Modeling COVID-19 variants of concern emergence and dynamics and impact of public health measures.

Evolutionary analyses starting from time- and location- annotated virus genomes can be a powerful tool for understanding the SARS-CoV-2 epidemic spread and to evaluate the effectiveness of public health measures. The emergence of new variants of SARS-CoV-2 herald a new phase of the pandemic. In this proposal, we aim to identify drivers of the SARS-CoV-2 variants of concern (VOC) spread in California and across the United States and to evaluate the impact of public health intervention on this virus's spread. \n We will reconstruct the timing and multiplicity of introductions within-California (between counties) and within the U.S. (between States) viral circulation history, using publicly available real time SARS-CoV-2 sequence and epidemiological data. Using an epoch extension of a phylogeography-based generalized linear model we plan to evaluate how human mobility and county/state/country-specific mobility restrictions impact the appearance and spread of emerging VOCs. The proposed analyses will provide near real time detection and tracking of new VOCs and will provide critical information for evaluating which public health interventions are most effective in controlling viral spread. The work will provide clear and timely information that can be used to hone the ongoing public health response.