Leveraging genomic sequencing data to evaluate disease surveillance strategies.
2023; 26 (12): 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.
View details for DOI 10.1016/j.isci.2023.108488
View details for PubMedID 38089591
View details for PubMedCentralID PMC10711492
- Improving adaptation to wildfire smoke and extreme heat in frontline communities: evidence from a community-engaged pilot study in the San Francisco Bay Area ENVIRONMENTAL RESEARCH LETTERS 2023; 18 (7)
Integrating social services with disease investigation: A randomized trial of COVID-19 high-touch contact tracing.
2023; 18 (5): e0285752
COVID-19 exposed and exacerbated health disparities, and a core challenge has been how to adapt pandemic response and public health in light of these disproportionate health burdens. Responding to this challenge, the County of Santa Clara Public Health Department designed a model of "high-touch" contact tracing that integrated social services with disease investigation, providing continued support and resource linkage for clients from structurally vulnerable communities. We report results from a cluster randomized trial of 5,430 cases from February to May 2021 to assess the ability of high-touch contact tracing to aid with isolation and quarantine. Using individual-level data on resource referral and uptake outcomes, we find that the intervention, randomized assignment to the high-touch program, increased the referral rate to social services by 8.4% (95% confidence interval, 0.8%-15.9%) and the uptake rate by 4.9% (-0.2%-10.0%), with the most pronounced increases in referrals and uptake of food assistance. These findings demonstrate that social services can be effectively combined with contact tracing to better promote health equity, demonstrating a novel path for the future of public health.
View details for DOI 10.1371/journal.pone.0285752
View details for PubMedID 37192191
View details for PubMedCentralID PMC10187910
Automated vs. manual case investigation and contact tracing for pandemic surveillance: Evidence from a stepped wedge cluster randomized trial.
2023; 55: 101726
Background: Case investigation and contact tracing (CICT) is an important tool for communicable disease control, both to proactively interrupt chains of transmission and to collect information for situational awareness. We run the first randomized trial of COVID-19 CICT to investigate the utility of manual (i.e., call-based) vs. automated (i.e., survey-based) CICT for pandemic surveillance.Methods: Between December 15, 2021 and February 5, 2022, a stepped wedge cluster randomized trial was run in which Santa Clara County ZIP Codes progressively transitioned from manual to automated CICT. Eleven individual-level data fields on demographics and disease dynamics were observed for non-response. The data contains 106,522 positive cases across 29 ZIP Codes.Findings: Automated CICT reduced overall collected information by 29 percentage points (SE=0.08, p<0.01), as well as the response rate for individual fields. However, we find no evidence of differences in information loss by race or ethnicity.Interpretations: Automated CICT can serve as a useful alternative to manual CICT, with no substantial evidence of skewing data along racial or ethnic lines, but manual CICT improves completeness of key data for monitoring epidemiologic patterns.Funding: This research was supported in part by the Stanford Office of Community Engagement and the Stanford Institute for Human-Centered Artificial Intelligence.
View details for DOI 10.1016/j.eclinm.2022.101726
View details for PubMedID 36386031
- How Redundant are Redundant Encodings? Blindness in the Wild and Racial Disparity when Race is Unobserved ASSOC COMPUTING MACHINERY. 2023: 667-686
Science Translation During the COVID-19 Pandemic: An Academic-Public Health Partnership to Assess Capacity Limits in California.
American journal of public health
1800; 112 (2): 308-315
On the basis of an extensive academic-public health partnership around COVID-19 response, we illustrate the challenge of science-policy translation by examining one of the most common nonpharmaceutical interventions: capacity limits. We study the implementation of a 20% capacity limit in retail facilities in the California Bay Area. Through a difference-in-differences analysis, we show that the intervention caused no material reduction in visits, using the same large-scale mobile device data on human movements (mobility data) originally used in the academic literature to support such limits. We show that the lack of effectiveness stems from a mismatch between the academic metric of capacity relative to peak visits and the policy metric of capacity relative to building code. The disconnect in metrics is amplified by mobility data losing predictive power after the early months of the pandemic, weakening the policy relevance of mobility-based interventions. Nonetheless, the data suggest that a better-grounded rationale for capacity limits is to reduce risk specifically during peak hours. To enhance the connection between science, policy, and public health in future times of crisis, we spell out 3 strategies: living models, coproduction, and shared metrics. (Am J Public Health. 2022;112(2):308-315. https://doi.org/10.2105/AJPH.2021.306576).
View details for DOI 10.2105/AJPH.2021.306576
View details for PubMedID 35080959
A language-matching model to improve equity and efficiency of COVID-19 contact tracing.
Proceedings of the National Academy of Sciences of the United States of America
2021; 118 (43)
Contact tracing is a pillar of COVID-19 response, but language access and equity have posed major obstacles. COVID-19 has disproportionately affected minority communities with many non-English-speaking members. Language discordance can increase processing times and hamper the trust building necessary for effective contact tracing. We demonstrate how matching predicted patient language with contact tracer language can enhance contact tracing. First, we show how to use machine learning to combine information from sparse laboratory reports with richer census data to predict the language of an incoming case. Second, we embed this method in the highly demanding environment of actual contact tracing with high volumes of cases in Santa Clara County, CA. Third, we evaluate this language-matching intervention in a randomized controlled trial. We show that this low-touch intervention results in 1) significant time savings, shortening the time from opening of cases to completion of the initial interview by nearly 14 h and increasing same-day completion by 12%, and 2) improved engagement, reducing the refusal to interview by 4%. These findings have important implications for reducing social disparities in COVID-19; improving equity in healthcare access; and, more broadly, leveling language differences in public services.
View details for DOI 10.1073/pnas.2109443118
View details for PubMedID 34686604
Evaluation of Allocation Schemes of COVID-19 Testing Resources in a Community-Based Door-to-Door Testing Program
JAMA HEALTH FORUM
2021; 2 (8): e212260
Overcoming social barriers to COVID-19 testing is an important issue, especially given the demographic disparities in case incidence rates and testing. Delivering culturally appropriate testing resources using data-driven approaches in partnership with community-based health workers is promising, but little data are available on the design and effect of such interventions.To assess and evaluate a door-to-door COVID-19 testing initiative that allocates visits by community health workers by selecting households in areas with a high number of index cases, by using uncertainty sampling for areas where the positivity rate may be highest, and by relying on local knowledge of the health workers.This cohort study was performed from December 18, 2020, to February 18, 2021. Community health workers visited households in neighborhoods in East San Jose, California, based on index cases or uncertainty sampling while retaining discretion to use local knowledge to administer tests. The health workers, also known as promotores de salud (hereinafter referred to as promotores) spent a mean of 4 days a week conducting door-to-door COVID-19 testing during the 2-month study period. All residents of East San Jose were eligible for COVID-19 testing. The promotores were selected from the META cooperative (Mujeres Empresarias Tomando Acción [Entrepreneurial Women Taking Action]).The promotores observed self-collection of anterior nasal swab samples for SARS-CoV-2 reverse transcriptase-polymerase chain reaction tests.A determination of whether door-to-door COVID-19 testing was associated with an increase in the overall number of tests conducted, the demographic distribution of the door-to-door tests vs local testing sites, and the difference in positivity rates among the 3 door-to-door allocation strategies.A total of 785 residents underwent door-to-door testing, and 756 were included in the analysis. Among the 756 individuals undergoing testing (61.1% female; 28.2% aged 45-64 years), door-to-door COVID-19 testing reached different populations than standard public health surveillance, with 87.6% (95% CI, 85.0%-89.8%) being Latinx individuals. The closest available testing site only reached 49.0% (95% CI, 48.3%-49.8%) Latinx individuals. Uncertainty sampling provided the most effective allocation, with a 10.8% (95% CI, 6.8%-16.0%) positivity rate, followed by 6.4% (95% CI, 4.1%-9.4%) for local knowledge, and 2.6% (95% CI, 0.7%-6.6%) for index area selection. The intervention was also associated with increased overall testing capacity by 60% to 90%, depending on the testing protocol.In this cohort study of 785 participants, uncertainty sampling, which has not been used conventionally in public health, showed promising results for allocating testing resources. Community-based door-to-door interventions and leveraging of community knowledge were associated with reduced demographic disparities in testing.
View details for DOI 10.1001/jamahealthforum.2021.2260
View details for Web of Science ID 000837103500002
View details for PubMedID 35977196
View details for PubMedCentralID PMC8796878
Rising Seas, Rising Inequity? Communities at Risk in the San Francisco Bay Area and Implications for Adaptation Policy
2021; 9 (7)
View details for DOI 10.1029/2020EF001963
When floods hit the road: Resilience to flood-related traffic disruption in the San Francisco Bay Area and beyond.
2020; 6 (32): eaba2423
As sea level rises, urban traffic networks in low-lying coastal areas face increasing risks of flood disruptions. Closure of flooded roads causes employee absences and delays, creating cascading impacts to communities. We integrate a traffic model with flood maps that represent potential combinations of storm surges, tides, seasonal cycles, interannual anomalies driven by large-scale climate variability such as the El Nino Southern Oscillation, and sea level rise. When identifying inundated roads, we propose corrections for potential biases arising from model integration. Our results for the San Francisco Bay Area show that employee absences are limited to the homes and workplaces within the areas of inundation, while delays propagate far inland. Communities with limited availability of alternate roads experience long delays irrespective of their proximity to the areas of inundation. We show that metric reach, a measure of road network density, is a better proxy for delays than flood exposure.
View details for DOI 10.1126/sciadv.aba2423
View details for PubMedID 32821823