Performance of colorimetric reverse transcription loop-mediated isothermal amplification as a diagnostic tool for SARS-CoV-2 infection during the fourth wave of COVID-19 in Thailand

Abstract

Background: COVID-19, which is caused by SARS-CoV-2 and its variants, poses an ongoing global threat, particularly in low-immunization coverage regions. Thus, rapid, accurate, and easy-to-perform diagnostic methods are in urgent demand to halt the spread of the virus.

Objectives: We aimed to validate the clinical performance of the FastProof 30 min-TTR SARS-CoV-2 reverse transcription loop-mediated isothermal amplification (RT-LAMP) method using leftover RNA samples extracted from 315 nasopharyngeal swabs. The sensitivity and specificity of RT-LAMP were determined in comparison with reverse transcriptase-polymerase chain reaction (RT-PCR).

Results: Of 315 nasopharyngeal swabs, viral RNA was detected in 154 samples (48.9%) by RT-PCR assay. Compared with RT-PCR, overall sensitivity and specificity of RT-LAMP were 81.82% (95% CI: 74.81-87.57) and 100% (95% CI: 97.73-100), respectively. A 100% positivity rate was achieved in samples with cycle threshold (Ct) <31 for RT-PCR targeting the ORF1ab gene. However, samples with Ct >31 accounted for false-negative results by RT-LAMP in 28 samples.

Conclusions: RT-LAMP reliably detected viral RNA with high sensitivity and specificity and has potential application for mass screening of patients with acute COVID-19 infection when viral load is high.

Keywords: COVID-19; Colorimetric RT-LAMP; RT-PCR; Sensitivity; Specificity.