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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
Additionally, other amplification methods for the detection of SARS-CoV-2 are under development or undergoing the process of commercialization. These methods involve technologies such as Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP), Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR), and molecular microarray assays. An overview of the nuclei acid–based diagnostic assays available for the diagnosis of COVID-19 infection is presented in Figure 6.2. The serological assays include the detection of viral protein in respiratory tract specimens. These are rapid tests that are based on Lateral Flow Immunoassays (LFI) and can be completed within 30 minutes. However, the sensitivity of LFI-based rapid tests is lower than for NAAT [9]. Moreover, false-positive results can also exist for the rapid tests if the antibodies on the test strip cross-react with the antigen of other viruses than SARS-CoV-2.
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).
Paracoccidioides Complex
Published in Rossana de Aguiar Cordeiro, Pocket Guide to Mycological Diagnosis, 2019
Zoilo Pires de Camargo, Anderson Messias Rodrigues
Loop mediated isothermal amplification (LAMP) is a single-tube technique for the amplification of DNA and was successfully used to detect in a specific manner the gp43 gene of P. brasiliensis (Endo et al., 2004) in a set of 22 clinical and 7 armadillo-derived isolates.
Updated considerations in the diagnosis and management of tuberculosis infection and disease: integrating the latest evidence-based strategies
Published in Expert Review of Anti-infective Therapy, 2023
Daniel S. Graciaa, Marcos Coutinho Schechter, Krystle B. Fetalvero, Lisa Marie Cranmer, Russell R. Kempker, Kenneth G. Castro
More affordable devices meant to be used in peripheral healthcare settings have also been endorsed by WHO, including the Loopamp MTBC assay and Truenat assays. Loop-mediated isothermal amplification (LAMP) uses an isothermal PCR amplification technique that requires minimal laboratory equipment and while endorsed as replacement to smear microscopy since 2016, has been underutilized to date. The Truenat assays including Truenat MTB Plus and Truenat MTB-RIF Dx (Molbio Diagnostics) run on the Truelab platform, which uses a chip-based, micro-real-time PCR technique that can provide results in 1 h [46]. Initial results are comparable to the Xpert Ultra and the WHO has a conditional recommendation to use Truenat as an initial test for Mtb and rifampicin resistance detection.
Molecular Diagnostic Tools for the Detection of SARS-CoV-2
Published in International Reviews of Immunology, 2021
Manali Datta, Desh Deepak Singh, Afsar R. Naqvi
Loop-mediated Isothermal Amplification (LAMP) is a single tube reaction generally used for the detection of DNA and RNA sequences. This technique uses a combination of 4–6 primers against different loci of target DNA sequences with the reaction temperature varying between 60 and 65 °C. The RT-LAMP assay has a significant edge given that SARS-CoV-2 is an RNA virus with length of about 30 kB and combined reverse transcription (RT) and LAMP together significantly diminishes detection time. An amplified product was detected via phenol red-based photometry whereby detection limit of the colorimetric RT-LAMP assay could detect a threshold cycle (CT) ≈ 30. Another group led by Xiaojing Li demonstrated that the RT-LAMP assay in clinical samples had a high specificity (99.5%), sensitivity (91.4%) and a positive predictive value (97.7%). An advanced methodology, swab-to-RT-LAMP assay, uses NPS and OPS and exhibited a high sensitivity for samples with a CT < 25. New England Biolabs (NEB) has developed a Quick Colorimetric LAMP Kit, which may be used to detect novel coronavirus RNA. The kit acts as a simple alternative to RT-qPCR and enables visual discovery of amplification of SARS-CoV-2 nucleic acid in only 30 min [33,34].
Loop-mediated isothermal amplification assay as a point-of-care diagnostic tool for Vibrio parahaemolyticus: recent developments and improvements
Published in Expert Review of Molecular Diagnostics, 2019
Karanth Padyana Anupama, Anirban Chakraborty, Iddya Karunasagar, Indrani Karunasagar, Biswajit Maiti
Loop-mediated isothermal amplification (LAMP) is a nucleic acid-based technique that enables DNA amplification under isothermal conditions. It requires a set of four specially designed primers that recognize six distinct regions of the target, and a Bst DNA polymerase with strand displacement activity [27–30]. LAMP assay has the potential to transform the landscape of the existing molecular-based diagnostic techniques. The assay can be done without any sophisticated equipment, without compromising the specificity and sensitivity levels. LAMP is capable of producing a large number of amplicons within an hour [27], and hence, it can be used as the point-of-care diagnostic technique for the identification of foodborne pathogens [28,31–33]. The assay can be carried out directly by eliminating the DNA extraction step [34–36], which has almost no impact as far as the sensitivity of the assay is concerned [27,37]. Unlike PCR assay, the LAMP assays are generally resistant to inhibitors like blood, serum and food ingredients [37–39]. LAMP assays are more sensitive and accurate compared to PCR assays including qPCR [29–32,40,41].