Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening

Abstract

In the context of social events reopening and economic relaunch, sanitary surveillance of SARS-CoV-2 infection is still required. Here, we evaluated the diagnostic performances of a rapid, extraction-free and connected reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay on saliva. Nasopharyngeal (NP) swabs and saliva from 443 outpatients were collected simultaneously and tested by reverse-transcription quantitative PCR (RT-qPCR) as reference standard test. Seventy-one individuals (16.0%) were positive by NP and/or salivary RT-qPCR. Sensitivity and specificity of salivary RT-LAMP were 85.9% (95%CI 77.8-94.0%) and 99.5% (98.7-100%), respectively. Performances were similar for symptomatic and asymptomatic participants. Moreover, SARS-CoV-2 genetic variants were analyzed and no dominant mutation in RT-LAMP primer region was observed during the period of the study. We demonstrated that this RT-LAMP test on self-collected saliva is reliable for SARS-CoV-2 detection. This simple connected test with optional automatic results transfer to health authorities is unique and opens the way to secure professional and social events in actual context of economics restart.

Figure 1

Study flow diagram. RT-LAMP, reverse transcription loop-mediated isothermal amplification; COVID, Coronavirus disease; TN, true negative; FN, false negative; TP, true positive; FP, false positive for salivary RT-LAMP.

Figure 2

(A) Sensitivity of salivary RT-LAMP evaluated against NP and salivary RT-qPCR Ct values. Ct value cutoffs indicate the infectious status of individuals considered as positive/negative. Dots show sensitivity (%) of RT-LAMP against salivary RT-qPCR (R² = 0.92). Triangles show sensitivity (%) of salivary RT-LAMP compared to NP RT-qPCR (R² = 0.61). RT-qPCR, reverse transcription quantitative polymerase chain reaction; RT-LAMP, reverse transcription loop-mediated isothermal amplification; NP, nasopharyngeal; Sal, salivary; Ct, cycle threshold. (B) Comparison of Ct Value between NP and salivary RT-qPCR. Dots represent experimentally measured Ct values of nasopharyngeal (X) and salivary (Y) RT-qPCR. Positive concordant individuals (positive for both NP and salivary RT-qPCR) are in down left white corner . Negative concordant individuals (Ct value ≥ 35 for both NP and salivary RT-qPCR) are in upper right white corner . Discordant results (negative for one specimen and positive for the other in RT-qPCR) are on the grey zones of the graphic (NP+/Sal- ; NP-/Sal+).