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

Joshua S. Bloom(Howard Hughes Medical Institute), Laila Sathe(University of California, Los Angeles), Chetan Munugala(Howard Hughes Medical Institute), 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(California Institute of Technology), Oliver F. Brandenberg(Howard Hughes Medical Institute), Longhua Guo(Howard Hughes Medical Institute), James Boocock(Howard Hughes Medical Institute), Myles Hochman, Scott W. Simpkins, Isabella Lin(University of California, Los Angeles), Nathan LaPierre(Samueli Institute), Duke Hong, Yi Zhang(University of California, Los Angeles), Gabriel Oland(University of California, Los Angeles), Bianca Judy Choe(University of California, Los Angeles), Sukantha Chandrasekaran(University of California, Los Angeles), Evann E. Hilt(University of California, Los Angeles), Manish J. Butte(University of California, Los Angeles), Robert Damoiseaux(California NanoSystems Institute), Clifford Kravit(Digital Science (United States)), Aaron Cooper, Yi Yin(University of California, Los Angeles), Lior Pachter(California Institute of Technology), Omai B. Garner(University of California, Los Angeles), Jonathan Flint(University of California, Los Angeles), Eleazar Eskin(University of California, Los Angeles), Chongyuan Luo(University of California, Los Angeles), Sriram Kosuri(University of California, Los Angeles), Leonid Kruglyak(Howard Hughes Medical Institute), Valerie A. Arboleda(University of California, Los Angeles)
Nature Biomedical Engineering
July 1, 2021
10.1038/s41551-021-00754-5
Cited by 75Open Access
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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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