tetano
Editor, Senior Moderator
EClinicalMedicine
. 2021 Aug 28;40:101101.
doi: 10.1016/j.eclinm.2021.101101. eCollection 2021 Oct.
Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa
Marycelin Mandu Baba[SUP] 1 [/SUP], Molalegne Bitew[SUP] 2 [/SUP], Joseph Fokam[SUP] 3 4 [/SUP], Eric Agola Lelo[SUP] 5 [/SUP], Ahmed Ahidjo[SUP] 1 [/SUP], Kominist Asmamaw[SUP] 2 [/SUP], Grace Angong Beloumou[SUP] 3 [/SUP], Wallace Dimbuson Bulimo[SUP] 5 [/SUP], Emanuele Buratti[SUP] 6 [/SUP], Collins Chenwi[SUP] 3 [/SUP], Hailu Dadi[SUP] 2 [/SUP], Pierlanfranco D'Agaro[SUP] 7 8 [/SUP], Laura De Conti[SUP] 6 [/SUP], Nadine Fainguem[SUP] 3 [/SUP], Galadima Gadzama[SUP] 1 [/SUP], Paolo Maiuri[SUP] 9 [/SUP], Janet Majanja[SUP] 5 [/SUP], Wadegu Meshack[SUP] 5 [/SUP], Alexis Ndjolo[SUP] 3 [/SUP], Celine Nkenfou[SUP] 3 [/SUP], Bamidele Soji Oderinde[SUP] 1 [/SUP], Silvanos Mukunzi Opanda[SUP] 5 [/SUP], Ludovica Segat[SUP] 7 [/SUP], Cristiana Stuani[SUP] 6 [/SUP], Samwel L Symekher[SUP] 5 [/SUP], Desire Takou[SUP] 3 [/SUP], Kassahun Tesfaye[SUP] 2 [/SUP], Gianluca Triolo[SUP] 6 [/SUP], Keyru Tuki[SUP] 2 [/SUP], Serena Zacchigna[SUP] 6 [/SUP], Alessandro Marcello[SUP] 6 [/SUP]
Affiliations
Abstract
Background: 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). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS.
Methods: This 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).
Findings: The 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.
Interpretation: In 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.
. 2021 Aug 28;40:101101.
doi: 10.1016/j.eclinm.2021.101101. eCollection 2021 Oct.
Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa
Marycelin Mandu Baba[SUP] 1 [/SUP], Molalegne Bitew[SUP] 2 [/SUP], Joseph Fokam[SUP] 3 4 [/SUP], Eric Agola Lelo[SUP] 5 [/SUP], Ahmed Ahidjo[SUP] 1 [/SUP], Kominist Asmamaw[SUP] 2 [/SUP], Grace Angong Beloumou[SUP] 3 [/SUP], Wallace Dimbuson Bulimo[SUP] 5 [/SUP], Emanuele Buratti[SUP] 6 [/SUP], Collins Chenwi[SUP] 3 [/SUP], Hailu Dadi[SUP] 2 [/SUP], Pierlanfranco D'Agaro[SUP] 7 8 [/SUP], Laura De Conti[SUP] 6 [/SUP], Nadine Fainguem[SUP] 3 [/SUP], Galadima Gadzama[SUP] 1 [/SUP], Paolo Maiuri[SUP] 9 [/SUP], Janet Majanja[SUP] 5 [/SUP], Wadegu Meshack[SUP] 5 [/SUP], Alexis Ndjolo[SUP] 3 [/SUP], Celine Nkenfou[SUP] 3 [/SUP], Bamidele Soji Oderinde[SUP] 1 [/SUP], Silvanos Mukunzi Opanda[SUP] 5 [/SUP], Ludovica Segat[SUP] 7 [/SUP], Cristiana Stuani[SUP] 6 [/SUP], Samwel L Symekher[SUP] 5 [/SUP], Desire Takou[SUP] 3 [/SUP], Kassahun Tesfaye[SUP] 2 [/SUP], Gianluca Triolo[SUP] 6 [/SUP], Keyru Tuki[SUP] 2 [/SUP], Serena Zacchigna[SUP] 6 [/SUP], Alessandro Marcello[SUP] 6 [/SUP]
Affiliations
- PMID: 34476394
- PMCID: PMC8401528
- DOI: 10.1016/j.eclinm.2021.101101
Abstract
Background: 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). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS.
Methods: This 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).
Findings: The 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.
Interpretation: In 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.