4.7 Article

Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing

期刊

JOURNAL OF CLINICAL MICROBIOLOGY
卷 59, 期 6, 页码 -

出版社

AMER SOC MICROBIOLOGY
DOI: 10.1128/JCM.03271-20

关键词

diagnosis; LamPORE; nanopore sequencing; SARS-CoV-2

资金

  1. National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford
  2. Public Health England (PHE)
  3. NIHR Oxford Biomedical Research Centre
  4. Wellcome Trust [110110/Z/15/Z, 110058/Z/15/Z]
  5. Wellcome Trust [110058/Z/15/Z] Funding Source: Wellcome Trust

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LamPORE is a novel diagnostic platform for detecting SARS-CoV-2 RNA with high sensitivity and specificity, making it suitable for high-throughput testing.
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.

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