Abstract
LamPORE is a novel diagnostic platform for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA combining loop-mediated isothermal amplification with nanopore sequencing, which could potentially be used to analyze thousands of samples per day on a single instrument. We evaluated the performance of LamPORE against reverse transcriptase PCR (RT-PCR) using RNA extracted from spiked respiratory samples and stored nose and throat swabs collected at two UK hospitals. The limit of detection of LamPORE was 10 genome copies/ml of extracted RNA, which is above the limit achievable by RT-PCR, but was not associated with a significant reduction of sensitivity in clinical samples. Positive clinical specimens came mostly from patients with acute symptomatic infection, and among them, LamPORE had a diagnostic sensitivity of 99.1% (226/228; 95% confidence interval [CI], 96.9% to 99.9%). Among negative clinical specimens, including 153 with other respiratory pathogens detected, LamPORE had a diagnostic specificity of 99.6% (278/279; 98.0% to 100.0%). Overall, 1.4% (7/514; 0.5% to 2.9%) of samples produced an indeterminate result on first testing, and repeat LamPORE testing on the same RNA extract had a reproducibility of 96.8% (478/494; 94.8% to 98.1%). LamPORE has a similar performance as RT-PCR for the diagnosis of SARS-CoV-2 infection in symptomatic patients and offers a promising approach to high-throughput testing.
| Original language | English |
|---|---|
| Article number | ARTN e03271-20 |
| Number of pages | 9 |
| Journal | Journal of Clinical Microbiology |
| Volume | 59 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - Jun 2021 |
Bibliographical note
Funding Information: We are grateful to all the clinical microbiology and virology staff at OUH and STH who helped to process the specimens used in this evaluation and to Kevin Bewley, PHE Porton Down, for providing the cultured virus. Materials for the evaluation were supplied by Oxford Nanopore Technologies, but allexperiments and analyses were conducted independently by the investigators. D.W.E. declares lecture fees from Gilead, outside the submitted work. All other authors declare no competing interests. This work was supported by the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in partnership with Public Health England (PHE) and the NIHR Oxford Biomedical Research Centre. L.P. is an NIHR clinical lecturer. D.W.E. is a Robertson Foundation Fellow and Oxford NIHR Senior Research Fellow. P.C.M. is funded by the Wellcome Trust (110110/Z/15/Z). T.I.D.S. is a supported by a Wellcome Trust Intermediate Clinical Fellowship (110058/Z/15/Z). This report presents independent research. The views expressed in this publication are those of the authors and not necessarily those of the NHS, NIHR, the Department of Health, or PHE. The funding source had no role in study design, in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the paper for publication.
Open Access: This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Publisher Copyright: © 2021 Peto et al.
Citation: Peto L, Rodger G, Carter DP, Osman KL, Yavuz M, Johnson K, Raza M, Parker MD, Wyles MD, Andersson M, Justice A, Vaughan A, Hoosdally S, Stoesser N, Matthews PC, Eyre DW, Peto TEA, Carroll MW, de Silva TI, Crook DW, Evans CM, Pullan ST. 2021. Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing. J Clin Microbiol 59:e03271-20.
DOI: https://doi.org/10.1128/JCM.03271-20.
Keywords
- Diagnosis
- LamPORE
- Nanopore sequencing
- SARS-CoV-2
- nanopore sequencing
- ASSAY
- diagnosis
- RAPID DETECTION