Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples
Open Access
- 5 August 2021
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 16 (8), e0255690
- https://doi.org/10.1371/journal.pone.0255690
Abstract
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.Funding Information
- David and Lucile Packard Foundation
- Shurl and Kay Curci Foundation
- Julia Burke Foundation
- Jane Coffin Childs Memorial Fund for Medical Research
- Cancer Research Institute
- National Science Foundation (DGE175814)
- National Institute on Aging (1F99AG068343-01)
- Howard Hughes Medical Institute
- Defense Advanced Research Projects Agency (N660012024033)
This publication has 14 references indexed in Scilit:
- Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater.Published by Cold Spring Harbor Laboratory ,2020
- Detection of SARS-CoV-2 from Saliva as Compared to Nasopharyngeal Swabs in OutpatientsViruses, 2020
- Saliva Alternative to Upper Respiratory Swabs for SARS-CoV-2 DiagnosisEmerging Infectious Diseases, 2020
- Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Coronavirus Disease 2019 DetectionClinical Infectious Diseases, 2020
- Saliva or Nasopharyngeal Swab Specimens for Detection of SARS-CoV-2The New England Journal of Medicine, 2020
- Prevalence of Asymptomatic SARS-CoV-2 InfectionAnnals of Internal Medicine, 2020
- Comparing Nasopharyngeal Swab and Early Morning Saliva for the Identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)Clinical Infectious Diseases, 2020
- Assessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United StatesJAMA Network Open, 2020
- Blueprint for a pop-up SARS-CoV-2 testing labNature Biotechnology, 2020
- Age-dependent effects in the transmission and control of COVID-19 epidemicsNature Medicine, 2020