Leveraging genomic sequencing data to evaluate disease surveillance strategies

Abstract

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.

Keywords: Public health; Virology.

Graphical abstract

Figure 1

Informational value of disease surveillance strategies Author’s analysis of Santa Clara County CalCONNECT and genomic sequencing data from May 1 to December 31, 2021. For each disease surveillance strategy, we show: the informational value (proportion of sequenced case pairs which are plausible transmission links according to whole-genome sequence data); the 95% confidence interval on informational value; and the number of proposed links which are sequenced. Contact Tracing: identified as close contacts by contact tracing. Same Address: shared home address. SaTScan: assigned to the same cluster by spatiotemporal analysis. All Mandated Reporting: linked through mandated reporting in a high-risk setting; School, Long-Term Care Facility, Jail, and Workplace Reporting are sufficiently numerous and sequenced to also be presented on their own. The following five strategies are based on matching results from the case interview or survey. Location History: matching location visited within the same time period. School: same school name, school type, and school location. Occupation Location: same workplace location, usually an address. Supervisor: same supervisor name, phone number, or e-mail. Employer Name: same employer name. CI, confidence interval; CT, contact tracing; LTCF, long-term care facility. See also Figures S1–S4.