Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples,Nature Biomedical Engineering

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Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples
Nature Biomedical Engineering ( IF 28.1 ) Pub Date : 2021-07-01 , DOI: 10.1038/s41551-021-00754-5
Joshua S Bloom _{1,

2,

3} , Laila Sathe ₄ , Chetan Munugala _{1,

2} , Eric M Jones ₃ , Molly Gasperini ₃ , Nathan B Lubock ₃ , Fauna Yarza ₃ , Erin M Thompson ₃ , Kyle M Kovary ₃ , Jimin Park ₃ , Dawn Marquette ₅ , Stephania Kay ₅ , Mark Lucas ₅ , TreQuan Love ₅ , A Sina Booeshaghi ₆ , Oliver F Brandenberg _{1,

2,

7} , Longhua Guo _{1,

2,

7} , James Boocock _{1,

2,

7} , Myles Hochman ₃ , Scott W Simpkins ₃ , Isabella Lin _{1,

4} , Nathan LaPierre ₈ , Duke Hong ₅ , Yi Zhang ₁ , Gabriel Oland ₉ , Bianca Judy Choe ₁₀ , Sukantha Chandrasekaran ₄ , Evann E Hilt ₄ , Manish J Butte _{11,

12} , Robert Damoiseaux _{13,

14,

15} , Clifford Kravit ₁₆ , Aaron R Cooper ₃ , Yi Yin ₁ , Lior Pachter ₁₇ , Omai B Garner ₄ , Jonathan Flint _{1,

18} , Eleazar Eskin _{1,

5,

8} , Chongyuan Luo ₁ , Sriram Kosuri _{3,

19} , Leonid Kruglyak _{1,

2,

7} , Valerie A Arboleda _{1,

4}

Affiliation

Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Howard Hughes Medical Institute, Chevy Chase, MD, USA.
Octant Inc., Emeryville, CA, USA.
Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Mechanical Engineering, Caltech, Pasadena, CA, USA.
Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA.
Department of Surgery, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Emergency Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, CA, USA.
California NanoSystems Institute, UCLA, Los Angeles, CA, USA.
Department of Bioengineering, Samueli School of Engineering, UCLA, Los Angeles, CA, USA.
Department of Medical and Molecular Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Digital Technology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Division of Biology and Bioengineering, Department of Computing and Mathematical Sciences, Caltech, Pasadena, CA, USA.
Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.

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.

中文翻译：

通过对混合和条形码化的鼻腔和唾液样本进行下一代测序，大规模扩大 SARS-CoV-2 RNA 检测

对无严重急性呼吸系统综合症冠状病毒 2 (SARS-CoV-2) 症状的人群进行频繁和广泛的检测对于减轻病毒的传播至关重要。尽管最近检测能力有所提高，但基于定量聚合酶链反应 (qPCR) 检测的检测无法轻松部署到全人群筛查所需的规模。在这里，我们展示了对标有样本特异性分子条形码的混合样本进行下一代测序，无需提取 RNA 即可在单次运行中检测数以千计的鼻腔或唾液样本中的 SARS-CoV-2 RNA。我们将其命名为 SwabSeq 的检测结合了一种合成 RNA 标准，该标准有助于终点量化和真阴性的检出，并降低了对自动化的要求，纯化和样品间标准化。我们使用 SwabSeq 在不到两个月的时间内进行了 80,000 次测试，分析灵敏度和特异性与传统 qPCR 测试相当或更好，周转时间不到 24 小时。SwabSeq 可以快速适应其他病原体的检测。

更新日期：2021-07-01

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