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Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing
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 e...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8315953/ https://www.ncbi.nlm.nih.gov/pubmed/33782112 http://dx.doi.org/10.1128/JCM.03271-20 |
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author | Peto, Leon Rodger, Gillian Carter, Daniel P. Osman, Karen L. Yavuz, Mehmet Johnson, Katie Raza, Mohammad Parker, Matthew D. Wyles, Matthew D. Andersson, Monique Justice, Anita Vaughan, Alison Hoosdally, Sarah Stoesser, Nicole Matthews, Philippa C. Eyre, David W. Peto, Timothy E. A. Carroll, Miles W. de Silva, Thushan I. Crook, Derrick W. Evans, Cariad M. Pullan, Steven T. |
author_facet | Peto, Leon Rodger, Gillian Carter, Daniel P. Osman, Karen L. Yavuz, Mehmet Johnson, Katie Raza, Mohammad Parker, Matthew D. Wyles, Matthew D. Andersson, Monique Justice, Anita Vaughan, Alison Hoosdally, Sarah Stoesser, Nicole Matthews, Philippa C. Eyre, David W. Peto, Timothy E. A. Carroll, Miles W. de Silva, Thushan I. Crook, Derrick W. Evans, Cariad M. Pullan, Steven T. |
author_sort | Peto, Leon |
collection | PubMed |
description | 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/μl 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. |
format | Online Article Text |
id | pubmed-8315953 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-83159532021-11-19 Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing Peto, Leon Rodger, Gillian Carter, Daniel P. Osman, Karen L. Yavuz, Mehmet Johnson, Katie Raza, Mohammad Parker, Matthew D. Wyles, Matthew D. Andersson, Monique Justice, Anita Vaughan, Alison Hoosdally, Sarah Stoesser, Nicole Matthews, Philippa C. Eyre, David W. Peto, Timothy E. A. Carroll, Miles W. de Silva, Thushan I. Crook, Derrick W. Evans, Cariad M. Pullan, Steven T. J Clin Microbiol Virology 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/μl 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. American Society for Microbiology 2021-05-19 /pmc/articles/PMC8315953/ /pubmed/33782112 http://dx.doi.org/10.1128/JCM.03271-20 Text en Copyright © 2021 Peto et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Virology Peto, Leon Rodger, Gillian Carter, Daniel P. Osman, Karen L. Yavuz, Mehmet Johnson, Katie Raza, Mohammad Parker, Matthew D. Wyles, Matthew D. Andersson, Monique Justice, Anita Vaughan, Alison Hoosdally, Sarah Stoesser, Nicole Matthews, Philippa C. Eyre, David W. Peto, Timothy E. A. Carroll, Miles W. de Silva, Thushan I. Crook, Derrick W. Evans, Cariad M. Pullan, Steven T. Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing |
title | Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing |
title_full | Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing |
title_fullStr | Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing |
title_full_unstemmed | Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing |
title_short | Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing |
title_sort | diagnosis of sars-cov-2 infection with lampore, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing |
topic | Virology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8315953/ https://www.ncbi.nlm.nih.gov/pubmed/33782112 http://dx.doi.org/10.1128/JCM.03271-20 |
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