Self-Sampled Gargle Water Direct RT-LAMP as a Screening Method for the Detection of SARS-CoV-2 Infections

Abstract

We assessed the viability of self-sampled gargle water direct RT-LAMP (LAMP) for detecting SARS-CoV-2 infections by estimating its sensitivity with respect to the gold standard indirect RT-PCR of paired oro-nasopharyngeal swab samples. We also assessed the impact of symptom onset to test time (STT)-i.e., symptom days at sampling, on LAMP. In addition, we appraised the viability of gargle water self-sampling versus oro-nasopharyngeal swab sampling, by comparing paired indirect RT-PCR results. 202 oro-nasopharyngeal swab and paired self-sampled gargle water samples were collected from hospital patients with COVID-19 associated symptoms. LAMP, indirect and direct RT-PCR were performed on all gargle water samples, and indirect RT-PCR was performed on all oro-nasopharyngeal samples. LAMP presented a sensitivity of 80.8% (95% CI: 70.8-90.8%) for sample pairs with sub-25 Ct oro-nasopharyngeal indirect RT-PCR results, and 77.6% (66.2-89.1%) sensitivity for sub-30 Ct samples with STT ≤ 7 days. STT, independently of Ct value, correlated negatively with LAMP performance. 80.7% agreement was observed between gargle water and oro-nasopharyngeal indirect RT-PCR results. In conclusion, LAMP presents an acceptable sensitivity for low Ct and low STT samples. Gargle water may be considered as a viable sampling method, and LAMP as a screening method, especially for symptomatic persons with low STT values.

Keywords: COVID-19; LAMP; RT-PCR; SARS-CoV-2; direct RT-LAMP; gargle water; loop-mediated isothermal amplification; self-sampling; viral diseases.

Figure 1

The cumulative sensitivity of LAMP displays a negative correlation with increasing Ct value cut-offs. The cut-offs were applied on the Ct values derived from the RT-PCR of paired oro-nasopharyngeal samples. The orange band presents 95% Wilson score (confidence) intervals for the sensitivities with respect to the given Ct value cut-offs. The black line presents the center values of these intervals. The numbers directly above the black center-value line indicate the number of sample pairs satisfying a given Ct value cut-off.

Figure 2

The RT-PCR Ct values and LAMP results for sample pairs with at least one positive RT-PCR result. The sample pairs where both the gargle water and swab yielded positive (sub 40 Ct) indirect RT-PCR results are distributed across the bottom left 2-D plane. For sample pairs where only one out of the two samples yielded a positive RT-PCR result, the corresponding data-point is situated on the 1-D line indicating its Ct value. For all data points, the color of the point indicates the gargle water LAMP result, with yellow corresponding to a positive result and purple to a negative result.