tetano
Editor, Senior Moderator
Open Forum Infect Dis
. 2023 Mar 18;10(4)
fad147.
doi: 10.1093/ofid/ofad147. eCollection 2023 Apr.
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
Chrysovalantis Stafylis[SUP] 1 [/SUP], Olivier Pernet[SUP] 2 [/SUP], Cassidy Hernandez-Tamayo[SUP] 1 [/SUP], Andrea Kovacs[SUP] 2 [/SUP], Jane Emerson[SUP] 3 [/SUP], Pamela M Ward[SUP] 3 [/SUP], Sarah Van Orman[SUP] 4 [/SUP], Frank Gilliland[SUP] 1 [/SUP], David Conti[SUP] 1 [/SUP], Maia Weisenhaus[SUP] 2 [/SUP], Angie Ghanem-Uzqueda[SUP] 4 [/SUP], Daniel Yepez[SUP] 1 [/SUP], Sofia Stellar[SUP] 1 [/SUP], Aditya P Tadanki[SUP] 1 [/SUP], Jillian Max[SUP] 1 [/SUP], Honour Fottrell[SUP] 1 [/SUP], Ethan Ong[SUP] 1 [/SUP], Sabrina Navarro[SUP] 1 [/SUP], Kaelyn Moses[SUP] 1 [/SUP], Michael Akaolisa[SUP] 1 [/SUP], Bijan Hosseini[SUP] 1 [/SUP], Shaleen Sunesara[SUP] 1 [/SUP], Yuzhu Wang[SUP] 1 [/SUP], Earl Strum[SUP] 5 [/SUP], Yolee Casagrande[SUP] 5 [/SUP], Nathalie Arenas[SUP] 5 [/SUP], Christopher Williams[SUP] 1 [/SUP], Paul Thomas[SUP] 1 [/SUP], Tara Chu[SUP] 1 [/SUP], Howard Hu[SUP] 1 [/SUP], Jeffrey D Klausner[SUP] 1 [/SUP]
Affiliations
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.
Keywords: COVID-19; SARS-CoV-2; surveillance; university; variants.
. 2023 Mar 18;10(4)
fad147.doi: 10.1093/ofid/ofad147. eCollection 2023 Apr.
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
Chrysovalantis Stafylis[SUP] 1 [/SUP], Olivier Pernet[SUP] 2 [/SUP], Cassidy Hernandez-Tamayo[SUP] 1 [/SUP], Andrea Kovacs[SUP] 2 [/SUP], Jane Emerson[SUP] 3 [/SUP], Pamela M Ward[SUP] 3 [/SUP], Sarah Van Orman[SUP] 4 [/SUP], Frank Gilliland[SUP] 1 [/SUP], David Conti[SUP] 1 [/SUP], Maia Weisenhaus[SUP] 2 [/SUP], Angie Ghanem-Uzqueda[SUP] 4 [/SUP], Daniel Yepez[SUP] 1 [/SUP], Sofia Stellar[SUP] 1 [/SUP], Aditya P Tadanki[SUP] 1 [/SUP], Jillian Max[SUP] 1 [/SUP], Honour Fottrell[SUP] 1 [/SUP], Ethan Ong[SUP] 1 [/SUP], Sabrina Navarro[SUP] 1 [/SUP], Kaelyn Moses[SUP] 1 [/SUP], Michael Akaolisa[SUP] 1 [/SUP], Bijan Hosseini[SUP] 1 [/SUP], Shaleen Sunesara[SUP] 1 [/SUP], Yuzhu Wang[SUP] 1 [/SUP], Earl Strum[SUP] 5 [/SUP], Yolee Casagrande[SUP] 5 [/SUP], Nathalie Arenas[SUP] 5 [/SUP], Christopher Williams[SUP] 1 [/SUP], Paul Thomas[SUP] 1 [/SUP], Tara Chu[SUP] 1 [/SUP], Howard Hu[SUP] 1 [/SUP], Jeffrey D Klausner[SUP] 1 [/SUP]
Affiliations
- PMID: 37089777
- PMCID: PMC10117372
- DOI: 10.1093/ofid/ofad147
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.
Keywords: COVID-19; SARS-CoV-2; surveillance; university; variants.