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

By Joshua S. Bloom, Laila Sathe, ... Leonid Kruglyak and Valerie A. Arboleda | Nature Biomedical Engineering 

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.

By Joshua S. Bloom, Laila Sathe, Chetan Munugala, Eric M. Jones, Molly Gasperini3, 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. Brandenberg, Longhua Guo, James Boocock, Myles Hochman, Scott W. Simpkins, Isabella Lin, Nathan LaPierre, Duke Hong, Yi Zhang, Gabriel Oland, Bianca Judy Choe, Sukantha Chandrasekaran, 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 and Valerie A. Arboleda