Leveraging genomic sequencing data to evaluate disease surveillance strategies
Summary: In the face of scarce public health resources, it is critical to understand which disease surveillance strategies are effective, yet such validation has historically been difficult. From May 1 to December 31, 2021, a cohort study was carried out in Santa Clara County, California, in which 1...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2023-12-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004223025658 |
| _version_ | 1797388720354099200 |
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| author | Benjamin Anderson Derek Ouyang Alexis D’Agostino Brandon Bonin Emily Smith Vit Kraushaar Sarah L. Rudman Daniel E. Ho |
| author_facet | Benjamin Anderson Derek Ouyang Alexis D’Agostino Brandon Bonin Emily Smith Vit Kraushaar Sarah L. Rudman Daniel E. Ho |
| author_sort | Benjamin Anderson |
| collection | DOAJ |
| description | Summary: In the face of scarce public health resources, it is critical to understand which disease surveillance strategies are effective, yet such validation has historically been difficult. From May 1 to December 31, 2021, a cohort study was carried out in Santa Clara County, California, in which 10,131 high-quality genomic sequences from COVID-19 polymerase chain reaction tests were merged with disease surveillance data. We measured the informational value, the fraction of sequenced links surfaced that are biologically plausible according to genomic sequence data, of different disease surveillance strategies. Contact tracing appeared more effective than spatiotemporal methods at uncovering nonresidential spread settings, school reporting appeared more fruitful than workplace reporting, and passively retrieved links through survey information presented some promise. Given the rapidly dwindling cost of sequencing, the informational value metric may enable near real-time, readily available evaluation of strategies by public health authorities to fight viral diseases beyond COVID-19. |
| first_indexed | 2024-03-08T22:44:54Z |
| format | Article |
| id | doaj.art-044f11d88110437b9ee2d89a064d4d6c |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-03-08T22:44:54Z |
| publishDate | 2023-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-044f11d88110437b9ee2d89a064d4d6c2023-12-17T06:40:58ZengElsevieriScience2589-00422023-12-012612108488Leveraging genomic sequencing data to evaluate disease surveillance strategiesBenjamin Anderson0Derek Ouyang1Alexis D’Agostino2Brandon Bonin3Emily Smith4Vit Kraushaar5Sarah L. Rudman6Daniel E. Ho7Stanford University, Stanford, CA 94305, USAStanford University, Stanford, CA 94305, USACounty of Santa Clara Public Health Department, San Jose, CA 95126, USACounty of Santa Clara Public Health Department, San Jose, CA 95126, USATheiagen Genomics, Highlands Ranch, Colorado 80129, USACalifornia Department of Public Health, Sacramento, CA 95814, USACounty of Santa Clara Public Health Department, San Jose, CA 95126, USAStanford University, Stanford, CA 94305, USA; Corresponding authorSummary: In the face of scarce public health resources, it is critical to understand which disease surveillance strategies are effective, yet such validation has historically been difficult. From May 1 to December 31, 2021, a cohort study was carried out in Santa Clara County, California, in which 10,131 high-quality genomic sequences from COVID-19 polymerase chain reaction tests were merged with disease surveillance data. We measured the informational value, the fraction of sequenced links surfaced that are biologically plausible according to genomic sequence data, of different disease surveillance strategies. Contact tracing appeared more effective than spatiotemporal methods at uncovering nonresidential spread settings, school reporting appeared more fruitful than workplace reporting, and passively retrieved links through survey information presented some promise. Given the rapidly dwindling cost of sequencing, the informational value metric may enable near real-time, readily available evaluation of strategies by public health authorities to fight viral diseases beyond COVID-19.http://www.sciencedirect.com/science/article/pii/S2589004223025658Public healthVirology |
| spellingShingle | Benjamin Anderson Derek Ouyang Alexis D’Agostino Brandon Bonin Emily Smith Vit Kraushaar Sarah L. Rudman Daniel E. Ho Leveraging genomic sequencing data to evaluate disease surveillance strategies iScience Public health Virology |
| title | Leveraging genomic sequencing data to evaluate disease surveillance strategies |
| title_full | Leveraging genomic sequencing data to evaluate disease surveillance strategies |
| title_fullStr | Leveraging genomic sequencing data to evaluate disease surveillance strategies |
| title_full_unstemmed | Leveraging genomic sequencing data to evaluate disease surveillance strategies |
| title_short | Leveraging genomic sequencing data to evaluate disease surveillance strategies |
| title_sort | leveraging genomic sequencing data to evaluate disease surveillance strategies |
| topic | Public health Virology |
| url | http://www.sciencedirect.com/science/article/pii/S2589004223025658 |
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