Abstract
We are interested in using phylodynamics to better understand molecular clusters of HIV within the state of Florida, USA. To our knowledge, there is currently no study using such methodology to understand the epidemic in Florida. Viral sequences collected from 2007 to 2017 (about 50,000) will be linked with individual-level data (demographics—sex, race/ethnicity—and mode of transmission) accessed through the Patient Reporting Investigating Surveillance Manager (PRISM), and the Enhanced HIV/AIDS Reporting System (eHARS) via the Florida Department of Health (FDOH). Through the use of HIV-TRACE, which analyzes genetic distance matrices, we will create molecular transmission networks including data on mode of transmission, race/ethnicity, and sex. Furthermore, a maximum likelihood phylogenetic tree will be created using software (e.g. IQ-Tree, PhyML, and FastTree2) run on a high-performance cluster. Phylogenetic comparative analysis will be performed to assess the association between phylogenetic clades and demographics (including extended demographics like syphilis and other comorbidities queried from PRISM and eHARS).