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

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; Tre Quan 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; Valerie A. Arboleda

doi:10.1038/s41551-021-00754-5

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

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, Tre Quan Love, A. Sina Booeshaghi, Oliver F. Brandenberg, Longhua Guo, James Boocock, Myles Hochman, Scott W. SimpkinsIsabella 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, Valerie A. Arboleda

Research output: Contribution to journal › Article › peer-review

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.

Original language	English (US)
Pages (from-to)	657-665
Number of pages	9
Journal	Nature Biomedical Engineering
Volume	5
Issue number	7
DOIs	https://doi.org/10.1038/s41551-021-00754-5
State	Published - Jul 2021
Externally published	Yes

Bibliographical note

Funding Information:
We thank J. Semel for her support. We also thank the staff at the Held Foundation and the Carol Moss Foundation for their support of this project; staff at the UCLA David Geffen School of Medicine’s Dean’s Office for their support; Fast Grants Inc. for funding this work; L. Starita, B. Martin, J. Gehring, S. Srivatsan, J. Shendure and the members of the Covid Testing Scaleup Slack for their input, guidance and openness in sharing their processes; M. Berro for her guidance with the FDA EUA201963; the clinical laboratory scientists at the UCLA Clinical Microbiology laboratory for their assistance in collecting and processing the remnant specimens and data; our staff at the UCLA SwabSeq COVID19 Testing laboratory for deploying our CLIA test; and L. Yost and A. Martin for their advice and guidance during our scaling process. This work was supported by funding from the Howard Hughes Medical Institute (to L.K.) and DP5OD024579 (to V.A.A.). I.L. is supported by T32GM008042. Figures 1a,f and 3b created with BioRender.com.

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.

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Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

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Bloom, J. S., Sathe, L., Munugala, C., Jones, E. M., Gasperini, M., Lubock, N. B., Yarza, F., Thompson, E. M., Kovary, K. M., Park, J., Marquette, D., Kay, S., Lucas, M., Love, T. Q., Sina Booeshaghi, A., Brandenberg, O. F., Guo, L., Boocock, J., Hochman, M., ... Arboleda, V. A. (2021). Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nature Biomedical Engineering, 5(7), 657-665. https://doi.org/10.1038/s41551-021-00754-5

Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. / Bloom, Joshua S.; Sathe, Laila; Munugala, Chetan; Jones, Eric M.; Gasperini, Molly; Lubock, Nathan B.; Yarza, Fauna; Thompson, Erin M.; Kovary, Kyle M.; Park, Jimin; Marquette, Dawn; Kay, Stephania; Lucas, Mark; Love, Tre Quan; Sina Booeshaghi, A.; Brandenberg, Oliver F.; Guo, Longhua; Boocock, James; Hochman, Myles; Simpkins, Scott W.; Lin, Isabella; LaPierre, Nathan; Hong, Duke; Zhang, Yi; Oland, Gabriel; Choe, Bianca Judy; Chandrasekaran, Sukantha; Hilt, Evann E.; Butte, Manish J.; Damoiseaux, Robert; Kravit, Clifford; Cooper, Aaron R.; Yin, Yi; Pachter, Lior; Garner, Omai B.; Flint, Jonathan; Eskin, Eleazar; Luo, Chongyuan; Kosuri, Sriram; Kruglyak, Leonid; Arboleda, Valerie A.

In: Nature Biomedical Engineering, Vol. 5, No. 7, 07.2021, p. 657-665.

Research output: Contribution to journal › Article › peer-review

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, TQ, 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 2021, 'Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples', Nature Biomedical Engineering, vol. 5, no. 7, pp. 657-665. https://doi.org/10.1038/s41551-021-00754-5

Bloom, Joshua S. ; Sathe, Laila ; Munugala, Chetan ; Jones, Eric M. ; Gasperini, Molly ; Lubock, Nathan B. ; Yarza, Fauna ; Thompson, Erin M. ; Kovary, Kyle M. ; Park, Jimin ; Marquette, Dawn ; Kay, Stephania ; Lucas, Mark ; Love, Tre Quan ; Sina Booeshaghi, A. ; Brandenberg, Oliver F. ; Guo, Longhua ; Boocock, James ; Hochman, Myles ; Simpkins, Scott W. ; Lin, Isabella ; LaPierre, Nathan ; Hong, Duke ; Zhang, Yi ; Oland, Gabriel ; Choe, Bianca Judy ; Chandrasekaran, Sukantha ; Hilt, Evann E. ; Butte, Manish J. ; Damoiseaux, Robert ; Kravit, Clifford ; Cooper, Aaron R. ; Yin, Yi ; Pachter, Lior ; Garner, Omai B. ; Flint, Jonathan ; Eskin, Eleazar ; Luo, Chongyuan ; Kosuri, Sriram ; Kruglyak, Leonid ; Arboleda, Valerie A. / Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. In: Nature Biomedical Engineering. 2021 ; Vol. 5, No. 7. pp. 657-665.

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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.",

author = "Bloom, {Joshua S.} and Laila Sathe and Chetan Munugala and Jones, {Eric M.} and Molly Gasperini and Lubock, {Nathan B.} and Fauna Yarza and Thompson, {Erin M.} and Kovary, {Kyle M.} and Jimin Park and Dawn Marquette and Stephania Kay and Mark Lucas and Love, {Tre Quan} and {Sina Booeshaghi}, A. and Brandenberg, {Oliver F.} and Longhua Guo and James Boocock and Myles Hochman and Simpkins, {Scott W.} and Isabella Lin and Nathan LaPierre and Duke Hong and Yi Zhang and Gabriel Oland and Choe, {Bianca Judy} and Sukantha Chandrasekaran and Hilt, {Evann E.} and Butte, {Manish J.} and Robert Damoiseaux and Clifford Kravit and Cooper, {Aaron R.} and Yi Yin and Lior Pachter and Garner, {Omai B.} and Jonathan Flint and Eleazar Eskin and Chongyuan Luo and Sriram Kosuri and Leonid Kruglyak and Arboleda, {Valerie A.}",

note = "Funding Information: We thank J. Semel for her support. We also thank the staff at the Held Foundation and the Carol Moss Foundation for their support of this project; staff at the UCLA David Geffen School of Medicine{\textquoteright}s Dean{\textquoteright}s Office for their support; Fast Grants Inc. for funding this work; L. Starita, B. Martin, J. Gehring, S. Srivatsan, J. Shendure and the members of the Covid Testing Scaleup Slack for their input, guidance and openness in sharing their processes; M. Berro for her guidance with the FDA EUA201963; the clinical laboratory scientists at the UCLA Clinical Microbiology laboratory for their assistance in collecting and processing the remnant specimens and data; our staff at the UCLA SwabSeq COVID19 Testing laboratory for deploying our CLIA test; and L. Yost and A. Martin for their advice and guidance during our scaling process. This work was supported by funding from the Howard Hughes Medical Institute (to L.K.) and DP5OD024579 (to V.A.A.). I.L. is supported by T32GM008042. Figures 1a,f and 3b created with BioRender.com. Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature Limited.",

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

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