Abstract
BackgroundManagement and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS.MethodsThis is a multicenter prospective observational study of diagnostic accuracy, conducted from October 2020 to February 2021 in four African Countries: Cameroon, Ethiopia, Kenya and Nigeria; and in Italy. We enroled 1657 individuals who were either COVID-19 suspect cases, or asymptomatic and presented for screening. RNA extracted from pharyngeal swabs was tested in parallel by a colorimetric RT-LAMP and by a standard real time polymerase chain reaction (RT-PCR).FindingsThe sensitivity and specificity of index RT LAMP compared to standard RT-PCR on 1657 prospective specimens from infected individuals was determined. For a subset of 1292 specimens, which underwent exactly the same procedures in different countries, we obtained very high specificity (98%) and positive predictive value (PPV = 99%), while the sensitivity was 87%, with a negative predictive value NPV = 70%, Stratification of RT-PCR data showed superior sensitivity achieved with an RT-PCR cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35.InterpretationIn this field trial, RT-LAMP appears to be a reliable assay, comparable to RT-PCR, particularly with medium-high viral loads (Ct < 35). Hence, RT-LAMP can be deployed in RLS for timely management and prevention of COVID-19, without compromising the quality of output.FundingBill & Melinda Gates Foundation [Grant No. INV-022,816].
Highlights
Such logistic and technical challenges are frequent in low- and middle-income countries (LMICs) and least developed countries (LDCs) in sub-Saharan Africa (SSA) [5], which contain 17.2% of the world’s population and yet have reported to date only around 3% (4 million) of the global COVID-19 infections (»130 million)
These data indicate that the reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a very good assay compared with gold-standard real time polymerase chain reaction (RT-PCR), except for samples with very low viral RNA (
Results from standardized protocols for RNA extraction, RT-PCR and RT-LAMP were in line with the other Countries, while standard of diagnosis (SoD) suffered from poor performance, emphasising the importance of better and more standardized assays for routine analysis
Summary
Management and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) of SARS-CoV-2 genomes is a nucleic acid test alternative to gold-standard RT-PCR. This technology attracted a lot of attention as a diagnostic tool, for deployment in resource-limited settings. Colorimetric RT-LAMP represents a formidable alternative to RT-PCR, but comprehensive clinical studies are still required for evidence-based decision-making towards its broad implementation across geographical settings Such findings would help in closing the gaps in SARS-CoV-2 diagnosis in RLS, and would accelerate result delivery due to the short turnaround-time and the user-friendly procedure of the RT-LAMP assay. With the goal of contributing to the accuracy in detecting SARS-CoV2 in RLS, we sought to evaluate the diagnostic performance of RTLAMP (index test) in terms of intrinsic (sensitivity, specificity) and extrinsic (positive and negative predictive values) characteristics, according to SARS-CoV-2 viral load estimates provided by the conventional RT-PCR (reference test) in LMIC/LDC of SSA
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