The COVID-19 pandemic has infected tens of millions of people and has caused nearly a million deaths worldwide. Along with many other states and countries, California has issued a shelter-in-place policy for all residents. These unprecedented measures have disrupted daily life significantly for approximately 40 million inhabitants in the state indefinitely. We face an extraordinary situation where real-time tracking of SARS-CoV-2, the virus that causes COVID-19, is critical to prevent further spread.

Our goal is to sequence SARS-CoV-2 genomes from infected patients throughout Northern California. We will provide real-time monitoring to aid in the public health epidemiologic response by informing the deployment of limited resources for testing, contact tracing, and containment. Real-time genomic surveillance is critically needed to support the public health infrastructure to get society back to work. As all of the methods, data, and results will be shared immediately and publicly, our impact on the COVID-19 outbreak in California will also serve as a model for other states and countries, which may have a delayed outbreak trajectory.