key: cord-0879481-t8twpynk authors: Cella, E.; Ali, S.; Schmedes, S. E.; Rife, B.; Marini, S.; Salemi, M.; Blanton, J.; Azarian, T. title: Early emergence phase of SARS-CoV-2 Delta variant in Florida date: 2022-02-22 journal: nan DOI: 10.1101/2022.02.18.22271195 sha: 0dfac8c6b977ce67e7315c29b430a057a49e117f doc_id: 879481 cord_uid: t8twpynk SARS-CoV-2, the causative agent of COVID-19, emerged in late 2020. The highly contagious B.1.617.2 (Delta) Variant of Concern (VOC) was first identified in October 2020 in India and subsequently disseminated worldwide, later becoming the dominant lineage in the U.S. Despite considerable genomic analysis of SARS-CoV-2 in the U.S., several gaps in the understanding of the local dynamics during early introductions remain, which when elucidated could translate the results of viral genomic epidemiology to actionable mitigation efforts. Here, we explore the early emergence of the Delta variant in Florida, U.S. using phylogenetic analysis of representative Florida and globally sampled genomes. We find multiple independent introductions into Florida primarily from North America and Europe, with a minority originating from Asia. These introductions lead to three distinct clades that demonstrated varying relative rates of transmission and possessed five distinct substitutions that were 3-21 times more prevalent in the Florida sample as compared to the global sample. Our results underscore the benefits of routine viral genomic surveillance to monitor epidemic spread and support the need for more comprehensive genomic epidemiology studies of emerging variants. In addition, we provide a model of epidemic spread of newly emerging VOCs that can inform future public health responses. Compared to its predecessor Alpha, the Delta variant possesses 12 notable mutations in the 80 genomic region encoding the spike protein that provide a fitness advantage. In particular, the 81 D614G substitution, which is shared with other VOCs including Alpha, Beta, Gamma and the 82 more recently emerging Omicron, has been associated with increased transmissibility, infectivity, CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) analyzing SARS-CoV-2 viral genome sequence data from Florida in the context of global data. Our findings provide insight into the introduction dynamics of future SARS-CoV-2 variants. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . 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