Leveraging genomic sequencing data to evaluate disease surveillance strategies

• Published in: iScience 2023-12, Vol.26 (12), p.108488-108488, Article 108488
• Main Authors: Anderson, Benjamin, Ouyang, Derek, D’Agostino, Alexis, Bonin, Brandon, Smith, Emily, Kraushaar, Vit, Rudman, Sarah L., Ho, Daniel E.
• Format: Article
• Language: English
• Subjects: Public health; Virology
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2023.108488

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. [Display omitted] •We analyzed 10,131 high-quality SARS-CoV-2 viral sequences from Santa Clara County•Informational value is the fraction of sequenced links with plausible transmission•Contact tracing and spatiotemporal clustering both yielded high informational value•School, long-term care facility, and jail reporting yielded more than at workplaces Public health; Virology