1
|
Baba MM, Bitew M, Fokam J, Lelo EA, Ahidjo A, Asmamaw K, Beloumou GA, Bulimo WD, Buratti E, Chenwi C, Dadi H, D'Agaro P, De Conti L, Fainguem N, Gadzama G, Maiuri P, Majanja J, Meshack W, Ndjolo A, Nkenfou C, Oderinde BS, Opanda SM, Segat L, Stuani C, Symekher SL, Takou D, Tesfaye K, Triolo G, Tuki K, Zacchigna S, Marcello A. Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa. EClinicalMedicine 2021; 40:101101. [PMID: 34476394 PMCID: PMC8401528 DOI: 10.1016/j.eclinm.2021.101101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
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.
Collapse
Affiliation(s)
- Marycelin Mandu Baba
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | - Molalegne Bitew
- Ethiopian Biotechnology Institute (EBTI), Addis Ababa, Ethiopia
| | - Joseph Fokam
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
- Department of Medical Laboratory Science, Faculty of Health Science, University of Buea, Buea, Cameroon
| | - Eric Agola Lelo
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Ahmed Ahidjo
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | | | | | | | - Emanuele Buratti
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Collins Chenwi
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Hailu Dadi
- Ethiopian Biotechnology Institute (EBTI), Addis Ababa, Ethiopia
| | - Pierlanfranco D'Agaro
- Azienda Sanitaria Universitaria Integrata di Trieste, UCO Igiene e Sanità Pubblica, Trieste, Italy
- Dipartimento di Scienze Mediche Chirurgiche e della Salute, Università di Trieste, Italy
| | - Laura De Conti
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Nadine Fainguem
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Galadima Gadzama
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | - Paolo Maiuri
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, Milano 20139, Italy
| | - Janet Majanja
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Wadegu Meshack
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Alexis Ndjolo
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Celine Nkenfou
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Bamidele Soji Oderinde
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | | | - Ludovica Segat
- Azienda Sanitaria Universitaria Integrata di Trieste, UCO Igiene e Sanità Pubblica, Trieste, Italy
| | - Cristiana Stuani
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Samwel L. Symekher
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Desire Takou
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | | | - Gianluca Triolo
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Keyru Tuki
- Ethiopian Biotechnology Institute (EBTI), Addis Ababa, Ethiopia
| | - Serena Zacchigna
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Alessandro Marcello
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| |
Collapse
|