scholarly journals Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP)

Author(s):  
Lukas Bokelmann ◽  
Olaf Nickel ◽  
Tomislav Maricic ◽  
Svante Paabo ◽  
Matthias Meyer ◽  
...  

Efforts to contain the spread of SARS-CoV-2 have spurred the need for reliable, rapid, and cost-effective diagnostic methods which can easily be applied to large numbers of people. However, current standard protocols for the detection of viral nucleic acids while sensitive, require a high level of automation, sophisticated laboratory equipment and trained personnel to achieve throughputs that allow whole communities to be tested on a regular basis. Here we present Cap-iLAMP (capture and improved loop-mediated isothermal amplification). This method combines a hybridization capture-based RNA extraction of non-invasive gargle lavage samples to concentrate samples and remove inhibitors with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. In contrast to direct addition of the sample to improved LAMP (iLAMP), Cap-iLAMP does not result in false positives and single infected samples can be detected in a pool among 25 uninfected samples, thus reducing the technical cost per test to ~1 Euro per individual.

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lukas Bokelmann ◽  
Olaf Nickel ◽  
Tomislav Maricic ◽  
Svante Pääbo ◽  
Matthias Meyer ◽  
...  

AbstractEfforts to contain the spread of SARS-CoV-2 have spurred the need for reliable, rapid, and cost-effective diagnostic methods which can be applied to large numbers of people. However, current standard protocols for the detection of viral nucleic acids while sensitive, require a high level of automation and sophisticated laboratory equipment to achieve throughputs that allow whole communities to be tested on a regular basis. Here we present Cap-iLAMP (capture and improved loop-mediated isothermal amplification) which combines a hybridization capture-based RNA extraction of gargle lavage samples with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. In contrast to direct addition of the sample to improved LAMP (iLAMP), Cap-iLAMP prevents false positives and allows single positive samples to be detected in pools of 25 negative samples, reducing the reagent cost per test to ~1 Euro per individual.


2021 ◽  
Author(s):  
Lukas Bokelmann ◽  
Olaf Nickel ◽  
Tomislav Maricic ◽  
Svante Pääbo ◽  
Matthias Meyer ◽  
...  

Abstract Here we present a step-by-step protocol for Cap-iLAMP (capture and improved ‎loop-mediated isothermal amplification) which combines a hybridization capture-based RNA extraction of gargle lavage samples with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. The sensitivity is 97% and the specificity is 99%. In contrast to direct addition of the sample to improved LAMP (iLAMP), Cap-iLAMP prevents false positives and allows single positive samples to be detected in pools of 25 negative samples.


Diagnostics ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 9
Author(s):  
Meysam Rezaei ◽  
Sajad Razavi Bazaz ◽  
Sareh Zhand ◽  
Nima Sayyadi ◽  
Dayong Jin ◽  
...  

The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its associated serious respiratory disease, coronavirus disease 2019 (COVID-19), poses a major threat to global public health. Owing to the lack of vaccine and effective treatments, many countries have been overwhelmed with an exponential spread of the virus and surge in the number of confirmed COVID-19 cases. Current standard diagnostic methods are inadequate for widespread testing as they suffer from prolonged turn-around times (>12 h) and mostly rely on high-biosafety-level laboratories and well-trained technicians. Point-of-care (POC) tests have the potential to vastly improve healthcare in several ways, ranging from enabling earlier detection and easier monitoring of disease to reaching remote populations. In recent years, the field of POC diagnostics has improved markedly with the advent of micro- and nanotechnologies. Due to the COVID-19 pandemic, POC technologies have been rapidly innovated to address key limitations faced in existing standard diagnostic methods. This review summarizes and compares the latest available POC immunoassay, nucleic acid-based and clustered regularly interspaced short palindromic repeats- (CRISPR)-mediated tests for SARS-CoV-2 detection that we anticipate aiding healthcare facilities to control virus infection and prevent subsequent spread.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shan Wei ◽  
Esther Kohl ◽  
Alexandre Djandji ◽  
Stephanie Morgan ◽  
Susan Whittier ◽  
...  

AbstractThe COVID-19 pandemic has resulted in an urgent need for a rapid, point of care diagnostic testing that could be rapidly scaled on a worldwide level. We developed and tested a highly sensitive and robust assay based on reverse transcription loop mediated isothermal amplification (RT-LAMP) that uses readily available reagents and a simple heat block using contrived spike-in and actual clinical samples. RT-LAMP testing on RNA-spiked samples showed a limit of detection (LoD) of 2.5 copies/μl of viral transport media. RT-LAMP testing directly on clinical nasopharyngeal swab samples in viral transport media had an 85% positive percentage agreement (PPA) (17/20), and 100% negative percentage agreement (NPV) and delivered results in 30 min. Our optimized RT-LAMP based testing method is a scalable system that is sufficiently sensitive and robust to test for SARS-CoV-2 directly on clinical nasopharyngeal swab samples in viral transport media in 30 min at the point of care without the need for specialized or proprietary equipment or reagents. This cost-effective and efficient one-step testing method can be readily available for COVID-19 testing world-wide, especially in resource poor settings.


2019 ◽  
Author(s):  
Lee E. Korshoj ◽  
Prashant Nagpal

AbstractAdvances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multi-omics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances towards such diagnostics. However, the inability to squeeze light with several hundred-nanometer wavelengths into angstrom-scale volume for single nucleotide measurements has hindered further progress. Recently, a block optical sequencing (BOS) method has been shown for determining relative nucleobase content in DNA k-mer blocks with Raman spectroscopy, and a block optical content scoring (BOCS) algorithm was developed for robust content-based genetic biomarker database searching. Here, we performed BOS measurements on positively-charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in DNA k-mer blocks (where k=10), as well as measurements on RNA and chemically-modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy BOS measurements were then used with BOCS to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 content measurements (<15% coverage) of the gene. These results prove the integration of BOS/BOCS as a diagnostic optical sequencing platform. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.


2020 ◽  
Author(s):  
Paula Demétrio de Souza França ◽  
Susanne Kossatz ◽  
Christian Brand ◽  
Daniella Karassawa Zanoni ◽  
Sheryl Roberts ◽  
...  

AbstractPurposeVisual inspection and biopsy is the current standard of care for oral cancer diagnosis, but is subject to misinterpretation and consequently to misdiagnosis. Topically applied PARPi-FL is a molecularly specific, fluorescent contrast-based approach that may fulfil the unmet need for a simple, in vivo, non-invasive, cost-effective, point-of-care method for the early diagnosis of oral cancer. Here, we present results from a phase I safety and feasibility study on fluorescent, topically applied PARPi-FL.Patients and MethodsTwelve patients with a histologically proven squamous cell carcinoma of the oral cavity (OSCC) gargled a PARPi-FL solution for 60 seconds (15 mL, 100 nM, 250 nM, 500 nM, or 1000 nM), followed by gargling a clearing solution for 60 seconds. Fluorescence measurements of the lesion and surrounding oral mucosa were taken before PARPi-FL application, after PARPi-FL application and after clearing. Blood pressure, oxygen levels, clinical chemistry and CBC were obtained before and after tracer administration.ResultsPARPi-FL was well-tolerated by all patients without any safety concerns. When analyzing the fluorescence signal, all malignant lesions showed a significant differential in contrast after administration of PARPi-FL, with the highest increase occurring at the highest dose level (1000 nM), where all patients had a tumor-to-margin fluorescence signal ratio of > 3. A clearing step was essential to increase signal specificity, as it clears unbound PARPi-FL trapped in normal anatomical structures. PARPi-FL tumor cell specificity was confirmed by ex vivo tabletop confocal microscopy. We have demonstrated that the fluorescence signal arose from the nuclei of tumor cells, endorsing our macroscopic findings.ConclusionsA PARPi-FL swish & spit solution is a rapid and non-invasive diagnostic tool that preferentially localizes fluorescent contrast to OSCC. This technique holds promise for the early detection of OSCC based on in vivo optical evaluation and targeted biopsy of suspicious lesions in the oral cavity.Translational RelevanceDespite their accessible location, oral cavity cancers are often diagnosed late, especially in low-resource areas where their incidence is typically high. The high prevalence of premalignant and benign oral lesions in these populations contributes to a number of issues that make early detection of oral cancer difficult: even in experienced hands, it can be difficult to differentiate cancer from premalignant or benign lesions during routine clinical examination; and biopsy-based histopathology, the current standard of care, is invasive, prone to sampling error, and requires geographic access to appropriate health care professionals, including a highly trained pathologist. While seemingly impenetrable economic and infrastructure barriers have confounded the early diagnosis of oral cancer for most of the world’s population, these could be circumvented by a simple, in vivo, non-invasive, cost-effective, point-of-care method of diagnosis. We are attempting to address this unmet clinical need by using topically applied PARPi-FL — a molecularly specific, fluorescent contrast-based approach — to detect oral cancer.FundingThis work was supported by National Institutes of Health grants P30 CA008748, R01 CA204441 (TR) and R43 CA228815 (CB and TR). Dr. Valero was sponsored by a grant from Fundación Alfonso Martín Escudero. The funding sources were not involved in study design, data collection and analysis, writing of the report, or the decision to submit this article for publication.Disclosure of Potential Conflicts of InterestC.B., S.K., S.P. and T.R. are shareholders of Summit Biomedical Imaging, LLC. S.K., S.P. and T.R. are co-inventors on PCT application WO2016164771. T.R. is co-inventor on PCT application WO2012074840. T.R. is a paid consultant for Theragnostics, Inc. All the other authors have no relevant conflict to declare. This arrangement has been reviewed and approved by Memorial Sloan Kettering Cancer Center in accordance with its conflict of interest policies.


Sensors ◽  
2019 ◽  
Vol 19 (22) ◽  
pp. 5003 ◽  
Author(s):  
Hussein Alawieh ◽  
Trishia El Chemaly ◽  
Samir Alam ◽  
Massoud Khraiche

Heart failure is a class of cardiovascular diseases that remains the number one cause of death worldwide with a substantial economic burden of around $18 billion incurred by the healthcare sector in 2017 due to heart failure hospitalization and disease management. Although several laboratory tests have been used for early detection of heart failure, these traditional diagnostic methods still fail to effectively guide clinical decisions, prognosis, and therapy in a timely and cost-effective manner. Recent advances in the design and development of biosensors coupled with the discovery of new clinically relevant cardiac biomarkers are paving the way for breakthroughs in heart failure management. Natriuretic neurohormone peptides, B-type natriuretic peptide (BNP) and N-terminal prohormone of BNP (NT-proBNP), are among the most promising biomarkers for clinical use. Remarkably, they result in an increased diagnostic accuracy of around 80% owing to the strong correlation between their circulating concentrations and different heart failure events. The latter has encouraged research towards developing and optimizing BNP biosensors for rapid and highly sensitive detection in the scope of point-of-care testing. This review sheds light on the advances in BNP and NT-proBNP sensing technologies for point-of-care (POC) applications and highlights the challenges of potential integration of these technologies in the clinic. Optical and electrochemical immunosensors are currently used for BNP sensing. The performance metrics of these biosensors—expressed in terms of sensitivity, selectivity, reproducibility, and other criteria—are compared to those of traditional diagnostic techniques, and the clinical applicability of these biosensors is assessed for their potential integration in point-of-care diagnostic platforms.


2020 ◽  
Vol 9 (7) ◽  
pp. 433
Author(s):  
Eugene Levin ◽  
Roman Shults ◽  
Reza Habibi ◽  
Zhongming An ◽  
William Roland

In spite of the tremendous success in artificial intelligence technology and a high level of automation in geospatial data obtaining processes, there is still a need for topographical field data collection by professional surveyors. Understanding terrain topology and topography is a cognitive skill set that has to be demonstrated by geospatial Subject Matter Experts (SME) for the productive work in the topographic surveying field. For training of the mentioned above skillset, one has to be exposed to the theory and must also practice with surveying instruments in field conditions. The challenge of any surveying/geospatial engineering workforce training is to expose students to field conditions which might be limited due to equipment expenses and meteorological conditions that prevent good data collection. To meet this challenge, the Integrated Geospatial Technology research group is working on a geospatial virtual reality (VR) project which encompasses the following components: (a) immersive visualization of terrain; (b) virtual total station instrument; (c) virtual surveyor with reflector installed on the virtual rod. The application scenario of the technology we are working with has the following stages: (1) student is installing total station on the optimal location; (2) students move virtual surveyor on the sampling points they consider to be important (3) contours are generated and displayed in 3D being superimposed on 3D terrain; (4) accuracy of terrain modeling is observable and measurable by comparing the sampling model with initial one.


2013 ◽  
Vol 62 (10) ◽  
pp. 1540-1544 ◽  
Author(s):  
Rachana Solanki ◽  
Lavanya Vanjari ◽  
Nagapriyanka Ede ◽  
Akhila Gungi ◽  
Amarendranath Soory ◽  
...  

Carbapenem-resistant pathogens cause infections associated with significant morbidity and mortality. This study evaluates the use of the loop-mediated isothermal amplification (LAMP) assay for rapid and cost-effective detection of bla NDM-1 and bla KPC genes among carbapenem-resistant Gram-negative bacteria in comparison with conventional PCR and existing phenotypic methods. A total of 60 carbapenem-resistant clinical isolates [Escherichia coli (15), Klebsiella pneumoniae (22), Acinetobacter baumannii (23)] were screened for the presence of carbapenemases (bla KPC and bla NDM-1) using phenotypic methods such as the modified Hodge test (MHT) and combined disc test (CDT) and molecular methods such as conventional PCR and LAMP assay. In all, 47/60 isolates (78.3 %) were MHT positive while 48 isolates were positive by CDT [46.6 % positive with EDTA, 30 % with 3′ aminophenylboronic acid (APB) plus EDTA and 1.6 % with APB alone]. Isolates showing CDT positivity with EDTA or APB contained bla NDM-1 and bla KPC genes, respectively. bla NDM-1 was present as a lone gene in 28 isolates (46.7 %) and present together with the bla KPC gene in 19 isolates (31.7 %). Only one E. coli isolate had a lone bla KPC gene. The LAMP assay detected either or both bla NDM-1 and bla KPC genes in four isolates that were missed by conventional PCR. Neither gene could be detected in 12 (20 %) isolates. The LAMP assay has greater sensitivity, specificity and rapidity compared to the phenotypic methods and PCR for the detection of bla NDM-1 and bla KPC. With a turnaround time of only 2–3 h, the LAMP assay can be considered a point-of-care assay.


Author(s):  
Pazhanimuthu Annamalai ◽  
Madhu Kanta ◽  
Pazhanivel Ramu ◽  
Baskar Ravi ◽  
Kokilavani Veerapandian ◽  
...  

AbstractThe recent outbreak of the newly emerged novel coronavirus (SARS-CoV-2) presents a big challenge for public health laboratories as virus isolates are not available while there is an increasing evidence that the epidemic is more widespread than initially thought, as well as spreading internationally across borders through travellers does already happen warranting a methodology for the rapid detection of the infection to control SARS-CoV-2. Aim: We intended to develop and deploy a robust and rapid diagnostic methodology using LAMP assay for use in point of care settings to detect SARS-COV-2 infection. Methodology: In the present study, we have developed a validated rapid diagnostic procedure to detect SARS-CoV-2 using LAMP assay, its design relying on isothermal amplification of the nucleic acids of the SARS-CoV-2. Results: The LAMP assay developed detects SARS-CoV-2 infection rapidly with high sensitivity and reliability. The data generated by LAMP assay were comparable and at par with the data generated by real-time PCR method. Conclusion: The present study demonstrates that the LAMP assay developed was a rapid, reliable, sensitive and cost effective method to detect SARS-CoV-2 infection in a point of care as well as in laboratory settings.


Sign in / Sign up

Export Citation Format

Share Document