scholarly journals Isothermal Amplification of Nucleic Acids: The Race for the Next “Gold Standard”

2021 ◽  
Vol 2 ◽  
Author(s):  
Beatriz B. Oliveira ◽  
Bruno Veigas ◽  
Pedro Viana Baptista

Nucleic acid amplification technologies (NAATs) have become fundamental tools in molecular diagnostics, due to their ability to detect small amounts of target molecules. Since its development, Polymerase Chain Reaction (PCR) has been the most exploited method, being stablished as the “gold standard” technique for DNA amplification. However, the requirement for different working temperatures leads to the need of a thermocycler machine or complex thermal apparatus, which have been preventing its application in novel integrated devices for single workflow and high throughput analysis. Conversely, isothermal amplification methods have been gaining attention, especially for point-of-care diagnosis and applications. These non-PCR based methods have been developed by mimicking the in vivo amplification mechanisms, while performing the amplification with high sensitivity, selectivity and allowing for high-throughput analysis. These favorable capabilities have pushed forward the implementation and commercialization of several platforms that exploit isothermal amplification methods, mostly against virus, bacteria and other pathogens in water, food, environmental and clinical samples. Nevertheless, the future of isothermal amplification methods is still dependent on achieving technical maturity and broader commercialization of enzymes and reagents.

2020 ◽  
Author(s):  
Pierre Garneret ◽  
Etienne Coz ◽  
Elian Martin ◽  
Jean-Claude Manuguerra ◽  
Elodie Brient-Litzler ◽  
...  

In order to respond to the urgent request of massive testing, developed countries perform nucleic acid amplification tests (NAAT) of SARS-CoV-2 in centralized laboratories. Real-time RT - PCR (Reverse transcription - Polymerase Chain Reaction) is used to amplify the viral RNA and enable its detection. Although PCR is 37 years old, it is still considered, without dispute, as the gold standard. PCR is an efficient process, but the complex engineering required for automated RNA extraction and temperature cycling makes it incompatible for use in point of care settings. In the present work, by harnessing progress made in the past two decades in DNA amplification, microfluidics and membrane technologies, we succeeded to create a portable test, in which SARS-CoV-2 RNA is extracted, amplified isothermally by RT - LAMP (Loop-mediated Isothermal Amplification), and detected using intercalating dyes or highly fluorescent probes. Depending on the viral load, the detection takes between twenty minutes and one hour. Using pools of naso-pharyngal clinical samples, we estimated a sensitivity comparable to RT-qPCR (up to a Cycle threshold of 39, equivalent to <0.1 TCID50 per mL) and a 100% specificity, for other human coronaviruses and eight respiratory viruses currently circulating in Europe. We designed and fabricated an easy-to-use portable device called COVIDISC to carry out the test at the point of care. The low cost of the materials along with the absence of complex equipment paves the way towards a large dissemination of this device. The perspective of a reliable SARS-CoV-2 point of care detection, highly performing, that would deliver on-site results in less than one hour opens up a new efficient approach to manage the pandemics.


2021 ◽  
Vol 22 (11) ◽  
pp. 5743
Author(s):  
Igor P. Oscorbin ◽  
Georgiy Yu. Shevelev ◽  
Ksenia A. Pronyaeva ◽  
Andrey A. Stepanov ◽  
Darya V. Shamovskaya ◽  
...  

Loop-mediated isothermal amplification (LAMP) is a method of nucleic acid amplification that is more stable and resistant to DNA amplification inhibitors than conventional PCR. LAMP multiplexing with reverse transcription allows for the single-tube amplification of several RNA fragments, including an internal control sample, which provides the option of controlling all analytical steps. We developed a method of SARS-CoV-2 viral RNA detection based on multiplex reverse-transcription LAMP, with single-tube qualitative analysis of SARS-CoV-2 RNA and MS2 phage used as a control RNA. The multiplexing is based on the differences in characteristic melting peaks generated during the amplification process. The developed technique detects at least 20 copies of SARS-CoV-2 RNA per reaction on a background of 12,000 MS2 RNA copies. The total time of analysis does not exceed 40 min. The method validation, performed on 125 clinical samples of patients’ nasal swabs, showed a 97.6% concordance rate with the results of real-time (RT)-PCR assays. The developed multiplexed LAMP can be employed as an alternative to PCR in diagnostic practice to save personnel and equipment time.


Author(s):  
Paola Petrini ◽  
Daniela Pacheco ◽  
Francesco Briatico Vangosa ◽  
Cosmin S. Butnarasu ◽  
Livia Visai ◽  
...  

An airway mucus model is proposed thus serving as an in vitro screening tool with the aim to reduce the number of noneffective drugs reaching the preclinical trials. The engineered mucus model is an easy-to-use and easy-to-produce tool that can be easily coupled to state-of-art diffusion models and it is compatible with high throughput analysis. This platform will serve as the basis to implement the complexity of the model in terms of components, also including the effect of bacteria


2015 ◽  
Vol 11 (4) ◽  
pp. 233-238 ◽  
Author(s):  
Luciano Cardoso ◽  
Suellen Cordeiro ◽  
Marcio Fronza ◽  
Denise Endringer ◽  
Tadeu de Andrade ◽  
...  

Author(s):  
Ruoxing Lei ◽  
Erin A. Akins ◽  
Kelly C. Y. Wong ◽  
Nicole A. Repina ◽  
Kayla J. Wolf ◽  
...  

The Analyst ◽  
2021 ◽  
Author(s):  
Jiawei Qi ◽  
Pinhua Rao ◽  
Lele Wang ◽  
Li Xu ◽  
Yanli Wen ◽  
...  

Pattern recognition, also called “array sensing” is a recognition strategy with a wide and expandable analysis range, based on the high-throughput analysis data. In this work, we constructed a sensor...


Author(s):  
Xiaojia Jiang ◽  
Mingsong Zang ◽  
Fei Li ◽  
Chunxi Hou ◽  
Quan Luo ◽  
...  

Biological nanopore-based techniques have attracted more and more attention recently in the field of single-molecule detection, because they allow the real-time, sensitive, high-throughput analysis. Herein, we report an engineered biological...


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