Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing.

Autor: Bloom JS; Department of Human Genetics, David Geffen School of Medicine, UCLA.; Howard Hughes Medical Institute, HHMI.; Octant, Inc., Sathe L; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA., Munugala C; Department of Human Genetics, David Geffen School of Medicine, UCLA.; Howard Hughes Medical Institute, HHMI., Jones EM; Octant, Inc., Gasperini M; Octant, Inc., Lubock NB; Octant, Inc., Yarza F; Octant, Inc., Thompson EM; Octant, Inc., Kovary KM; Octant, Inc., Park J; Octant, Inc., Marquette D; Department of Computational Medicine, David Geffen School of Medicine, UCLA., Kay S; Department of Computational Medicine, David Geffen School of Medicine, UCLA., Lucas M; Department of Computational Medicine, David Geffen School of Medicine, UCLA., Love T; Department of Computational Medicine, David Geffen School of Medicine, UCLA., Booeshaghi AS; Department of Mechanical Engineering, Caltech., Brandenberg OF; 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., Guo L; 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., Boocock J; 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., Hochman M; Octant, Inc., Simpkins SW; Octant, Inc., Lin I; Department of Human Genetics, David Geffen School of Medicine, UCLA.; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA., LaPierre N; Department of Computer Science, Samueli School of Engineering, UCLA., Hong D; Department of Computational Medicine, David Geffen School of Medicine, UCLA., Zhang Y; Department of Human Genetics, David Geffen School of Medicine, UCLA., Oland G; Department of Surgery, David Geffen School of Medicine, UCLA., Choe BJ; Department of Emergency Medicine, David Geffen School of Medicine, UCLA., Chandrasekaran S; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA., Hilt EE; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA., Butte MJ; Department of Pediatrics, David Geffen School of Medicine, UCLA.; Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, UCLA., Damoiseaux R; California NanoSystems Institute, UCLA.; Department of Bioengineering, Samueli School of Engineering, UCLA.; David Geffen School of Medicine, Research Information Technology., Kravit C; David Geffen School of Medicine, Research Information Technology., Cooper AR; Octant, Inc., Yin Y; Department of Human Genetics, David Geffen School of Medicine, UCLA., Pachter L; Division of Biology and Bioengineering & Department of Computing and Mathematical Sciences, Caltech., Garner OB; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA., Flint J; Department of Human Genetics, David Geffen School of Medicine, UCLA.; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, UCLA., Eskin E; 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., Luo C; Department of Human Genetics, David Geffen School of Medicine, UCLA., Kosuri S; Octant, Inc.; Department of Chemistry and Biochemistry, UCLA., Kruglyak L; 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., Arboleda VA; Department of Human Genetics, David Geffen School of Medicine, UCLA.; Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA.
Jazyk: angličtina
Zdroj: MedRxiv : the preprint server for health sciences [medRxiv] 2021 Mar 09. Date of Electronic Publication: 2021 Mar 09.
DOI: 10.1101/2020.08.04.20167874
Abstrakt: 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 transmission 1,2 . 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.
Databáze: MEDLINE
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