Surveillance of SARS-CoV-2 and variants using digital droplet polymerase chain reaction at a large university and healthcare system in California

Abstract Background 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 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 droplet digital reverse transcriptase PCR to analyze 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 de-identified health information from positive cases including demographics, history of COVID-19 (e.g., symptoms, hospitalizations, and repeat infections) and COVID-19 vaccination status. Results We reviewed 1169 cases and determined the variant type of 482 specimens: 77 as original strain, 119 as ‘Delta’, 165 as ‘Omicron’. The original strain was detected during the third and fourth quarters of 2020. The ‘Delta’ variant appeared during the second quarter of 2021, while ‘Omicron’ appeared in the fourth quarter of 2021. Conclusions 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.