Scientific Reports (Feb 2023)
A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva
- Kaitlyn Wagner,
- Phil Fox,
- Elizabeth Gordon,
- Westen Hahn,
- Kenzie Olsen,
- Alex Markham,
- Dylan Buglewicz,
- Platon Selemenakis,
- Avery Lessard,
- Daniella Goldstein,
- Alissa Threatt,
- Luke Davis,
- Jake Miller-Dawson,
- Halie Stockett,
- Hailey Sanders,
- Kristin Rugh,
- Houston Turner,
- Michelle Remias,
- Maggie Williams,
- Jorge Chavez,
- Gabriel Galindo,
- Charlotte Cialek,
- Amanda Koch,
- Alex Fout,
- Bailey Fosdick,
- Bettina Broeckling,
- Mark D. Zabel
Affiliations
- Kaitlyn Wagner
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Phil Fox
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Elizabeth Gordon
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Westen Hahn
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Kenzie Olsen
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Alex Markham
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Dylan Buglewicz
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Platon Selemenakis
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Avery Lessard
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Daniella Goldstein
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Alissa Threatt
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Luke Davis
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Jake Miller-Dawson
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Halie Stockett
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Hailey Sanders
- Colorado State University
- Kristin Rugh
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Houston Turner
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Michelle Remias
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Maggie Williams
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Jorge Chavez
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Gabriel Galindo
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Charlotte Cialek
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Amanda Koch
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Alex Fout
- Department of Statistics, Colorado State University
- Bailey Fosdick
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus
- Bettina Broeckling
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- Mark D. Zabel
- Prion Research Center, Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences
- DOI
- https://doi.org/10.1038/s41598-023-29858-5
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 17
Abstract
Abstract In response to the SARS-CoV-2 pandemic, we developed a multiplexed, paired-pool droplet digital PCR (MP4) screening assay. Key features of our assay are the use of minimally processed saliva, 8-sample paired pools, and reverse-transcription droplet digital PCR (RT-ddPCR) targeting the SARS-CoV-2 nucleocapsid gene. The limit of detection was determined to be 2 and 12 copies per µl for individual and pooled samples, respectively. Using the MP4 assay, we routinely processed over 1,000 samples a day with a 24-h turnaround time and over the course of 17 months, screened over 250,000 saliva samples. Modeling studies showed that the efficiency of 8-sample pools was reduced with increased viral prevalence and that this could be mitigated by using 4-sample pools. We also present a strategy for, and modeling data supporting, the creation of a third paired pool as an additional strategy to employ under high viral prevalence.
