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Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Sina Booeshaghi A, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nat Biomed Eng 2021; 5:657-665. [PMID: 34211145 PMCID: PMC10810734 DOI: 10.1038/s41551-021-00754-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/20/2021] [Indexed: 02/02/2023]
Abstract
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.
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Affiliation(s)
- Joshua S Bloom
- 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.
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | | | | | | | | | | | - Dawn Marquette
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Stephania Kay
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Mark Lucas
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - TreQuan Love
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Oliver F Brandenberg
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | | | - Isabella Lin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
| | - Duke Hong
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Gabriel Oland
- Department of Surgery, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Bianca Judy Choe
- Department of Emergency Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sukantha Chandrasekaran
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Manish J Butte
- Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, CA, USA
| | - Robert Damoiseaux
- 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
| | - Clifford Kravit
- Department of Digital Technology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Lior Pachter
- Division of Biology and Bioengineering, Department of Computing and Mathematical Sciences, Caltech, Pasadena, CA, USA
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Human Genetics, 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 Computer Science, Samueli School of Engineering, UCLA, Los Angeles, CA, USA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Sriram Kosuri
- Octant Inc., Emeryville, CA, USA.
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, USA.
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte MJ, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. medRxiv 2021. [PMID: 32909008 PMCID: PMC7480060 DOI: 10.1101/2020.08.04.20167874] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission1,2. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens.
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Affiliation(s)
- Joshua S Bloom
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Octant, Inc
| | - Laila Sathe
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Chetan Munugala
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI
| | | | | | | | | | | | | | | | - Dawn Marquette
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Stephania Kay
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Mark Lucas
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - TreQuan Love
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | | | - Oliver F Brandenberg
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - Longhua Guo
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | | | | | - Isabella Lin
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Nathan LaPierre
- Department of Computer Science, Samueli School of Engineering, UCLA
| | - Duke Hong
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Yi Zhang
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Gabriel Oland
- Department of Surgery, David Geffen School of Medicine, UCLA
| | - Bianca Judy Choe
- Department of Emergency Medicine, David Geffen School of Medicine, UCLA
| | | | - Evann E Hilt
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Manish J Butte
- Department of Pediatrics, David Geffen School of Medicine, UCLA.,Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, UCLA
| | - Robert Damoiseaux
- California NanoSystems Institute, UCLA.,Department of Bioengineering, Samueli School of Engineering, UCLA.,David Geffen School of Medicine, Research Information Technology
| | - Clifford Kravit
- David Geffen School of Medicine, Research Information Technology
| | | | - Yi Yin
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Lior Pachter
- Division of Biology and Bioengineering & Department of Computing and Mathematical Sciences, Caltech
| | - Omai B Garner
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Jonathan Flint
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA
| | - Eleazar Eskin
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Computer Science, Samueli School of Engineering, UCLA.,Department of Computational Medicine, David Geffen School of Medicine, UCLA
| | - Chongyuan Luo
- Department of Human Genetics, David Geffen School of Medicine, UCLA
| | - Sriram Kosuri
- Octant, Inc.,Department of Chemistry and Biochemistry, UCLA
| | - Leonid Kruglyak
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Howard Hughes Medical Institute, HHMI.,Department of Biological Chemistry, David Geffen School of Medicine, UCLA
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA
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