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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.
The Precision Medicine Approach in Oncology
Published in David E. Thurston, Ilona Pysz, Chemistry and Pharmacology of Anticancer Drugs, 2021
The test works by specifically detecting the level of expression of cytokeratin-19 (CK19), an epithelial marker associated with breast cancer which is normally not present in healthy lymph node tissue. Crucially, the levels of cytokeratin-19 correlate with the number of metastatic cells present. The test involves homogenization of sentinel lymph node tissue followed by analysis of the CK19 mRNA using RT-LAMP (Reverse Transcription Loop Mediated Isothermal Amplification). The system does not require mRNA to be extracted from the tissue and purified before analysis which is a significant advantage in an operating theater environment, and the reason why previous attempts to carry out such intraoperative molecular-based tests during surgery failed.
Chikungunya 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
Singhal et al. (2018) have developed a genosensor based on 2D MoS2 nanosheets for the detection of CHIKV. The genosensor exhibited a linear range of 0.1 nm to 0.1 µM, and the MoS2-based genosensor was highly specific, sensitive, and efficient for detecting CHIKV. Lopez-Jimena et al. (2018) have developed a uni-tube one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for quick investigation of CHIKV, which is based on targeting the conserved 6K-E1. The assay has been tested with sera obtained from a CHIKV outbreak in Senegal in 2015.
Advances in RT-LAMP for COVID-19 testing and diagnosis
Published in Expert Review of Molecular Diagnostics, 2023
Gihoon Choi, Taylor J. Moehling, Robert J. Meagher
The SARS-CoV-2 pandemic has brought the need for viral diagnostics into the spotlight. Terms like ‘PCR tests’ and ‘rapid antigen tests’ have entered the everyday lexicon in the United States. Rapid antigen tests have made at-home testing for infectious diseases routine for many people. The need for frequent diagnostic testing has also expanded interest in reverse transcription loop-mediated isothermal amplification (RT-LAMP) for research and clinical applications. LAMP has long been positioned as a lower-complexity alternative to PCR for use in low-resource settings, for neglected tropical diseases and plant and animal pathogens in locations where quantitative PCR (qPCR) is too costly or inaccessible. Early in the SARS-CoV-2 pandemic, RT-qPCR laboratory capacity was severely strained, and suddenly the entire world, including developed nations with advanced medical systems, had a need for novel diagnostic capabilities. SARS-CoV-2 thus generated unprecedented interest in RT-LAMP, as exemplified by hundreds of scientific publications describing new RT-LAMP assays, including new instruments and microfluidic devices, and simplified workflows. All these publications aimed to expand testing capability beyond RT-qPCR.
Diagnostic accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins in pharyngeal swabs compared to RT-PCR as a reference test
Published in Expert Review of Molecular Diagnostics, 2022
Milad Shirvaliloo, Roghayeh Sheervalilou, Ehsan Ahmadpour, Saeid Safiri, Hossein Bannazadeh Baghi
Regardless of the sample type, time and time again, RT-PCR is either replaced or complemented with other diagnostic modalities, including reverse transcription loop-mediated isothermal amplification (RT-LAMP), IgM/IgG antibody assays, and CRISPR/Cas, the latter of which is less-studied than the formers [42]. As an independent platform, RT-LAMP is still subject to a two-fold higher rate of false negatives than RT-PCR [43]. Anti-SARS-CoV-2 antibody assays, on the other hand, are far from being perfect as a result of temporal changes in serum levels of antibodies, they can be used for ruling out COVID-19 in individuals suspected to have false negative RT-PCR results or follow-up of patients who had the disease in the past [44]. Nevertheless, it should be noted that even RT-PCR itself is not 100% reliable. According to a number of investigations, RT-PCR might falsely identify a COVID-19 patient as a healthy individual 0.2–5.8% of instances, depending on the regional prevalence of disease. The rate of misdiagnosis may go as high as 29% when the prevalence is 50%, i.e. one out of two individuals is infected [45]. Despite certain limitations, PCR is a highly flexible technology that can be incorporated into newer platforms like droplet digital PCR (ddPCR), which is believed to be more accurate than its conventional counterpart [46].
Molecular diagnostic assays for COVID-19: an overview
Published in Critical Reviews in Clinical Laboratory Sciences, 2021
Parham Habibzadeh, Mohammad Mofatteh, Mohammad Silawi, Saeid Ghavami, Mohammad Ali Faghihi
Reverse transcription loop-mediated isothermal amplification (RT-LAMP), which uses four to six sets of primers specifically designed to bind to distinct target regions, allows the identification of RNA sequences of interest [45,46] (Figure 3). The higher number of primers used in this method leads to an overall increase in the specificity of this assay [45]. Detection methods include measurement of turbidity caused by magnesium pyrophosphate precipitation during the reaction or use of fluorescent dyes [47]. RT-LAMP, which was used for the detection of the previous Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) global outbreaks, has also been shown to be an efficient diagnostic assay for SARS-CoV-2 [48–50]. In a study that analyzed 130 clinical specimens of individuals suspected to be infected with SARS-CoV-2 and compared the diagnostic accuracy of RT-LAMP with RT-PCR as the reference standard, RT-LAMP had a sensitivity of 100% (95% confidence interval [CI] 92.3-100%) and specificity of 100% (95% CI 93.7–100%); notably, the RT-LAMP assay detected the virus in a mean duration of 26.28 min while the RT-PCR assay required 1–2 h after viral RNA extraction [48].