Summary Background The coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has killed millions of people worldwide. The current crisis has created an unprecedented demand for rapid test of SARS-CoV-2 infection. Methods Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a fast and convenient method to amplify and identify the transcripts of a targeted pathogen. However, the sensitivity and specificity of RT-LAMP were generally regarded as inferior when compared with the gold standard RT-qPCR. To address this issue, we combined bioinformatic and experimental analyses to improve the assay performance for COVID-19 diagnosis. Findings First, by experimental screening as well as high-throughput sequencing studies, we discovered new primer features that impacted LAMP sensitivity and specificity. These features were then used to build an improved bioinformatics algorithm to design LAMP primers targeting SARS-CoV-2. We further rigorously validated these new assays for their efficacy and specificity. We demonstrated that multiplexed RT-LAMP assay could directly detect as low as 1.5 copies/µL of SARS-CoV-2 particles in saliva, without the need of RNA isolation. We further tested this ultra-sensitive and specific RT-LAMP assay using saliva samples from COVID-19 patients. Clinical validation results indicated that the new RT-LAMP assay was comparable to standard RT-qPCR in overall assay sensitivity and specificity. Interpretation In summary, our new LAMP primer design algorithm along with the validated assays provide a fast and reliable method for the diagnosis of COVID-19 cases. Funding National Institutes of Health.
【저자키워드】 COVID-19, SARS-CoV-2, RT-LAMP, diagnostic assay, 【초록키워드】 coronavirus disease, Saliva, Coronavirus disease 2019, Efficacy, SARS-COV-2 infection, Sequencing, Transcription, bioinformatics, RT-LAMP, specificity, RT-qPCR, pathogen, Rapid test, Sensitivity and specificity, Loop-mediated isothermal amplification, LAMP, clinical, Algorithm, COVID-19 diagnosis, gold, isothermal amplification, funding, COVID-19 patients, Analysis, COVID-19 cases, gold standard, transcripts, primer, saliva samples, finding, SARS-CoV-2 particles, transcript, feature, RNA isolation, IMPROVE, tested, identify, detect, caused, indicated, amplify, demonstrated, comparable, impacted, build, diagnosis of COVID-19, SARS-CoV-2 particle, 【제목키워드】 Developing, diagnosis of SARS-CoV-2,