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

• DOI: 10.1101/2020.08.04.20167874
• Publication Date: 2020-08-06T16:30:53Z
• Authors: Joshua S. Bloom; Laila Sathe; Chetan Munugala; Eric M. Jones; Molly Gasperini; Nathan B. Lubock; Fauna Yarza; Erin M. Thompson; Kyle M. Kovary; Jimin Park; Dawn Marquette; Stephania Kay; Mark Lucas; TreQuan Love; A. Sina Booeshaghi; Oliver F. Branden...; Longhua Guo; James Boocock; Myles Hochman; Scott W. Simpkins; Isabella Lin; Nathan LaPierre; Duke Hong; Yi Zhang; Gabriel Oland; Bianca Judy Choe; Sukantha Chandras...; Evann E. Hilt; Manish J. Butte; Robert Damoiseaux; Clifford Kravit; Aaron R. Cooper; Yi Yin; Lior Pachter; Omai B. Garner; Jonathan Flint; Eleazar Eskin; Chongyuan Luo; Sriram Kosuri; Leonid Kruglyak; Valerie A. Arboleda
• Keywords: Amplicon

ABSTRACT The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates transmission by individuals who are asymptomatic at time 1, . Frequent, widespread testing population for SARS-CoV-2 essential suppress viral transmission. Despite increases in capacity, multiple challenges remain deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests scale required screening individuals. We have developed SwabSeq, a high-throughput platform that uses next-generation sequencing as readout. SwabSeq employs sample-specific molecular barcodes enable thousands samples be combined simultaneously analyzed presence or absence single run. Importantly, incorporates an vitro RNA standard mimics amplicon, but can distinguished sequencing. This allows end-point rather than PCR, improves quantitation, reduces requirements automation sample-to-sample normalization, enables purification-free detection, gives better ability call true negatives. After setting up high-complexity CLIA laboratory, we performed more 80,000 COVID-19 less two months, confirming real world inexpensively delivers highly sensitive specific results scale, with turn-around 24 hours. Our clinical laboratory test both nasal saliva without extraction, while maintaining analytical sensitivity comparable RT-qPCR tests. Moving forward, rapidly mitigate devastating novel pathogens.