Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2
Abstract Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has caused a global pandemics. To facilitate the detection of SARS-CoV-2 infection, various RT-LAMP assays using 19 sets of primers had been developed, but never been compared. We performed comparative evaluation of the 19 sets of pri...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-020-80314-0 |
| _version_ | 1818843019320754176 |
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| author | Yajuan Dong Xiuming Wu Shenwei Li Renfei Lu Yingxue Li Zhenzhou Wan Jianru Qin Guoying Yu Xia Jin Chiyu Zhang |
| author_facet | Yajuan Dong Xiuming Wu Shenwei Li Renfei Lu Yingxue Li Zhenzhou Wan Jianru Qin Guoying Yu Xia Jin Chiyu Zhang |
| author_sort | Yajuan Dong |
| collection | DOAJ |
| description | Abstract Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has caused a global pandemics. To facilitate the detection of SARS-CoV-2 infection, various RT-LAMP assays using 19 sets of primers had been developed, but never been compared. We performed comparative evaluation of the 19 sets of primers using 4 RNA standards and 29 clinical samples from COVID-19 patients. Six of 15 sets of primers were firstly identified to have faster amplification when tested with four RNA standards, and were further subjected to parallel comparison with the remaining four primer sets using 29 clinical samples. Among these 10 primer sets, Set-4 had the highest positive detection rate of SARS-CoV-2 (82.8%), followed by Set-10, Set-11, and Set-13 and Set-17 (75.9%). Set-14 showed the fastest amplification speed (Tt value < 8.5 min), followed by Set-17 (Tt value < 12.5 min). Based on the overall detection performance, Set-4, Set-10, Set-11, Set-13, Set-14 and Set-17 that target Nsp3, S, S, E, N and N gene regions of SARS-CoV-2, respectively, were determined to be better than the other primer sets. Two RT-LAMP assays with the Set-4 primers in combination with any one of four other primer sets (Set-14, Set-10, Set-11, and Set-13) were recommended to be used in the COVID-19 surveillance. |
| first_indexed | 2024-12-19T04:51:13Z |
| format | Article |
| id | doaj.art-0f6ac97a74bd4c4ab10af69a7a6331d7 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T04:51:13Z |
| publishDate | 2021-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-0f6ac97a74bd4c4ab10af69a7a6331d72022-12-21T20:35:20ZengNature PortfolioScientific Reports2045-23222021-02-0111111110.1038/s41598-020-80314-0Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2Yajuan Dong0Xiuming Wu1Shenwei Li2Renfei Lu3Yingxue Li4Zhenzhou Wan5Jianru Qin6Guoying Yu7Xia Jin8Chiyu Zhang9Shanghai Public Health Clinical Center, Fudan UniversityPathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of SciencesShanghai International Travel Healthcare CenterClinical Laboratory, Nantong Third Hospital Affiliated To Nantong UniversityShanghai Public Health Clinical Center, Fudan UniversityMedical Laboratory of Taizhou Fourth People’s HospitalCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityShanghai Public Health Clinical Center, Fudan UniversityShanghai Public Health Clinical Center, Fudan UniversityAbstract Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has caused a global pandemics. To facilitate the detection of SARS-CoV-2 infection, various RT-LAMP assays using 19 sets of primers had been developed, but never been compared. We performed comparative evaluation of the 19 sets of primers using 4 RNA standards and 29 clinical samples from COVID-19 patients. Six of 15 sets of primers were firstly identified to have faster amplification when tested with four RNA standards, and were further subjected to parallel comparison with the remaining four primer sets using 29 clinical samples. Among these 10 primer sets, Set-4 had the highest positive detection rate of SARS-CoV-2 (82.8%), followed by Set-10, Set-11, and Set-13 and Set-17 (75.9%). Set-14 showed the fastest amplification speed (Tt value < 8.5 min), followed by Set-17 (Tt value < 12.5 min). Based on the overall detection performance, Set-4, Set-10, Set-11, Set-13, Set-14 and Set-17 that target Nsp3, S, S, E, N and N gene regions of SARS-CoV-2, respectively, were determined to be better than the other primer sets. Two RT-LAMP assays with the Set-4 primers in combination with any one of four other primer sets (Set-14, Set-10, Set-11, and Set-13) were recommended to be used in the COVID-19 surveillance.https://doi.org/10.1038/s41598-020-80314-0 |
| spellingShingle | Yajuan Dong Xiuming Wu Shenwei Li Renfei Lu Yingxue Li Zhenzhou Wan Jianru Qin Guoying Yu Xia Jin Chiyu Zhang Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2 Scientific Reports |
| title | Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2 |
| title_full | Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2 |
| title_fullStr | Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2 |
| title_full_unstemmed | Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2 |
| title_short | Comparative evaluation of 19 reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2 |
| title_sort | comparative evaluation of 19 reverse transcription loop mediated isothermal amplification assays for detection of sars cov 2 |
| url | https://doi.org/10.1038/s41598-020-80314-0 |
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