A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection

Abstract

The COVID-19 pandemic has illustrated the importance of simple, rapid and accurate diagnostic testing. This study describes the validation of a new rapid SARS-CoV-2 RT-LAMP assay for use on extracted RNA or directly from swab offering an alternative diagnostic pathway that does not rely on traditional reagents that are often in short supply during a pandemic. Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1 × 10¹ and 1 × 10² copies per reaction when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care rRT-PCR. When a C_T cut-off of 33 was employed, above which increasingly evidence suggests there is a low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct RT-LAMP (that does not require RNA extraction) was 67% and 97%, respectively. When setting C_T cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively, time from swab-to-result, C_T < 25, was < 15 min. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increased sample throughput and Direct RT-LAMP as a near-patient screening tool to rapidly identify highly contagious individuals within emergency departments and care homes during times of increased disease prevalence ensuring negative results still get laboratory confirmation.

Keywords: COVID-19; Direct RNA detection; Near patient testing; RT-LAMP; Rapid diagnostics; SARS-CoV-2.

Fig. 1

RNA RT-LAMP time to positivity (Tp: ss:mm:hh) of individual samples plotted against rRT-PCR C_T values. Data points represent 86 SARS-CoV-2 positive (C_T ≤45) clinical samples (as determined by rRT-PCR).

Fig. 2

Direct RT-LAMP time to positivity (Tp: ss:mm:hh) plotted against rRT-PCR C_T. Data points represent 49 SARS-CoV-2 positive clinical samples (as determined by rRT-rPCR).

Fig. 3

Pre- and post-test probability of infection and the use of Direct RT-LAMP. Probabilities are shown as mean (points) and 95% confidence intervals (error bars). Four risk categories of patients are considered (x axis): 1) Symp_contact = symptomatic patient with history of contact with an infected person, 2) Symp_no_contact = symptomatic patient who had no contact with an infected or sick person, 3) Asymp_contact = asymptomatic patient with history of contact with an infected Aldermaston Roadperson and 4) Asymp_no_contact = asymptomatic patient who had no contact with an infected or sick person. Post-test probability negative values ≤ 0.05 are also shown in the figure.