Evaluation of the efficacy of LAMP-based SARS-CoV-2 detection with simple RNA extraction from nasopharyngeal swabs: A prospective observational study

Abstract

The Loopamp SARS-CoV-2 Detection Kit is used for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Loop-mediated isothermal amplification (LAMP) is based on a measurement principle that can be used with a relatively simple device. Detection using this kit requires viral RNA extraction from samples with the QIAGEN QIAamp Viral Mini Kit (QIAGEN extraction) or the Loopamp Viral RNA Extraction Kit (Eiken extraction), which are recommended by the manufacturer. However, the efficacy of LAMP-based SARS-CoV-2 detection using these extraction methods has not been compared. In this study, we aimed to compare the results of genome extraction and detection from nasopharyngeal swab samples using the QIAGEN and Eiken extraction kits. The present study involved patients who presented to the Rinku General Medical Center with suspected COVID-19 (25 positive and 26 negative cases). A comparison of the results obtained using each extraction method with those obtained via PCR showed that the positive, negative, and overall concordance rates between QIAGEN extraction and PCR were 96.0% (24/25 samples), 100% (26/26), and 98.0% (50/51; κ = 0.96, 95% CI = 0.69-1.00), respectively. Results with Eiken extraction were also favorable, with positive, negative, and overall concordance rates of 88.0% (22/25), 100% (26/26), and 94.1% (48/51; κ = 0.88, 95% CI = 0.61-1.00), respectively. Favorable results were obtained using both QIAGEN and Eiken extraction kits. Since Eiken extraction can be completed in a few minutes, it enables prompt and reliable testing for SARS-CoV-2 detection.

Fig 1. Relation between PCR and LAMP deviations and timing of specimen collection.

For all PCR-positive cases, the Ct values of PCR and the days after the onset of symptoms were plotted. White and black circles indicate the E-LAMP-positive and -negative cases, respectively. The days after onset of symptoms and Ct values according to PCR for the E-LAMP-negative cases are indicated in the figure.

Fig 2. Trend for the Tt value with LAMP, with focus on the time since onset.

(A) Tt values of LAMP and the number of days elapsed since the onset of disease in Q-LAMP-and E-LAMP-positive cases are shown. Black and white triangles indicate the Q-LAMP- and E-LAMP-positive cases, respectively. (B) The difference is calculated between the Tt values for LAMP performed using the two extraction methods and represented along with the days after onset of symptoms. Samples R-001, R-038, and R-044 were excluded (ref. Table 2).

Fig 3. Correlation between the Ct value with PCR and Tt value with LAMP.

(A) The Tt values with LAMP and Ct values with RT-PCR in Q-LAMP- and E-LAMP-positive cases are presented. Black and white triangles indicate the Q-LAMP- and E-LAMP-positive cases, respectively. (B) The gap in the Tt values calculated in 2B is shown along with the Ct value with PCR. Samples R-001, R-038, and R-044 were excluded (ref. Table 2).

Fig 4. The turnaround time of the detection test for SARS-CoV-2 using E-LAMP.

The number of LAMP tests per indicated TAT (bar graph; left axis) and the cumulative percentage of all samples (line graph; right axis) are presented.