Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 and Variants Using Digital Droplet Polymerase Chain Reaction at a Large University and Healthcare System in California
Author:
Stafylis Chrysovalantis1ORCID, Pernet Olivier2, Hernandez-Tamayo Cassidy1, Kovacs Andrea2, Emerson Jane3, Ward Pamela M3, Van Orman Sarah4, Gilliland Frank1, Conti David1, Weisenhaus Maia2, Ghanem-Uzqueda Angie4, Yepez Daniel1, Stellar Sofia1, Tadanki Aditya P1, Max Jillian1, Fottrell Honour1, Ong Ethan1, Navarro Sabrina1, Moses Kaelyn1, Akaolisa Michael1, Hosseini Bijan1, Sunesara Shaleen1, Wang Yuzhu1, Strum Earl5, Casagrande Yolee5, Arenas Nathalie5, Williams Christopher1, Thomas Paul1ORCID, Chu Tara1, Hu Howard1, Klausner Jeffrey D1
Affiliation:
1. Department of Population and Public Health Sciences, University of Southern California , Los Angeles, California , USA 2. Maternal, Child and Adolescent Center for Infectious Diseases, University of Southern California , Los Angeles, California , USA 3. Department of Pathology and Laboratory Medicine in Keck, University of Southern California , Los Angeles, California , USA 4. Department of Family Medicine, University of Southern California , Los Angeles, California , USA 5. Keck Hosptial of USC, Employee Health , Los Angeles, California , USA
Abstract
Abstract
Background
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with different infectivity, transmission potential, and morbidity change the characteristics of local epidemics and affect vaccine effectiveness. As part of the University of Southern California COVID-19 Pandemic Research Center's efforts to understand, control, and inform local community on coronavirus disease 2019 (COVID-19), we implemented a SARS-CoV-2 surveillance program among students, employees, and USC Keck Medical Center patients. We present the epidemiology and distribution of SARS-CoV-2 and its variants among the population.
Methods
We used digital droplet reverse-transcriptase polymerase chain reaction (PCR) to analyze in real-time remnant SARS-CoV-2 PCR-positive saliva specimens stored at the USC Keck Medicine laboratory between September 2020 and April 2022. Samples were tested for the original strain (A20) and 9 SARS-CoV-2 variants: α(B.1.1.7, Q.1–Q.8), β(B.1.351, B.1.351.2, B.1.351.3), γ(P.1, P.1.1, P.1.2), δ(B.1.617.2), δ+(or δ417N), ε(B.1.427 and B.1.429), η(B.1.525), λ(C.37) and ο(B.1.1.529, ΒΑ.1, BA.2). We reviewed deidentified health information from positive cases including demographics, history of COVID-19 (eg, symptoms, hospitalizations, and repeat infections), and COVID-19 vaccination status.
Results
We reviewed 1169 cases and determined the variant type of 482 specimens: 77 specimens were original strain, 119 “Delta”, 165 “Omicron”. The original strain was detected during the third and fourth quarters of 2020. The Delta variant appeared during the second quarter of 2021, whereas Omicron appeared in the fourth quarter of 2021.
Conclusions
Prospectively tracking SARS-CoV-2 variants in a university population and a hospital system, utilizing a low-cost, high-throughput PCR assay, was feasible. Local variant monitoring remains important to inform prevention and control efforts among university and clinical settings.
Funder
William M. Keck Foundation Southern California Clinical and Translational Science Institute National Center for Advancing Translational Science US National Institutes of Health
Publisher
Oxford University Press (OUP)
Subject
Infectious Diseases,Oncology
Cited by
1 articles.
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