Using digital traces to build prospective and real-time county-level early warning systems to anticipate COVID-19 outbreaks in the United States

The ongoing COVID-19 pandemic continues to affect communities around the world. To date, almost 6 million people have died as a consequence of COVID-19, and more than one-quarter of a billion people are estimated to have been infected worldwide. The design of appropriate and timely mitigation strategies to curb the effects of this and future disease outbreaks requires close monitoring of their spatio-temporal trajectories. We present machine learning methods to anticipate sharp increases in COVID-19 activity in US counties in real-time. Our methods leverage Internet-based digital traces -- e.g., disease-related Internet search activity from the general population and clinicians, disease-relevant Twitter micro-blogs, and outbreak trajectories from neighboring locations -- to monitor potential changes in population-level health trends. Motivated by the need for finer spatial-resolution epidemiological insights to improve local decision-making, we build upon previous retrospective research efforts originally conceived at the state level and in the early months of the pandemic. Our methods -- tested in real-time and in an out-of-sample manner on a subset of 97 counties distributed across the US -- frequently anticipated sharp increases in COVID-19 activity 1-6 weeks before the onset of local outbreaks (defined as the time when the effective reproduction number $R_t$ becomes larger than 1 consistently). Given the continued emergence of COVID-19 variants of concern -- such as the most recent one, Omicron -- and the fact that multiple countries have not had full access to vaccines, the framework we present, while conceived for the county-level in the US, could be helpful in countries where similar data sources are available.