학술논문
A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva
Document Type
article
Author
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
Source
Scientific Reports, Vol 13, Iss 1, Pp 1-17 (2023)
Subject
Language
English
ISSN
2045-2322
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.