Detection of SARS-CoV-2 RNA in Urine by RT-LAMP: A Very Rare Finding

Abstract

Detection of SARS-CoV-2 is routinely performed in naso/oropharyngeal swabs samples from patients via RT-qPCR. The RT-LAMP technology has also been used for viral RNA detection in respiratory specimens with both high sensitivity and specificity. Recently, we developed a novel RT-LAMP test for SARS-CoV-2 RNA detection in nasopharyngeal swab specimens (named, N15-RT-LAMP) that can be performed as a single-tube colorimetric method, in a real-time platform, and as dry-LAMP. To date, there has been very little success in detecting SARS-CoV-2 RNA in urine by RT-qPCR, and the information regarding urine viral excretion is still scarce and not comprehensive. Here, we tested our N15-RT-LAMP on the urine of 300 patients admitted to the Hospital of Salamanca, Spain with clinical suspicion of COVID-19, who had a nasopharyngeal swab RT-qPCR-positive (n = 100), negative (n = 100), and positive with disease recovery (n = 100) result. The positive group was also tested by RT-qPCR for comparison to N15-RT-LAMP. Only a 4% positivity rate was found in the positive group via colorimetric N15-RT-LAMP and 2% via RT-qPCR. Our results are consistent with those obtained in other studies that the presence of SARS-CoV-2 RNA in urine is a very rare finding. The absence of SARS-CoV-2 RNA in urine in the recovered patients might suggest that the urinary route is very rarely used for viral particle clearance.

Keywords: COVID-19; RT-LAMP; RT-qPCR; SARS-CoV-2; molecular diagnostics; urine.

Figure 1

Flowchart describing the process of patient group selection and urine sample analysis strategy. RT-qPCR, reverse transcription-polymerase chain reaction; RT-LAMP, reverse transcription loop-mediated isothermal amplification.

Figure 2

Detection of SARS-CoV-2 RNA in urine samples by colorimetric and real-time N15-RT-LAMP. (a) Colorimetric N15-RT-LAMP: results detected with SYBR Green I. Green/yellow, positive results; orange, negative results. (b) Real-time N15-RT-LAMP: results detected by fluorescence in a Genie III device. PTC, positive template control (2 μL of RNA purified from a nasopharyngeal swab from a patient with a RT-qPCR-positive result for SARS-CoV-2; Ct = 25 for ORF1ab); PP21, PP36, PP58, and PP80, patient urine samples; NTC, negative template control (2 μL of ultrapure water instead RNA).