CDC awarded $2.5 million contract to fund one of the largest SARS-CoV-2 surveillance programs in the United States

A team led by scientists from Scripps Research has been awarded a contract by the US Centers for Disease Control & Prevention (CDC) to support one of the largest SARS-CoV-2 surveillance programs in the United States.

The two-year, $2.5 million contract funds large-scale, near-real-time sequencing of SARS-CoV-2 isolates from hospitals and local health authorities in San Diego and nearby northwestern Mexico, as well as development of software to track progress and geographic distribution of SARS-CoV-2 variants.

The contract, an extension of a contract originally awarded in 2020, is being conducted by the San Diego Epidemiology and Research for COVID Health (SEARCH) Alliance, co-founded by Scripps Research, the University of California San Diego (UC San Diego) and Rady Children’s Hospital-San Diego.

CDC support for SEARCH’s genomic surveillance program has already resulted in significant advances in COVID-19 public health as well as new scientific knowledge on SARS-CoV-2, and we expect many more advances in both areas.”

Kristian Andersen, PhD, Principal Investigator, Professor, Division of Immunology and Microbiology at Scripps Research

Since the beginning of the pandemic, SEARCH has conducted genomic surveillance of SARS-CoV-2 using clinical samples collected from hospitals in San Diego and from sources across the border in Baja California. SEARCH has also developed key protocols and analytical tools to track the emergence and spread of SARS-CoV-2 variants in wastewater. Additionally, SEARCH investigators are actively involved in understanding the origins of SARS-CoV-2 and have found evidence of initial spread from animals sold at the Huanan Market in Wuhan, China, in several high-profile publications .

SEARCH’s efforts include several collaborations, including with the CDC, San Diego County’s Health & Human Services Agency, the California Department of Health, Sharp Health, Scripps Health, virus surveillance company Helix, and health network Salud Digna in Mexico. Since the beginning of the pandemic, these efforts have resulted in the publication and analysis of more than 70,000 SARS-CoV-2 sequences.

Under the new contract, SEARCH will accelerate its virus sequencing workflow to provide more timely and actionable information on local virus spread and evolution, including the emergence of new variants and subvariants of concern.

“The current process of collecting, sequencing, and analyzing a panel of virus samples from local hospital cases and sewage treatment plants can take several weeks,” says Mark Zeller, PhD, project scientist at the Andersen lab. “We aim to reduce that to a few days, which would allow us to monitor transmission chains in near real-time for localized outbreaks.”

In collaboration with the County of San Diego, the State of California and Mexican health laboratories, the researchers will continue to analyze the transmission of SARS-CoV-2 across the busy California-Baja border. Additionally, they will expand their genomic surveillance efforts to additional Mexican border states and popular tourist destinations, including Puerto Vallarta. The team will continue to publish their analysis on SEARCH’s online dashboards.

The project involves the further development of open-source software tools to support the tracking of local development and transmission of SARS-CoV-2.

“The tools we’ve developed over the past few years are already widely used by the public health community for sequencing and analysis of SARS-CoV-2,” says Joshua Levy, PhD, a postdoctoral fellow in the Andersen lab. “As part of this new contract, we will develop the technology to permanently transform the way genomic surveillance is used to strengthen our public health response.”

These open source software tools are available at https://andersen-lab.com/secrets/code/. The SEARCH Alliance SARS-CoV-2 surveillance dashboards can be found at https://searchcovid.info/Dashboards/.