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. 2020 Oct 28;16(10):e1008966.
doi: 10.1371/journal.ppat.1008966. eCollection 2020 Oct.

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB

Emily D Crawford  1   2 , Irene Acosta  1 , Vida Ahyong  1 , Erika C Anderson  3 , Shaun Arevalo  3 , Daniel Asarnow  3 , Shannon Axelrod  1 , Patrick Ayscue  1 , Camillia S Azimi  3 , Caleigh M Azumaya  3 , Stefanie Bachl  3 , Iris Bachmutsky  3 , Aparna Bhaduri  3 , Jeremy Bancroft Brown  3 , Joshua Batson  1 , Astrid Behnert  3 , Ryan M Boileau  3 , Saumya R Bollam  3 , Alain R Bonny  4 , David Booth  4 , Michael Jerico B Borja  1 , David Brown  3 , Bryan Buie  3 , Cassandra E Burnett  3 , Lauren E Byrnes  3 , Katelyn A Cabral  3   5 , Joana P Cabrera  1 , Saharai Caldera  1   6 , Gabriela Canales  3 , Gloria R Castañeda  1 , Agnes Protacio Chan  3 , Christopher R Chang  3 , Arthur Charles-Orszag  3   7 , Carly Cheung  1 , Unseng Chio  3 , Eric D Chow  4 , Y Rose Citron  8 , Allison Cohen  3 , Lillian B Cohn  1   9 , Charles Chiu  10 , Mitchel A Cole  3 , Daniel N Conrad  3 , Angela Constantino  3 , Andrew Cote  3 , Tre'Jon Crayton-Hall  1 , Spyros Darmanis  1 , Angela M Detweiler  1 , Rebekah L Dial  4 , Shen Dong  3 , Elias M Duarte  3 , David Dynerman  1 , Rebecca Egger  1 , Alison Fanton  8 , Stacey M Frumm  3 , Becky Xu Hua Fu  3 , Valentina E Garcia  4 , Julie Garcia  3 , Christina Gladkova  3   7 , Miriam Goldman  3 , Rafael Gomez-Sjoberg  1 , M Grace Gordon  3 , James C R Grove  3 , Shweta Gupta  3 , Alexis Haddjeri-Hopkins  3 , Pierce Hadley  3   5 , John Haliburton  1 , Samantha L Hao  1 , George Hartoularos  3 , Nadia Herrera  3 , Melissa Hilberg  10 , Kit Ying E Ho  1 , Nicholas Hoppe  3 , Shayan Hosseinzadeh  1 , Conor J Howard  3 , Jeffrey A Hussmann  3 , Elizabeth Hwang  3 , Danielle Ingebrigtsen  3 , Julia R Jackson  1 , Ziad M Jowhar  3 , Danielle Kain  1 , James Y S Kim  1 , Amy Kistler  1 , Oriana Kreutzfeld  3 , Jessie Kulsuptrakul  1 , Andrew F Kung  3 , Charles Langelier  1   6 , Matthew T Laurie  4 , Lena Lee  1 , Kun Leng  3 , Kristoffer E Leon  11 , Manuel D Leonetti  1 , Sophia R Levan  3 , Sam Li  4 , Aileen W Li  3 , Jamin Liu  4 , Heidi S Lubin  12 , Amy Lyden  1 , Jennifer Mann  1 , Sabrina Mann  1 , Gorica Margulis  1 , Diana M Marquez  3 , Bryan P Marsh  3 , Calla Martyn  3 , Elizabeth E McCarthy  3 , Aaron McGeever  1 , Alexander F Merriman  11 , Lauren K Meyer  3 , Steve Miller  10 , Megan K Moore  3 , Cody T Mowery  11 , Tanzila Mukhtar  3 , Lusajo L Mwakibete  1 , Noelle Narez  1 , Norma F Neff  1 , Lindsay A Osso  3 , Diter Oviedo  1 , Suping Peng  3 , Maira Phelps  1 , Kiet Phong  3 , Peter Picard  1 , Lindsey M Pieper  3 , Neha Pincha  3 , Angela Oliveira Pisco  1 , Angela Pogson  3 , Sergei Pourmal  4 , Robert R Puccinelli  1 , Andreas S Puschnik  1 , Elze Rackaityte  4 , Preethi Raghavan  1 , Madhura Raghavan  4 , James Reese  3 , Joseph M Replogle  3 , Hanna Retallack  4 , Helen Reyes  3 , Donald Rose  3 , Marci F Rosenberg  3 , Estella Sanchez-Guerrero  1 , Sydney M Sattler  3 , Laura Savy  1 , Stephanie K See  3 , Kristin K Sellers  3 , Paula Hayakawa Serpa  1   6 , Maureen Sheehy  1 , Jonathan Sheu  1 , Sukrit Silas  3 , Jessica A Streithorst  3 , Jack Strickland  3 , Doug Stryke  10 , Sara Sunshine  4 , Peter Suslow  10 , Renaldo Sutanto  3 , Serena Tamura  3 , Michelle Tan  1 , Jiongyi Tan  3 , Alice Tang  3 , Cristina M Tato  1 , Jack C Taylor  3 , Iliana Tenvooren  3 , Erin M Thompson  3 , Edward C Thornborrow  10 , Eric Tse  13 , Tony Tung  1 , Marc L Turner  3 , Victoria S Turner  3 , Rigney E Turnham  3 , Mary J Turocy  3 , Trisha V Vaidyanathan  3 , Ilia D Vainchtein  3 , Manu Vanaerschot  1 , Sara E Vazquez  4 , Anica M Wandler  3 , Anne Wapniarski  3 , James T Webber  1 , Zara Y Weinberg  3 , Alexandra Westbrook  3 , Allison W Wong  3 , Emily Wong  3 , Gajus Worthington  1 , Fang Xie  3 , Albert Xu  3 , Terrina Yamamoto  3 , Ying Yang  3 , Fauna Yarza  3 , Yefim Zaltsman  3 , Tina Zheng  3 , Joseph L DeRisi  1   4
Affiliations

Rapid deployment of SARS-CoV-2 testing: The CLIAHUB

Emily D Crawford et al. PLoS Pathog. .
No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1
(A) Counties served by CLIAHUB and the growth of testing volume over the first 120 days of operation. The most frequent users of testing at CLIAHUB were the surrounding Bay Area counties; however, outlying areas, such as Placer and Lassen, were also frequent users despite the distance. (B) CLIAHUB testing workflow and approximate timing are shown on normalized to a single sample, for preanalytical (blue), analytical (red), and postanalytical (green/yellow). The time to process a batch of 84 samples was approximately 6.7 h, including preanalytical and postanalytical steps. Median TAT was 24 h, highlighting the variability in extrinsic factors not under laboratory control, such as medical courier delivery times. qPCR, quantitative polymerase chain reaction; TAT, turnaround time.
Fig 2
Fig 2. Concordance between RT-PCR Ct values for the E and N gene probes.
For 91% of samples, agreement between viral gene probe sets were within 5 Ct cycles, with the majority within 2 cycles. For 9% of samples, only 1 gene was detected (5% E gene only, 4% N gene only), leading to an indeterminate result. In all such cases, the sample extraction and RT-PCR was repeated; points plotted represent the retest result. Ct, cycle threshold; ND not detected; RT-PCR, reverse transcription polymerase chain reaction.
See this image and copyright information in PMC

References

    1. Chamie G, Marquez C, Crawford E, Peng J, Petersen M, Schwab D, et al. SARS-CoV-2 Community Transmission disproportionately affects Latinx population during Shelter-in-Place in San Francisco. Clin Infect Dis. 2020. 10.1093/cid/ciaa1234 - DOI - PMC - PubMed
    1. Coronavirus (COVID-19) Update: FDA Issues New Policy to Help Expedite Availability of Diagnostics. U.S. Food & Drug Administration; 2020. https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19...
    1. State of California ED. Executive Order N-25-20. https://www.gov.ca.gov/wp-content/uploads/2020/03/3.12.20-EO-N-25-20-COV...
    1. Lyden A, Crawford E, Ahyong V, Vanaerschot M, Hayakawa Serpa P, Raghavan P, et al. CLIAHUB Automated RNA Extraction & RT-PCR Protocol V2. https://www.protocols.io/view/cliahub-automated-rna-extraction-amp-rt-pc...

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