The Impact of Federal Funding Cuts on Public Health Surveillance in San Diego

In a significant blow to public health efforts, the San Diego Epidemiology and Research for COVID Health program (SEARCH) has been forced to halt its wastewater analysis, a critical tool in monitoring viral outbreaks in the community. This decision comes in the wake of a nationwide reduction in federal public health funding, which has impacted local initiatives aimed at tracking infectious diseases.

Since its inception in February 2021, SEARCH has been a collaborative effort among UC San Diego, the Scripps Research Institute, and Rady Children’s Hospital. Utilizing advanced genomic techniques, the program analyzed wastewater samples from three treatment plants serving San Diego County’s 3.3 million residents. Initially focused on detecting the coronavirus, the program expanded to include other pathogens such as MPOX and is exploring methods to identify influenza, hepatitis, and measles.

However, as of April 2025, the funding that supported SEARCH—approximately $400,000 annually from the county’s public health department—has been cut. This decision was part of broader reductions initiated by the Department of Government Efficiency, affecting the “Epidemiology and Laboratory Capacity” program managed by the U.S. Centers for Disease Control and Prevention (CDC). Although other wastewater testing services will continue, the detailed insights provided by SEARCH into the specific types of viruses circulating in the community will be lost.

Dr. Louise Laurent, a perinatal research director at UC San Diego, expressed disappointment over the abrupt end of funding. “We’re going to do one more batch, because we already purchased the reagents,” she noted, explaining that the lab’s routine of weekly sample deliveries has now concluded. The researchers had anticipated a more gradual transition, with plans for the county to incorporate wastewater surveillance into its operations, particularly with a new $93 million public health laboratory set to open in May.

The lack of an orderly transition process has raised concerns among researchers. Laurent highlighted the importance of having both UCSD and the county lab processing the same samples concurrently to ensure data accuracy. “Finding out… that your contract ended a week ago and that there is no transition time… that’s not the most efficient way to do this,” she lamented.

The county has acknowledged the challenges presented by the funding cuts. In an official statement, county representatives indicated that while they are working on establishing their in-house program, the lack of a seamless transition could complicate data comparisons. The county reiterated its commitment to moving forward with wastewater testing and expressed gratitude for the contributions made by UC San Diego and Scripps.

Despite the funding challenges, researchers remain committed to assisting the county as much as possible. Kristian Andersen, director of infectious disease genomics at Scripps Research, emphasized that the decision to cut funding is a federal issue rather than a local one. “We’re not angry with the county because we know that they don’t want to do this,” he stated, while also noting the limitations that come with reduced financial support.

The SEARCH project stands out for its detailed approach to wastewater analysis, providing insights beyond basic viral load measurements. Unlike other initiatives that report only the total viral genetic material found in wastewater, SEARCH employs genetic sequencing to identify specific variants present in the community. This level of detail is crucial for understanding the behavior of different variants, which can inform vaccine development and treatment strategies.

As the public health landscape continues to evolve, the cessation of the SEARCH program underscores the importance of sustained funding for innovative research initiatives. The ability to monitor and respond to viral outbreaks is vital for protecting community health, and the lessons learned from this situation may prompt future discussions on the necessity of robust public health funding at all levels of government.