Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples.

Autor: Hamilton JR; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Stahl EC; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Tsuchida CA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America.; San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, United States of America., Lin-Shiao E; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Tsui CK; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America., Pestal K; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America., Gildea HK; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America., Witkowsky LB; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Moehle EA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., McDevitt SL; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., McElroy M; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Keller A; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Sylvain I; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Hirsh A; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Ciling A; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Ehrenberg AJ; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America.; Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, United States of America., Ringeisen BR; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Huberty G; Washington Hospital Healthcare System Clinical Laboratory, Fremont, CA, United States of America., Urnov FD; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Giannikopoulos P; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America., Doudna JA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States of America.; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States of America.; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, United States of America.; Gladstone Institutes, San Francisco, CA, United States of America.; Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, United States of America.; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America.; Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States of America.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2021 Aug 05; Vol. 16 (8), pp. e0255690. Date of Electronic Publication: 2021 Aug 05 (Print Publication: 2021).
DOI: 10.1371/journal.pone.0255690
Abstrakt: Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against nasopharyngeal swab specimens and found saliva methods require further optimization to match this gold standard. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.
Competing Interests: J.A.D. is a cofounder of Caribou Biosciences, Editas Medicine, Scribe Therapeutics, Intellia Therapeutics and Mammoth Biosciences. J.A.D. is a scientific advisory board member of Caribou Biosciences, Intellia Therapeutics, eFFECTOR Therapeutics, Scribe Therapeutics, Mammoth Biosciences, Synthego, Algen Biotechnologies, Felix Biosciences and Inari. J.A.D. is a Director at Johnson & Johnson and has research projects sponsored by Biogen, Pfizer, AppleTree Partners and Roche. F.D.U. is a co-founder of Tune Therapeutics. P.G. is a cofounder and Director at NewCo Health. P.G. is the CLIA Laboratory Director for Coral Genomics and 3DMed. The other authors declare no competing interests. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje