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Ali S, Cella E, Johnston C, Rojas AC, Brown AN, Deichen M, Azarian T. Environmental surface monitoring as a noninvasive method for SARS-CoV-2 surveillance in community settings: Lessons from a university campus study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169456. [PMID: 38123097 DOI: 10.1016/j.scitotenv.2023.169456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Environmental testing of high-touch objects is a potential noninvasive approach for monitoring population-level trends of SARS-CoV-2 and other respiratory viruses within a defined setting. We aimed to determine the association between SARS-CoV-2 contamination on high-touch environmental surfaces, community level case incidence, and university student health data. Environmental swabs were collected from January 2022 to November 2022 from high-touch objects and surfaces from five locations on a large university campus in Florida, USA. RT-qPCR was used to detect and quantify viral RNA, and a subset of positive samples was analyzed by viral genome sequencing to identify circulating lineages. During the study period, we detected SARS-CoV-2 viral RNA on 90.7 % of 162 tested samples. Levels of environmental viral RNA correlated with trends in community-level activity and case reports from the student health center. A significant positive correlation was observed between the estimated viral gene copy number in environmental samples and the weekly confirmed cases at the university. Viral sequencing data from environmental samples identified lineages concurrently circulating in the local community and state based on genomic surveillance data. Further, we detected emerging variants in environmental samples prior to their identification by clinical genomic surveillance. Our results demonstrate the utility of viral monitoring on high-touch environmental surfaces for SARS-CoV-2 surveillance at a community level. In communities with delayed or limited testing facilities, immediate environmental surface testing may considerably inform epidemic dynamics.
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Affiliation(s)
- Sobur Ali
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Catherine Johnston
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Ana C Rojas
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Ashley N Brown
- Institute for Therapeutic Innovation, Department of Medicine, College of Medicine, University of Florida, Orlando, FL 32827, USA
| | - Michael Deichen
- Student Health Services, University of Central Florida, Orlando, FL, USA
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA.
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Cucina A, Contino F, Brunacci G, Orlando V, La Rocca M, Indelicato S, Di Gaudio F. The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance. Diagnostics (Basel) 2023; 13:3618. [PMID: 38132202 PMCID: PMC10742923 DOI: 10.3390/diagnostics13243618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/24/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
The COVID-19 pandemic has transformed laboratory management, with a surge in demand for diagnostic tests prompting the adoption of new diagnostic assays and the spread of variant surveillance tools. Rapid antigen tests (RATs) were initially used only for screening and later as suitable infection assessment tools. This study explores the feasibility of sequencing the SARS-CoV-2 genome from the residue of the nasopharyngeal swab extraction buffers of rapid antigen tests (RATs) to identify different COVID-19 lineages and sub-lineages. METHODS Viral RNA was extracted from the residue of the nasopharyngeal swab extraction buffers of RATs and, after a confirmation of positivity through a reaction of RT-PCR, viral genome sequencing was performed. RESULTS Overall, the quality of the sequences obtained from the RNA extracted from the residue of the nasopharyngeal swab extraction buffers of RATs was adequate and allowed us to identify the SARS-CoV-2 variants' circulation and distribution in a period when the use of molecular swabs had been drastically reduced. CONCLUSIONS This study demonstrates the potential for genomic surveillance by sequencing SARS-CoV-2 from the residue of the nasopharyngeal swab extraction buffers of RATs, highlighting alternative possibilities for tracking variants.
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Affiliation(s)
- Annamaria Cucina
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Flavia Contino
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Giuseppina Brunacci
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Valentina Orlando
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Mario La Rocca
- Regional Health Department, Department of Strategic Planning, Piazza Ottavio Ziino, 24, 90145 Palermo, Italy;
| | - Sergio Indelicato
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
| | - Francesca Di Gaudio
- Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Chromatography and Mass Spectrometry Section, Quality Control and Chemical Risk (CQRC), Via del Vespro, 133, 90127 Palermo, Italy; (A.C.); (F.C.); (G.B.); (V.O.)
- PROMISE-Promotion of Health, Maternal-Childhood, Internal and Specialized Medicine of Excellence “G. D’Alessandro”, University of Palermo, Piazza delle Cliniche, 2, 90127 Palermo, Italy
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