Simple RNA extraction method for reverse transcription loop-mediated amplification detection of SARS-CoV-2

Zulkefli, Nur Zulaikha and Bukhari, Fatma Diyana Mohd and Lai, Meng Yee and Suppiah, Jeyanthi and Thayan, Ravindran and Mat Isa, Mohd Khairi and Lau, Yee Ling (2022) Simple RNA extraction method for reverse transcription loop-mediated amplification detection of SARS-CoV-2. Southeast Asian Journal of Tropical Medicine and Public Health, 53 (3). pp. 345-355. ISSN 0125-1562,

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Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a robust and cost-effective assay for rapid diagnosis of SARS-CoV-2 compared to reverse transcription quantitative (RT-q) PCR. The study evaluated the performance of RT-LAMP technique that incorporated a simple Chelex 100 resin-based RNA extraction step for SARS-CoV-2 detection targeting virus E (encoding envelope protein) and RdRP (encoding RNA-dependent RNA polymerase). Using primer sets for E and RdRP, the developed RT-LAMP assay had a limit of detection (LOD) of 1 copy/mu l transcribed RNA. For nasopharyngeal and oropharyngeal swab samples (n = 58), in comparison to the gold standard RT-qPCR (amplifying E and RdRP) sensitivity, specificity, positive predictive value, and negative predictive value of SARS-CoV-2 RT-LAMP assay targeting E gene was 88% (95% confidence interval (CI): 75-96%), 87% (95% CI: 59-98%), 99% (95% CI: 97-100%), and 28% (95% CI: 14-48%), respectively and for RdRP gene was 67% (95% CI: 51-98%), 87% (95% CI: 59-98%), 100% (95% CI: 96-100%), and 12% (95% CI : 8-18%), respectively. The whole process of RT-LAMP assay was completed within similar to 60 minutes. This developed RT-LAMP method for on-site COVID-19 detection should be useful in resource limited settings.

Item Type: Article
Funders: Prototype Research Grant Scheme (PRGS), Ministry of Education, Malaysia [PR001-2020B (PRGS/2/2020/S K K 0 9/U M/0 2/1)], Ministry of Education, Malaysia
Uncontrolled Keywords: COVID-19; Chelex resin; Rapid detection; LAMP assay; SARS-CoV-2
Subjects: R Medicine
Divisions: Faculty of Medicine
Depositing User: Ms. Juhaida Abd Rahim
Date Deposited: 25 Sep 2023 02:43
Last Modified: 25 Sep 2023 02:43

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