Harnessing the Power of Genomic Sequencing for California Public Health

Introducing CZ GEN EPI, an Open-Source Tool To Help Departments of Public Health Track and Slow the Spread of COVID-19 and Prepare for Future Crises

Editor’s Note: This release post has been updated as of 12/7/21 with the new name of CZ GEN EPI (formerly Aspen).

As COVID-19 quickly spread across California and the U.S. in the spring of 2020, our teams at the Chan Zuckerberg Initiative (CZI) and the Chan Zuckerberg Biohub (CZ Biohub) believed that two approaches had the potential to significantly impact the spread of the virus. The first was increased availability of testing to help identify cases and better understand its spread in real time. The second was genomic analysis of positive samples to determine how and where the virus was mutating.

To address the testing shortage, CZI and CZ Biohub, along with hundreds of volunteers from UC San Francisco, turned an empty lab space adjacent to the Biohub into a CLIA-certified clinical testing lab in just eight days — a process that would normally take months. Over the next seven months, the “CLIAhub” processed over 165,000 free COVID-19 tests for California community clinics, safety net hospitals, Departments of Public Health (DPHs), and prisons, providing a critical bridge for California’s COVID-19 Testing Task Force as it ramped up its own testing capacity.

Through inspiring collaboration and innovation, CZ Biohub, CZI, and UCSF created one of the nation’s leading COVID-19 testing centers in only eight days — a process that would normally take months to complete.

At the same time last spring, CZI and CZ Biohub partnered with the state of California to launch California COVID Tracker, one of the first (and the largest) statewide SARS-CoV-2 tracking programs in the U.S. California COVID Tracker provided viral genomic data to local public health officials, many of whom did not have the in-house tools or capabilities to produce or analyze this type of information. Since the spring of 2020, California COVID Tracker has made whole-genome sequencing and analysis of the virus freely available to all DPHs in the state and to local health jurisdictions — at one point accounting for 45% of the genomic sequencing in the state and 5% nationwide.

With this actionable data, public health officers have been better able to map the spread of COVID-19 and institute practices and recommendations to help slow its spread. The information provided through California COVID Tracker enables officials to:

To date, this collaboration has resulted in more than 11,550 COVID-positive samples sequenced and analyzed by CZI and CZ Biohub teams to support public health surveillance and response.

Whole genome sequencing allows scientists to track mutations of the SARS-CoV-2 virus, which typically happens every 2–3 transmissions. These mutations are key to helping public health officials trace transmission sources.

We created California COVID Tracker with the goal of meeting the immediate needs of public health officials, and as we’ve transitioned through varying phases of the pandemic, their needs have evolved. It is clear that there is a continued need to build capacity at the local level for sequencing and interpreting genomic data — to continue to track the spread of COVID-19 and the variants of concern, and also to create a bridge towards strengthening our local public health infrastructure for the future.

Last week we launched Chan Zuckerberg GEN EPI (CZ GEN EPI), a new open-source free software tool that will increase access to powerful analysis tools built by the scientific community. CZ GEN EPI does not require coding or any local infrastructure build — it aggregates data and provides easy access to analytics and interpretation for scientists and non-scientists alike. CZ GEN EPI will ultimately allow public health departments and officials across the state to analyze and interpret data and draw important conclusions to keep their local communities safe and healthy.

Our goal is to make the powerful tools developed by the scientific community accessible to public health departments through a user-friendly, point-and-click interface.

Teams from CZI and CZ Biohub have worked closely with a group of partners at the California state and local health departments consisting of many epidemiologists, public health officers, and public health laboratory directors who have helped shape this project. More than 20 DPHs have gone through a training process at varying levels — weekly sessions, webinars, and ad-hoc support. DPHs have acquired sequencing machines, or established a partnership with another organization, to allow them to conduct genomic sequencing, analysis, and interpretation independently. Over the next few months, we expect this resource and training will become available to all DPHs in the state and eventually to others outside of California.

We hope that by making this tool available at no cost and providing training and support, we can build capacity and knowledge across the state, ultimately strengthening and supporting California’s collective ability to effectively track and slow the spread of COVID-19 and be ready for future crises.

Through this transition, and as a continuation of the successes built from California COVID Tracker, we will continue to work closely with Departments of Public Health across California as they take a leading role in this work. Furthermore, we are committed to supporting the California vision for genomic epidemiology, bridging the ability for the local DPHs to analyze data on their own. We look forward to being a continued partner and resource to ensure this transition results in a strong, collaborative system.

To learn more about CZ GEN EPI, email helloaspen@chanzuckerberg.com or contact Patrick Ayscue at patrick.ayscue@czbiohub.org or Sidney Bell at sidneymbell@chanzuckerberg.com