China
Africa
Explore chapters and articles related to this topic
Yellow Fever: Emergence and Reality
Published in Jagriti Narang, Manika Khanuja, Small Bite, Big Threat, 2020
Neelam Yadav, Bennet Angel, Jagriti Narang, Surender Singh Yadav, Vinod Joshi, Annette Angel
Conversely, direct detection methods for YFV provide a transferable, facile, and robust technique, which is convenient in limited resource settings as well as in diagnosis in the field as well during epidemic (Escadafal et al., 2014). Thus, novel molecular techniques based on isothermal amplification have been developed for the detection of YFV. These techniques include real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) (Kwallah et al., 2013) and helicase-dependent amplification assays (HDA) (Domingo et al., 2012), reverse transcriptase recombinase polymerase amplification (RPA) assay for YFV detection (Escadafal, et al., 2014).
Distribution
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
Meanwhile, the heterogeneous asymmetric recombinase polymerase amplification (haRPA) was applied for the phage MS2 detection in combination with the stepwise phage concentration from 1250 L drinking water into 1 mL (Elsäßer et al. 2018). Since then, digital PCR (dPCR) has become a promising technology for absolute quantification of nucleic acid without need of calibration curves. Following dPCR, various digital isothermal amplification methods were also developed which only required isothermal incubation. Among them, a loop-mediated isothermal amplification, or LAMP, became the most popular one and was adapted to the rapid enumeration of the phage MS2 as a model (Huang X et al. 2018; Lin et al. 2019).
The Evolution of COVID-19 Diagnostics
Published in Debmalya Barh, Kenneth Lundstrom, COVID-19, 2022
Praveen Rai, Ballamoole Krishna Kumar, Deekshit Vijaya Kumar, Prashant Kumar, Anoop Kumar, Shashi Kumar Shetty, Biswajit Maiti
RT-RPA is a technique developed using proteins involved in DNA synthesis, repair and recombination. In this technique, a recombinase protein uvsX from T4-like bacteriophages was used to bind to primers in the presence of ATP and a crowding agent (polyethylene glycol), forming a recombinase-primer complex. The complex is then allowed to interact with the double-stranded DNA with a homologous sequence that in turn promotes strand invasion by the primer. The proteins in the complex will stabilize the displaced DNA strand. Finally, the recombinase enzyme disassembles, and a strand displacing DNA polymerase binds to the 3′ end of the primer to elongate it in the presence of dNTPs. The process is then repeated in several cycles to achieve exponential amplification [38]. The technique has been widely used in combination with reverse transcription for the detection of SARS-CoV-2 on an OR-DETECTR platform that combines RPA and CRISPR/Cas12 technologies for two transcripts, the RdRp and N genes. The limit of detection for RdRp was found to be 20 copies/μl and 1 copy/μl of the N gene. A similar one-tube method based on RT-RPA and SHERLOCK (OR-SHERLOCK) combines RT-RPA and CRISPR/Cas13a detection with the same level of sensitivity and specificity as that of OR-DETECTR [39]. A microfluidic-integrated lateral flow recombinase polymerase amplification (MI-IF-RPA) assay was developed for rapid detection of SARS-CoV-2. The technique combines RT-RPA and a universal lateral flow (LF) dipstick detection system into a single microfluidic chip. The RT-RPA reaction components are mixed with running buffer and then delivered to the LF detection strips for biotin- and FAM-labeled amplified analyte sequences, which can provide easily interpreted positive or negative results. The technique showed the limit of detection of 1 copy/μl or 30 copies per sample with 97% to 100% specificity [40].
LAMP Diagnostics at the Point-of-Care: Emerging Trends and Perspectives for the Developer Community
Published in Expert Review of Molecular Diagnostics, 2021
Taylor J. Moehling, Gihoon Choi, Lawrence C. Dugan, Marc Salit, Robert J. Meagher
LAMP has its origins in the late 1990s, which was a period of innovation in isothermal molecular diagnostics. Many of the isothermal methods that were developed around the same time currently attract limited academic or commercial attention, while LAMP has been steadily increasing in popularity. In recent years, recombinase polymerase amplification (RPA) gained interest, with seemingly desirable performance characteristics, including very low limits of detection, rapid amplification, and low power requirements. But with the emergence of the COVID-19 pandemic and the ensuing gaps in reverse transcription quantitative polymerase chain reaction (RT-qPCR) diagnostic capabilities, it was RT-LAMP that emerged as the ‘PCR alternative’ of choice, with rapid development efforts by numerous academic and commercial test developers.
Advances in technologies for cervical cancer detection in low-resource settings
Published in Expert Review of Molecular Diagnostics, 2019
Kathryn A. Kundrod, Chelsey A. Smith, Brady Hunt, Richard A. Schwarz, Kathleen Schmeler, Rebecca Richards-Kortum
Other groups have developed paper platforms for individual components of nucleic acid testing including sample preparation, amplification, and detection, which are discussed in a recent review article [112]. Many of these devices use isothermal amplification of DNA with a single temperature heater, or body heat in the case of recombinase polymerase amplification (RPA), to reduce equipment and infrastructure needs [113]. Despite these advances, no truly point-of-care platform for DNA or RNA amplification has been validated with large-scale clinical studies in low-resource settings.
Diagnostic efficiency of RT-LAMP integrated CRISPR-Cas technique for COVID-19: A systematic review and meta-analysis
Published in Pathogens and Global Health, 2022
Akansha Bhatt, Gurvinder Singh Bumbrah, Munindra Ruwali, Saif Hameed, Zeeshan Fatima
The rapid, accessible, and accurate nature of diagnostic tests for coronavirus infections is crucial for patient management and to control the pandemic. Quantitative reverse transcription-polymerase chain reaction (RT-qPCR) is the mostly used detection method for SARS-CoV-2 with the application of Reverse transcription-Loop Associated mediated amplification (RT-LAMP) as a new addition to the diagnosis of the SARS-CoV2 [6, 7]. To fulfill the demand for rapid diagnosis during disease outbreaks, point-of-care tests (POCTs) are needed that are cheaper, faster, and deployable in the field. Various commercially and non-commercially developed tests have been reported since the pandemic started. Most of the commercially available kits are based on RT-qPCR. Non-commercially available tests are based on RT-LAMP, CRISPR, Biosensors, Sequencing-based tests, etc. These tests predominantly target five genes – ORF1 (Open Reading Frame 1), N (Nucleoprotein), E (Envelope), S (Spike), and RdRp (Recombinant dependent RNA polymerase) [8, 9]. Nucleic acid-based detections relying on isothermal amplification such as RT-LAMP and RT-RPA (Reverse Transcription-Recombinase polymerase amplification) obviate the need for a thermal cycler and these methods are also cost-effective, less time-consuming, and realistic [10, 11]. Simple amplification-based assay (SAMBA) uses DNA-dependent RNA polymerase and RNA-dependent DNA polymerase to alternately transcribe and reverse transcribe RNA target. CRISPR diagnosis combines isothermal amplification techniques (such as RT-LAMP and RT-RPA) with specific DNA or RNA targeting ability of crRNA and Cas12 [12, 13] or Cas13 [14, [5]Schermer et al., 2020] enzymes. The outputs of these detection techniques can be coupled with fluorescent or colorimetric reporters as well as lateral flow strip platforms to facilitate readout processes.