Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States

Joseph Fauver

Joseph Fauver, Yale School of Public Health


To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the U.S., we used the ARTIC Network pipeline on the Oxford Nanopore MinION to sequence nine viral genomes from first reported COVID-19 cases in Connecticut. Our phylogenetic analysis places most of these genomes with viruses sequenced from Washington state. Coupling our genomic data with domestic and international flight patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. This study provides evidence for widespread, sustained transmission of SARS-CoV-2 within the U.S. and highlights the critical need for local surveillance.


Dr. Joseph Fauver is a postdoctoral research associate at the Yale School of Public Health in Dr. Nathan Grubaugh’s laboratory, focused on the genomic epidemiology of mosquito-borne viruses including dengue, Zika, and West Nile virus. Previously, Joseph was a postdoc at Washington University in St. Louis where he used MinION sequencing to generate complete genome assemblies of filarial worms. Joseph is primarily interested in incorporating genomics into routine epidemiological surveillance programs, particularly in the Global South.