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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.
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1 Fudan University, Shanghai Public Health Clinical Center, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443); Henan Normal University, College of Life Sciences, Xinxiang, China (GRID:grid.462338.8) (ISNI:0000 0004 0605 6769)
2 Chinese Academy of Sciences, Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Shanghai, China (GRID:grid.9227.e) (ISNI:0000000119573309); Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China (GRID:grid.464493.8)
3 Shanghai International Travel Healthcare Center, Shanghai, China (GRID:grid.464493.8)
4 Nantong Third Hospital Affiliated To Nantong University, Clinical Laboratory, Nantong, China (GRID:grid.260483.b) (ISNI:0000 0000 9530 8833)
5 Fudan University, Shanghai Public Health Clinical Center, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443); Chinese Academy of Sciences, CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Suzhou, China (GRID:grid.9227.e) (ISNI:0000000119573309)
6 Medical Laboratory of Taizhou Fourth People’s Hospital, Taizhou, China (GRID:grid.490502.a)
7 Henan Normal University, College of Life Sciences, Xinxiang, China (GRID:grid.462338.8) (ISNI:0000 0004 0605 6769)
8 Fudan University, Shanghai Public Health Clinical Center, Shanghai, China (GRID:grid.8547.e) (ISNI:0000 0001 0125 2443)