Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK.
Institute of Cancer & Genomic Sciences, University of Birmingham, Birmingham, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK.
Clin Microbiol Infect. 2021 Sep;27(9):1348.e1-1348.e7. doi: 10.1016/j.cmi.2021.04.008. Epub 2021 Apr 24.
Rapid, high throughput diagnostics are a valuable tool, allowing the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations so as to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as quantitative RT-PCR (RT-qPCR), particularly throughout the first months of the coronavirus disease 2019 pandemic. We investigated the use of LamPORE, where loop-mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS-CoV-2 in symptomatic and asymptomatic populations.
In an asymptomatic prospective cohort, for 3 weeks in September 2020, health-care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self-swabbed with nasopharyngeal swabs weekly and supplied a saliva specimen daily. These samples were tested for SARS-CoV-2 RNA using the Oxford Nanopore LamPORE system and a reference RT-qPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza-like illness from March 2020 to June 2020 were similarly tested from nasopharyngeal swabs.
In the asymptomatic cohort a total of 1200 participants supplied 23 427 samples (3966 swab, 19 461 saliva) over a 3-week period. The incidence of SARS-CoV-2 detection using LamPORE was 0.95%. Diagnostic sensitivity and specificity of LamPORE was >99.5% (decreasing to approximately 98% when clustered estimation was used) in both swab and saliva asymptomatic samples when compared with the reference RT-qPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%.
LamPORE is a highly accurate methodology for the detection of SARS-CoV-2 in both symptomatic and asymptomatic population settings and can be used as an alternative to RT-qPCR.
快速、高通量的诊断是一种有价值的工具，可以在人群中检测到严重急性呼吸综合征冠状病毒 2（SARS-CoV-2），从而识别和隔离无症状和有症状感染的人。试剂短缺和对高通量检测解决方案的限制限制了常规检测方法的有效性，例如定量 RT-PCR（RT-qPCR），特别是在 2019 年冠状病毒病大流行的头几个月。我们研究了 LamPORE 在检测有症状和无症状人群中的 SARS-CoV-2 中的应用，其中环介导等温扩增（LAMP）与纳米孔测序技术相结合。
在 2020 年 9 月的 3 周无症状前瞻性队列中，来自四个地点（伯明翰、南安普敦、巴斯和曼彻斯特）的医护人员每周用鼻咽拭子自我拭子，每天提供唾液样本。这些样本使用牛津纳米孔 LamPORE 系统和提取样本 RNA 的参考 RT-qPCR 检测 SARS-CoV-2 RNA。从 2020 年 3 月至 6 月的 848 例流感样疾病患者的第二个回顾性队列也从鼻咽拭子中进行了类似的测试。
在无症状队列中，共有 1200 名参与者在 3 周内提供了 23427 份样本（3966 份拭子，19461 份唾液）。使用 LamPORE 检测 SARS-CoV-2 的发生率为 0.95%。与参考 RT-qPCR 检测相比，LamPORE 在拭子和唾液无症状样本中的诊断灵敏度和特异性均>99.5%（当使用聚类估计时，灵敏度和特异性分别降至约 98%）。在回顾性有症状队列中，发病率为 13.4%，灵敏度和特异性均为 100%。
LamPORE 是一种在有症状和无症状人群中检测 SARS-CoV-2 的高度准确方法，可作为 RT-qPCR 的替代方法。
