  
Diagnostic Tests ◽  
Large Scale ◽  
Point Of Care ◽  
Meta Analysis ◽  
Rapid Diagnostic Tests ◽  
Diagnostic Methods ◽  
Rt Pcr ◽  
Real World Data ◽  
Healthcare Facilities

SARS-CoV-2 is responsible for a highly contagious infection, known as COVID-19. SARS-CoV-2 was discovered in late December 2019 and, since then, has become a global pandemic. Timely and accurate COVID-19 laboratory testing is an essential step in the management of the COVID-19 outbreak. To date, assays based on the reverse-transcription polymerase chain reaction (RT-PCR) in respiratory samples are the gold standard for COVID-19 diagnosis. Unfortunately, RT-PCR has several practical limitations. Consequently, alternative diagnostic methods are urgently required, both for alleviating the pressure on laboratories and healthcare facilities and for expanding testing capacity to enable large-scale screening and ensure a timely therapeutic intervention. To date, few studies have been conducted concerning the potential utilization of rapid testing for COVID-19, with some conflicting results. Therefore, the present systematic review and meta-analysis was undertaken to explore the feasibility of rapid diagnostic tests in the management of the COVID-19 outbreak. Based on ten studies, we computed a pooled sensitivity of 64.8% (95%CI 54.5–74.0), and specificity of 98.0% (95%CI 95.8–99.0), with high heterogeneity and risk of reporting bias. We can conclude that: (1) rapid diagnostic tests for COVID-19 are necessary, but should be adequately sensitive and specific; (2) few studies have been carried out to date; (3) the studies included are characterized by low numbers and low sample power, and (4) in light of these results, the use of available tests is currently questionable for clinical purposes and cannot substitute other more reliable molecular tests, such as assays based on RT-PCR.

scholarly journals Detection of Flavescence Dorée Phytoplasma in Grapevine by Reverse-Transcription PCR

Plant Disease ◽  
2007 ◽  
Vol 91 (11) ◽  
pp. 1496-1501 ◽  
Author(s):  
P. Margaria ◽  
C. Rosa ◽  
C. Marzachì ◽  
M. Turina ◽  
S. Palmano
Keyword(s):  
Reverse Transcription ◽  
Large Scale ◽  
Diagnostic Methods ◽  
Kappa Index ◽  
Rt Pcr ◽  
Flavescence Dorée ◽  
Reverse Transcription Pcr ◽  
Novel Method ◽  
Pcr Method ◽  
Polymerase Chain

Flavescence dorée (FD) is the most serious phytoplasma disease of grapevine. This report describes a novel method of detecting FD phytoplasma based on reverse-transcription polymerase chain reaction (RT-PCR) on 16S ribosomal RNA (16SrRNA) which will greatly improve mass screening of infected grapevines. A rapid protocol for extracting sap from whole leaves or midveins and successive one-tube amplification by RT-PCR was applied to grapevine samples with or without symptoms collected from different areas of Piedmont (northwestern Italy). Results were compared with those obtained using one of the current diagnostic methods that utilizes nested PCR on phytoplasma DNA-enriched preparations. A Cohen's kappa index of 0.76 indicated a substantial agreement between the two sets of results. The RT-PCR method has the advantage of being a rapid, reliable, and sensitive assay for large-scale screening of grapevines.

scholarly journals Fast and low-cost detection of SARS-CoV-2 peptides by tandem mass spectrometry in clinical samples

2020 ◽  
Author(s):  
Karina Helena Morais Cardozo ◽  
Adriana Lebkuchen ◽  
Guilherme Goncalves Okai ◽  
Rodrigo Andrade Schuch ◽  
Luciana Godoy Viana ◽  
...  
Keyword(s):  
Real Time ◽  
Large Scale ◽  
Low Cost ◽  
Large Population ◽  
Virus Detection ◽  
Standard Test ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Fast Processing

Abstract The current outbreak of severe acute respiratory syndrome associated with coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Real-time reverse-transcription PCR (real-time RT-PCR) is the gold standard test for virus detection but the soaring demand for this test resulted in shortage of reagents and instruments, severely limiting its applicability to large-scale screening. To be used either as an alternative, or as a complement, to real-time RT-PCR testing, we developed a high-throughput targeted proteomics assay to detect SARS-CoV-2 proteins directly from clinical respiratory tract samples. Sample preparation was fully automated by using a modified magnetic particle-based proteomics approach implemented on a robotic liquid handler, enabling a fast processing of samples. The use of turbulent flow chromatography included four times multiplexed on-line sample cleanup and UPLC separation. MS/MS detection of three peptides from SARS-CoV-2 nucleoprotein and a 15N-labeled internal global standard was achieved within 2.5 min, enabling the analysis of more than 500 samples per day. The method was validated using 562 specimens previously analyzed by real-time RT-PCR and was able to detect over 83% of positive cases. No interference was found with samples from common respiratory viruses, including other coronaviruses (NL63, OC43, HKU1, and 229E). The strategy here presented has high sample stability and low cost and should be considered as an option to large population testing.

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