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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
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 Resea...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117372/ https://www.ncbi.nlm.nih.gov/pubmed/37089777 http://dx.doi.org/10.1093/ofid/ofad147 |
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author | Stafylis, Chrysovalantis Pernet, Olivier Hernandez-Tamayo, Cassidy Kovacs, Andrea Emerson, Jane Ward, Pamela M Van Orman, Sarah Gilliland, Frank Conti, David Weisenhaus, Maia Ghanem-Uzqueda, Angie Yepez, Daniel Stellar, Sofia Tadanki, Aditya P Max, Jillian Fottrell, Honour Ong, Ethan Navarro, Sabrina Moses, Kaelyn Akaolisa, Michael Hosseini, Bijan Sunesara, Shaleen Wang, Yuzhu Strum, Earl Casagrande, Yolee Arenas, Nathalie Williams, Christopher Thomas, Paul Chu, Tara Hu, Howard Klausner, Jeffrey D |
author_facet | Stafylis, Chrysovalantis Pernet, Olivier Hernandez-Tamayo, Cassidy Kovacs, Andrea Emerson, Jane Ward, Pamela M Van Orman, Sarah Gilliland, Frank Conti, David Weisenhaus, Maia Ghanem-Uzqueda, Angie Yepez, Daniel Stellar, Sofia Tadanki, Aditya P Max, Jillian Fottrell, Honour Ong, Ethan Navarro, Sabrina Moses, Kaelyn Akaolisa, Michael Hosseini, Bijan Sunesara, Shaleen Wang, Yuzhu Strum, Earl Casagrande, Yolee Arenas, Nathalie Williams, Christopher Thomas, Paul Chu, Tara Hu, Howard Klausner, Jeffrey D |
author_sort | Stafylis, Chrysovalantis |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10117372 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-101173722023-04-21 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 Stafylis, Chrysovalantis Pernet, Olivier Hernandez-Tamayo, Cassidy Kovacs, Andrea Emerson, Jane Ward, Pamela M Van Orman, Sarah Gilliland, Frank Conti, David Weisenhaus, Maia Ghanem-Uzqueda, Angie Yepez, Daniel Stellar, Sofia Tadanki, Aditya P Max, Jillian Fottrell, Honour Ong, Ethan Navarro, Sabrina Moses, Kaelyn Akaolisa, Michael Hosseini, Bijan Sunesara, Shaleen Wang, Yuzhu Strum, Earl Casagrande, Yolee Arenas, Nathalie Williams, Christopher Thomas, Paul Chu, Tara Hu, Howard Klausner, Jeffrey D Open Forum Infect Dis Major Article 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. Oxford University Press 2023-03-18 /pmc/articles/PMC10117372/ /pubmed/37089777 http://dx.doi.org/10.1093/ofid/ofad147 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Major Article Stafylis, Chrysovalantis Pernet, Olivier Hernandez-Tamayo, Cassidy Kovacs, Andrea Emerson, Jane Ward, Pamela M Van Orman, Sarah Gilliland, Frank Conti, David Weisenhaus, Maia Ghanem-Uzqueda, Angie Yepez, Daniel Stellar, Sofia Tadanki, Aditya P Max, Jillian Fottrell, Honour Ong, Ethan Navarro, Sabrina Moses, Kaelyn Akaolisa, Michael Hosseini, Bijan Sunesara, Shaleen Wang, Yuzhu Strum, Earl Casagrande, Yolee Arenas, Nathalie Williams, Christopher Thomas, Paul Chu, Tara Hu, Howard Klausner, Jeffrey D 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 |
title | 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 |
title_full | 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 |
title_fullStr | 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 |
title_full_unstemmed | 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 |
title_short | 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 |
title_sort | 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 |
topic | Major Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10117372/ https://www.ncbi.nlm.nih.gov/pubmed/37089777 http://dx.doi.org/10.1093/ofid/ofad147 |
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