Bloom Joshua S, Sathe Laila, Munugala Chetan, Jones Eric M, Gasperini Molly, Lubock Nathan B, Yarza Fauna, Thompson Erin M, Kovary Kyle M, Park Jimin, Marquette Dawn, Kay Stephania, Lucas Mark, Love TreQuan, Sina Booeshaghi A, Brandenberg Oliver F, Guo Longhua, Boocock James, Hochman Myles, Simpkins Scott W, Lin Isabella, LaPierre Nathan, Hong Duke, Zhang Yi, Oland Gabriel, Choe Bianca Judy, Chandrasekaran Sukantha, Hilt Evann E, Butte Manish J, Damoiseaux Robert, Kravit Clifford, Cooper Aaron R, Yin Yi, Pachter Lior, Garner Omai B, Flint Jonathan, Eskin Eleazar, Luo Chongyuan, Kosuri Sriram, Kruglyak Leonid, Arboleda Valerie A
Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Nat Biomed Eng. 2021 Jul;5(7):657-665. doi: 10.1038/s41551-021-00754-5. Epub 2021 Jul 1.
Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.
对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）无症状人群进行频繁且广泛的检测对于减轻病毒传播至关重要。尽管近期检测能力有所提高，但基于定量聚合酶链反应（qPCR）检测的方法难以按照全人群筛查所需的规模轻松部署。在此，我们表明，对带有样本特异性分子条形码的混合样本进行下一代测序，能够在单次运行中对数千份鼻拭子或唾液样本进行SARS-CoV-2 RNA检测，而无需进行RNA提取。我们将该检测方法命名为SwabSeq，它包含一种合成RNA标准品，有助于进行终点定量和判定真阴性，并且减少了对自动化、纯化以及样本间标准化的要求。我们使用SwabSeq在不到两个月的时间内进行了80000次检测，其分析灵敏度和特异性与传统qPCR检测相当或更佳，周转时间不到24小时。SwabSeq能够快速适用于检测其他病原体。
