Precision Population Health: Joining Forces to Reduce Disparities

Kim Rhoads, MD, MS, MPH, left, associate professor of Epidemiology & Biostatistics, Director, Office of Community Engagement and Associate Director for Community Outreach and Engagement, UCSF Helen Diller Family Comprehensive Cancer Center, and Diane Havlir, MD, professor of Medicine in HIV, Infectious Disease, and Global Medicine, Infectious Diseases, welcome and instruct health care workers before opening the doors to the COVID-19 testing site at Havard Early Education School in the Bayview neighborhood, District 10, in San Francisco. Photo: Susan Merrell.

By Sarah Paris

Since UCSF hosted the Precision Public Health Summit in 2016, the institution has advocated for a targeted approach to public health, in line with the principles of Precision Medicine. This strategy requires a close integration of community partnerships, the basic, clinical and social sciences, and large-scale computational tools. The struggle to stem the COVID-19 pandemic illustrates how this process works in practice.

Community Partnerships 

Partnerships with community leaders and organizations are the foundation of public health outreach. These alliances serve to build trust, to communicate with the public, and to craft interventions aligned with the lived experience of the people.  

In response to the outbreak of the epidemic in San Francisco, UCSF partnered with community-led Latino Task Force for COVID-19 to offer free testing in the Mission District and the Bayview/Sunnydale neighborhoods, areas that were most affected. This partnership, Unidos En Salud/United in Health, continues to inform and work with the community, building up relationships and credibility that will be crucial throughout the pandemic, including eventual study and deployment of new vaccines.

Targeted Testing and Response 

Test results from the initial studies in San Francisco confirmed the need to focus interventions on the Latinx population. Following the genomic trail of the virus (see Tracking the Virus below) demonstrated the high level of infection and transmission; it also showed that infections occurred initially in the workplace and were then brought back into households. With these insights, an intervention model emerged that is now being studied by other cities and abroad. The model combines community-mobilized, low barrier testing; following-up positive diagnoses with health information; help to access food and other resources; and importantly, financial protection, so workers will be able to quarantine at home. 

Groundwork For Public Policy

Equipped with this data, policy makers were in a position to take action. A city-wide Right to Recover program was launched by Supervisor Hillary Ronen. It guarantees up to four weeks of paid wages to anyone who tests positive and does not have alternative income or benefits during the recovery period. 

“This partnership between UCSF, the community, political leaders and policymakers showed how we could rapidly generate and share data that leads to policy change which directly affects the health of our community,” said Diane Havlir, MD, chief of the UCSF Division of HIV, Infectious Diseases and Global Medicine, who led the Mission District study.

Tracking The Virus

Processing thousands of tests every day would not have been possible without the Chan Zuckerberg Biohub. Under the leadership of its co-president, Joe DeRisi, PhD, a professor of biochemistry and biophysics at UCSF, the Biohub created a high-capacity covid-test lab in eight day at the beginning of March, an amazing feat made possible by a small army of volunteers. The lab now provides free COVID-19 testing to a majority of California's Departments of Public Health.

The lab has been using genomic sequencing to monitor the dynamics of viral transmission and circulation by tracking mutations across the population. In the process, the researchers were able to reconstruct the family tree of viruses and place them in the context of local epidemiology, setting the stage for intervention by local public health officials across the state. 

UCSF scientists Elizabeth McCarthy, center, Valentina Garcia, right, and Allison Wong, left, process COVID-19 test samples at a new UCSF diagnostic laboratory adjacent to the Chan Zuckerberg Biohub (CZ Biohub) on Friday, April 24, 2020, in San Francisco. Photo: Noah Berger

The Covid Corps: Grad Students Fuel The Science

The frantic effort to ramp of testing and genomic sequencing effort would have been impossible without the work of hundreds of grad students and postdocs, who put their science training and work on hold to serve as volunteers in the “COVID Corps,” as DeRisi proudly calls them. Valentina Garcia, a graduate student in the Tetrad Program, was among the first to step into the breach. She was already working in the DeRisi Lab, and when the plan to create the Biohub CLIA lab began to solidify, it was apparent to her they would need volunteers to help run the tests.  “With UCSF shutting down and the uncertainty of how the pandemic would evolve, I was eager to do something to help,” she said.
​Read more about the experience of the postdocs and grad students in the COVID lab >>>

Data Visualization For Public Health Departments

The CZ Biohub trained public health officials to use open software tools that allow them to visualize their metadata, so they can more easily identify hotspots and vectors of the disease in their area.  More recently, they launched “COVID Tracker”, a one-stop, state-wide platform for ongoing viral genomic sequencing and visualization to support public health response. The platform unifies no-cost sequencing, data visualization, and training to empower public health departments to act on genomic data.

“Providing those kinds of insights are the next level up from traditional epidemiology. Call it genomic epidemiology in the service of precision medicine," said DeRisi.

Open Data For Rapid Learning

Among the challenges the  SARS-CoV-2 has presented to scientists was its behavioral patterns, which are very different to previously known versions of coronavirus. By collecting the enormous amount of data from patients across the UC Health system and analyzing them through the power of today’s computational tools, researchers are steadily gaining more insights into these patterns to inform potential vaccines, treatments, and knowledge that might stem future pandemics.

Wide-spread collaboration across traditional silos and rapid sharing of data have become the rule, rather than the exception, and results are presented on platforms independent of the traditional publications for open access to all. “Everybody should be sharing data in real time. The community has been able to do much faster work because of faster communications and more transparency,” DeRisi commented. 

The Heart of Precision Public Health

“Harnessing all of the scientific and data tools available to us, as well as robust partnerships with community and public health to ensure a targeted and effective public health response – this is at the heart of precision public health," concludes Kirsten Bibbins-Domingo, PhD, MD, MAS, chair of the UCSF Department of Epidemiology and vice dean for population health and health equity at the UCSF School of Medicine. "It has also underscored the innovative and collaborative spirit at UCSF that is essential to these efforts.”