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

Bloom, Joshua S. and Sathe, Laila and Munugala, Chetan and Jones, Eric M. and Gasperini, Molly and Lubock, Nathan B. and Yarza, Fauna and Thompson, Erin M. and Kovary, Kyle M. and Park, Jimin and Marquette, Dawn and Kay, Stephania and Lucas, Mark and Love, TreQuan and Booeshaghi, A. Sina and Brandenberg, Oliver F. and Guo, Longhua and Boocock, James and Hochman, Myles and Simpkins, Scott W. and Lin, Isabella and LaPierre, Nathan and Hong, Duke and Zhang, Yi and Oland, Gabriel and Choe, Bianca Judy and Chandrasekaran, Sukantha and Hilt, Evann E. and Butte, Manish J. and Damoiseaux, Robert and Kravit, Clifford and Cooper, Aaron R. and Yin, Yi and Pachter, Lior and Garner, Omai B. and Flint, Jonathan and Eskin, Eleazar and Luo, Chongyuan and Kosuri, Sriram and Kruglyak, Leonid and Arboleda, Valerie A. (2020) Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20201119-132151980

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Abstract

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 transmission1,2. 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.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.08.04.20167874DOIDiscussion Paper
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7480060/PubMed CentralDiscussion Paper
https://github.com/joshsbloom/swabseqRelated ItemData/Code
https://github.com/joshsbloom/swabseqrRelated ItemData/Code
https://github.com/octantbio/SwabSeqRelated ItemData/Code
https://www.notion.so/Octant-COVID-License-816b04b442674433a2a58bff2d8288dfRelated ItemOctant COVID License
ORCID:
AuthorORCID
Bloom, Joshua S.0000-0002-7241-1648
Gasperini, Molly0000-0003-4559-8432
Lubock, Nathan B.0000-0001-8064-2465
Booeshaghi, A. Sina0000-0002-6442-4502
Brandenberg, Oliver F.0000-0001-5662-1234
Guo, Longhua0000-0001-9690-9750
Boocock, James0000-0003-0323-8818
Simpkins, Scott W.0000-0002-5997-2838
Butte, Manish J.0000-0002-4490-5595
Damoiseaux, Robert0000-0002-7611-7534
Cooper, Aaron R.0000-0003-4588-2513
Yin, Yi0000-0003-0963-2672
Pachter, Lior0000-0002-9164-6231
Garner, Omai B.0000-0002-7366-2692
Flint, Jonathan0000-0002-9427-4429
Eskin, Eleazar0000-0003-1149-4758
Luo, Chongyuan0000-0002-8541-0695
Kosuri, Sriram0000-0002-4661-0600
Kruglyak, Leonid0000-0002-8065-3057
Arboleda, Valerie A.0000-0002-9687-9122
Additional Information:The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Version 1 August 6, 2020; Version 2 September 3, 2020; Version 3 February 5, 2021; Version 4: March 9. 2021. We thank Jane Semel. Without her support this work would not have been possible. We also thank the Held Foundation and the Carol Moss Foundation for their support of this project. We thank the UCLA David Geffen School of Medicine’s Dean’s Office for their support, the Fast Grants, Inc for funding of this work. We also thank Lea Starita, Beth Martin, Jase Gehring, Sanjay Srivatsan, Jay Shendure, and the members of the Covid Testing Scaleup Slack for their input, guidance and openness in sharing their processes. This work was supported by funding from the Howard Hughes Medical Institute (to LK) and DP5OD024579 (to VA). IL is supported by T32GM008042. We thank Marlene Berro for her guidance with the FDA EUA201963. We also thank the clinical lab scientists in the UCLA Clinical Microbiology lab for their assistance in collecting and processing the remnant specimens and data and our wonderful staff in the UCLA SwabSeq COVID19 Testing laboratory for deploying our CLIA test. We thank Laura Yost and Alex Martin for their advice and guidance during our scaling process. Biorender.com was used to generate figures with cartoons. We thank all the video games and video game makers that have helped keep our loved ones sane as we spent all our time on SwabSeq. E.M.J, M.G., N.B.L., S.W.S. , F.Y., E.M.T., K.M.K., and J.P., and S.K. are employed by and hold equity, J.S.B. consults for and holds equity, and A.R.C holds equity in Octant Inc. which initially developed SwabSeq, and has filed for patents for some of the work here, though they have been made available under the Open Covid License: https://www.notion.so/Octant-COVID-License-816b04b442674433a2a58bff2d8288df. Software and Data: https://github.com/joshsbloom/swabseq (code for data and figure presented). https://github.com/joshsbloom/swabseqr (R package for fully automated analysis of patient samples). https://github.com/octantbio/SwabSeq (code for primer design and cross-reactivity). The core technology has been made available under the Open Covid Pledge, and software and data under the MIT license (UCLA) and Apache 2.0 license (Octant Inc.). Data Availability: Source data for all figures are available on https://github.com/joshsbloom/swabseq. All protocols and primers are available under an Open Covid License https://www.notion.so/Octant-COVID-License-816b04b442674433a2a58bff2d8288df. Code Availability: All code can be accessed on https://github.com/joshsbloom/swabseq . An R package to automate the resulting of patient samples can be found at https://github.com/joshsbloom/swabseqr. Author Contributions: JSB and VA wrote the manuscript with assistance from CL, JF, LK, EE, EJ, AC, NL, MG, SK. EJ, AC, NL, MG, SS, JSB, SK designed barcodes and performed early testing and analysis of protocols and reagents. CL, YY, YZ, LG, RD, MB provided early guidance and key automation resources. EE, DH, NLP and CK developed the registration webapp and IT infrastructure. LS, CM, MG, EJ, NL, SK, IL, OFB, VA, JSB performed and analyzed experiments. ASB and LP analyzed mis-assignment of index barcodes. VA, OG, SC, EH, GO, BJC collected and processed clinical samples. DM optimized operational protocols and, DM, SK, ML, TL, and EE optimized scale up. EE, LK, JF, CL, YY, YZ, JB provided helpful insight into protocols, software, and development and optimization of our specimen collection and handling. FY, EMT, KMK, JP, and MH developed the diversified S Spike mixture, N1 primers and flu primers.
Group:COVID-19
Funders:
Funding AgencyGrant Number
Held FoundationUNSPECIFIED
Carol Moss FoundationUNSPECIFIED
UCLAUNSPECIFIED
Fast Grants, Inc.UNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
NIHDP5OD024579
NIH Predoctoral FellowshipT32GM008042
PubMed Central ID:PMC7480060
Record Number:CaltechAUTHORS:20201119-132151980
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201119-132151980
Official Citation:Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing. Joshua S. Bloom, Eric M. Jones, Molly Gasperini, Nathan B. Lubock, Laila Sathe, Chetan Munugala, A. Sina Booeshaghi, Oliver F. Brandenberg, Longhua Guo, James Boocock, 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, Aaron R. Cooper, Yi Yin, Lior Pachter, Omai B. Garner, Jonathan Flint, Eleazar Eskin, Chongyuan Luo, Sriram Kosuri, Leonid Kruglyak, Valerie A. Arboleda. medRxiv 2020.08.04.20167874; doi: https://doi.org/10.1101/2020.08.04.20167874
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106738
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:19 Nov 2020 22:33
Last Modified:10 Mar 2021 23:59

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