A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples
The raging COVID-19 pandemic has created an unprecedented demand for frequent and widespread testing to limit viral transmission. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a promising diagnostic platform for rapid detection of SARS-CoV-2, in part because i...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2022
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| Online Access: | https://hdl.handle.net/10356/162367 |
| _version_ | 1826124784151298048 |
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| author | Ooi, Kean Hean Liu, Mengying Mandy Moo, Jia Rong Nimsamer, Pattaraporn Payungporn, Sunchai Kaewsapsak, Pornchai Tan, Meng How |
| author2 | School of Chemical and Biomedical Engineering |
| author_facet | School of Chemical and Biomedical Engineering Ooi, Kean Hean Liu, Mengying Mandy Moo, Jia Rong Nimsamer, Pattaraporn Payungporn, Sunchai Kaewsapsak, Pornchai Tan, Meng How |
| author_sort | Ooi, Kean Hean |
| collection | NTU |
| description | The raging COVID-19 pandemic has created an unprecedented demand for frequent and widespread testing to limit viral transmission. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a promising diagnostic platform for rapid detection of SARS-CoV-2, in part because it can be performed with simple instrumentation. However, isothermal amplification methods frequently yield spurious amplicons even in the absence of a template. Consequently, RT-LAMP assays can produce false positive results when they are based on generic intercalating dyes or pH-sensitive indicators. Here, we report the development of a sensitive RT-LAMP assay that leverages on a novel sequence-specific probe to guard against spurious amplicons. We show that our optimized fluorescent assay, termed LANTERN, takes only 30 min to complete and can be applied directly on swab or saliva samples. Furthermore, utilizing clinical RNA samples from 52 patients with COVID-19 infection and 21 healthy individuals, we demonstrate that our diagnostic test exhibits a specificity and positive predictive value of 95% with a sensitivity of 8 copies per reaction. Hence, our new probe-based RT-LAMP assay can serve as an inexpensive method for point-of-need diagnosis of COVID-19 and other infectious diseases. |
| first_indexed | 2024-10-01T06:26:20Z |
| format | Journal Article |
| id | ntu-10356/162367 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T06:26:20Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | ntu-10356/1623672022-10-17T04:00:42Z A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples Ooi, Kean Hean Liu, Mengying Mandy Moo, Jia Rong Nimsamer, Pattaraporn Payungporn, Sunchai Kaewsapsak, Pornchai Tan, Meng How School of Chemical and Biomedical Engineering School of Biological Sciences Genome Institute of Singapore, A*STAR Engineering::Bioengineering Diagnostics COVID-19 The raging COVID-19 pandemic has created an unprecedented demand for frequent and widespread testing to limit viral transmission. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has emerged as a promising diagnostic platform for rapid detection of SARS-CoV-2, in part because it can be performed with simple instrumentation. However, isothermal amplification methods frequently yield spurious amplicons even in the absence of a template. Consequently, RT-LAMP assays can produce false positive results when they are based on generic intercalating dyes or pH-sensitive indicators. Here, we report the development of a sensitive RT-LAMP assay that leverages on a novel sequence-specific probe to guard against spurious amplicons. We show that our optimized fluorescent assay, termed LANTERN, takes only 30 min to complete and can be applied directly on swab or saliva samples. Furthermore, utilizing clinical RNA samples from 52 patients with COVID-19 infection and 21 healthy individuals, we demonstrate that our diagnostic test exhibits a specificity and positive predictive value of 95% with a sensitivity of 8 copies per reaction. Hence, our new probe-based RT-LAMP assay can serve as an inexpensive method for point-of-need diagnosis of COVID-19 and other infectious diseases. Agency for Science, Technology and Research (A*STAR) Ministry of Education (MOE) Nanyang Technological University This work is supported by a Ministry of Education Academic Research Fund Tier 1 Grant (2017-T1-001-214 to M.H.T.), a Gap Fund from Ministry of Education (NGF-2020-08-015 to M.H.T.), a Gap Fund from A*STAR (ACCL/19-GAP064-R20H-N to M.H.T.), and a NTU Research Scholarship (to M.M.L.). 2022-10-17T04:00:42Z 2022-10-17T04:00:42Z 2022 Journal Article Ooi, K. H., Liu, M. M., Moo, J. R., Nimsamer, P., Payungporn, S., Kaewsapsak, P. & Tan, M. H. (2022). A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples. ACS Synthetic Biology, 11(1), 448-463. https://dx.doi.org/10.1021/acssynbio.1c00538 2161-5063 https://hdl.handle.net/10356/162367 10.1021/acssynbio.1c00538 34981924 2-s2.0-85122747755 1 11 448 463 en 2017-T1-001-214 NGF-2020-08-015 ACCL/19-GAP064-R20H-N ACS Synthetic Biology © 2022 American Chemical Society. All rights reserved. |
| spellingShingle | Engineering::Bioengineering Diagnostics COVID-19 Ooi, Kean Hean Liu, Mengying Mandy Moo, Jia Rong Nimsamer, Pattaraporn Payungporn, Sunchai Kaewsapsak, Pornchai Tan, Meng How A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples |
| title | A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples |
| title_full | A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples |
| title_fullStr | A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples |
| title_full_unstemmed | A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples |
| title_short | A sensitive and specific fluorescent RT-LAMP assay for SARS-CoV‑2 detection in clinical samples |
| title_sort | sensitive and specific fluorescent rt lamp assay for sars cov 2 detection in clinical samples |
| topic | Engineering::Bioengineering Diagnostics COVID-19 |
| url | https://hdl.handle.net/10356/162367 |
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