Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa

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.

An Ultrafast One-Step Quantitative Reverse Transcription–Polymerase Chain Reaction Assay for Detection of SARS-CoV-2

“…Additionally, the throughput of the Accula TM System for SARS-CoV-2 test is limited to 2 samples per run, which is significantly less than 96 and/or 384 samples per run in this ultrafast one-step qRT-PCR assay. Compared with RT-LAMP, this ultrafast one-step qRT-PCR assay achieved 100% clinical sensitivity and specificity, which is much better than that of RT-LAMP with reported specificity (98%) and sensitivity (87%) ( Baba et al, 2021 ). As such, we believe this work would be of interest to the general healthcare audience, especially those in the field of virus detection.…”

Molecular Detection of Infectious Laryngotracheitis Virus in Chickens with a Microfluidic Chip

“…Indeed, LAMP incubation can be carried out even electricity-free without any instrumentation with an exothermic reaction to provide heat and a phase change material to control incubation temperature [ 36 ]. Moreover, a previous study has demonstrated that the collective cost per LAMP reaction was roughly one third of that for PCR [ 37 ].…”

SARS-CoV-2 Genome Sequence Obtained from Ethiopia

“…There is a strong demand to know whether variants of concern are circulating in this country to inform authorities and to guide public health interventions ( 4 ). However, only five sequences from Ethiopia were available on public databases from December 2020 to March 2021, reinforcing the urgent need to increase molecular surveillance ( 5 ).…”

“…RNA was then suspended in RNase-free water, and then the RNA extracts were purified using an RNA clean and concentrator kit (Zymo Research, CA, USA) ( 6 ). The diagnostic detection of SARS-CoV-2 RNA was performed with the Beijing Genomic Institute (BGI) real-time fluorescent reverse transcriptase PCR (RT-qPCR) detection kit of SARS-CoV-2 (BGI, China) with primers targeting the ORF 1ab gene ( 5 ) A total of 15 samples with cycle threshold ( C T ) values of <30 were selected randomly for high-throughput genome sequencing. This technique is based mainly on PCR amplification of the genome ( 7 ).…”