Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses

Islam, Mamunul; Koirla, Dipak

doi:10.1016/j.aca.2021.339338

Cited by 31 publications

(20 citation statements)

References 336 publications

(373 reference statements)

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“…A response to those needs is the application of isothermal amplification methods that do not need thermocycling and have the potential to be applied in point-of-care tests. Isothermal amplification methods started to emerge within a few years after the invention of the PCR [ 11 ], but they have flourished as a diagnostic tool in the last few years.…”

Section: Discussionmentioning

confidence: 99%

Detection of SARS-CoV-2 Using Reverse Transcription Helicase Dependent Amplification and Reverse Transcription Loop-Mediated Amplification Combined with Lateral Flow Assay

et al. 2022

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Rapid and accurate detection and identification of pathogens in clinical samples is essential for all infection diseases. However, in the case of epidemics, it plays a key role not only in the implementation of effective therapy but also in limiting the spread of the epidemic. In this study, we present the application of two nucleic acid isothermal amplification methods—reverse transcription helicase dependent amplification (RT-HDA) and reverse transcription loop-mediated amplification (RT-LAMP)—combined with lateral flow assay as the tools for the rapid detection of SARS-CoV-2, the etiological agent of COVID-19, which caused the ongoing global pandemic. In order to optimize the RT-had, the LOD was 3 genome copies per reaction for amplification conducted for 10–20 min, whereas for RT-LAMP, the LOD was 30–300 genome copies per reaction for a reaction conducted for 40 min. No false-positive results were detected for RT-HDA conducted for 10 to 90 min, but false-positive results occurred when RT-LAMP was conducted for longer than 40 min. We concluded that RT-HDA combined with LFA is more sensitive than RT-LAMP, and it is a good alternative for the development of point-of-care tests for SARS-CoV-2 detection as this method is simple, inexpensive, practical, and does not require qualified personnel to perform the test and interpret its results.

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Section: Discussionmentioning

confidence: 99%

Detection of SARS-CoV-2 Using Reverse Transcription Helicase Dependent Amplification and Reverse Transcription Loop-Mediated Amplification Combined with Lateral Flow Assay

et al. 2022

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“…Other recent reviews have focused on different issues concerning related topics, such as on-chip cell lysis ( Grigorov et al, 2021 ; Chen Y. et al, 2022 ; Petrou and Ladame, 2022 ), the role of magnetic beads in these steps ( Chen et al, 2020a ), on-chip PCR methods ( Chen S. et al, 2022 ), the contribution of 3D printing to on-chip amplification ( Tzivelekis et al, 2021 ) and detection methods for all-in-one systems ( Li et al, 2021 ), and microfluidic sensors ( Sharma and Sharma, 2022 ). Several other reviews have also focused on these steps without limiting their scope to on-chip methods; these have covered topics such as sample preparation ( Jeon et al, 2018 ; Danaeifar, 2022 ), isothermal amplification ( Obande and Singh, 2020 ; Pumford et al, 2020 ; Islam and Koirla, 2021 ; Maiti et al, 2022 ), and detection ( Chiorcea-Paquim and Oliveira-Brett, 2021 ; Leonardo et al, 2021 ; Reyes et al, 2021 ; Bhat et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems

Wang

Jiang

Pan

et al. 2023

Front. Bioeng. Biotechnol.

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As nucleic acid testing is playing a vital role in increasingly many research fields, the need for rapid on-site testing methods is also increasing. The test procedure often consists of three steps: Sample preparation, amplification, and detection. This review covers recent advances in on-chip methods for each of these three steps and explains the principles underlying related methods. The sample preparation process is further divided into cell lysis and nucleic acid purification, and methods for the integration of these two steps on a single chip are discussed. Under amplification, on-chip studies based on PCR and isothermal amplification are covered. Three isothermal amplification methods reported to have good resistance to PCR inhibitors are selected for discussion due to their potential for use in direct amplification. Chip designs and novel strategies employed to achieve rapid extraction/amplification with satisfactory efficiency are discussed. Four detection methods providing rapid responses (fluorescent, optical, and electrochemical detection methods, plus lateral flow assay) are evaluated for their potential in rapid on-site detection. In the final section, we discuss strategies to improve the speed of the entire procedure and to integrate all three steps onto a single chip; we also comment on recent advances, and on obstacles to reducing the cost of chip manufacture and achieving mass production. We conclude that future trends will focus on effective nucleic acid extraction via combined methods and direct amplification via isothermal methods.

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“…Despite these advances, however, PCR still has a relatively long time-to-detection, and the requirement for thermocycling increases device complexity. As a possible solution to these shortcomings, isothermal amplification techniques are becoming increasingly popular in the development of point-of-use devices [ 9 , 10 , 11 ]. Of the many isothermal amplification techniques thus far developed, loop-mediated isothermal amplification (LAMP) has become popular due to its rapid, high-efficiency amplification of very low copy numbers of the template, and the theoretical potential for very high specificity [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification

Marangoni

Emadi

2023

Micromachines

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Loop-mediated isothermal amplification (LAMP) is rapidly developing into an important tool for the point-of-use detection of pathogens for both clinical and environmental samples, largely due to its sensitivity, rapidity, and adaptability to portable devices. Many methods are used to monitor LAMP, but not all are amenable to point-of-use applications. Common methods such as fluorescence often require bulky equipment, whereas colorimetric and turbidimetric methods can lack sensitivity. Electrochemical biosensors are becoming increasingly important for these applications due to their potential for low cost, high sensitivity, and capacity for miniaturization into integrated devices. This review provides an overview of the use of voltammetric sensors for monitoring LAMP, with a specific focus on how electroactive species are used to interface between the biochemical products of the LAMP reaction and the voltammetric sensor. Various strategies for the voltammetric detection of DNA amplicons as well as pyrophosphate and protons released during LAMP are presented, ranging from direct DNA binding by electroactive species to the creative use of pyrophosphate-detecting aptamers and pH-sensitive oligonucleotide structures. Hurdles for adapting these devices to point-of-use applications are also discussed.

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Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses

Cited by 31 publications

References 336 publications

Detection of SARS-CoV-2 Using Reverse Transcription Helicase Dependent Amplification and Reverse Transcription Loop-Mediated Amplification Combined with Lateral Flow Assay

Detection of SARS-CoV-2 Using Reverse Transcription Helicase Dependent Amplification and Reverse Transcription Loop-Mediated Amplification Combined with Lateral Flow Assay

Rapid on-site nucleic acid testing: On-chip sample preparation, amplification, and detection, and their integration into all-in-one systems

Strategies for the Voltammetric Detection of Loop-Mediated Isothermal Amplification

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