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Background: In the wake of the COVID-19 pandemic, scientists have scrambled to collect and analyze SARS-CoV-2 genomic data to inform public health responses to COVID-19 in real-time. Open-source phylogenetic and data visualization platforms for monitoring SARS-CoV-2 genomic epidemiology have rapidly gained popularity for their ability to illuminate spatial-temporal transmission patterns worldwide. However, the utility of such tools to inform public health decision-making for COVID-19 in real-time remains to be explored. Objective: The objective of this study was to convene experts in public health, infectious diseases, virology, and bioinformatics – many of whom were actively engaged in the COVID-19 response at the time of their participation – to discuss the application of phylodynamic tools to inform pandemic responses. Methods: A series of four virtual focus group discussions were hosted between June 2020 and June 2021, covering the pre- and post-variant and vaccination eras of the COVID-19 crisis. Audio recordings were transcribed verbatim, and an iterative, thematic qualitative framework was used for analysis. Results: Of the 41 individuals invited, 23 total participants (56.1%) agreed to participate. Across the four focus group sessions, 15 (65%) of the participants were female, 17 (74%) were white, and 5 (22%) were black. Participants were described as molecular epidemiologists (ME, n=9), clinician-researchers (n=3), infectious disease experts (ID, n=4), and public health professionals (PH) at the local (n=4), state (n=2), and federal (n=1) levels. Collectively, participants felt that successful uptake of phylodynamic tools relies on the strength of academic-public health partnerships. They called for interoperability standards in sequence data sharing and cited many resource issues that must be addressed, including timeliness and cost, in addition to improving issues related to sampling bias and the translation of phylodynamic findings into public health action. Conclusions: This was the first qualitative study to characterize the perspectives of key experts regarding the utility of phylodynamic tools for the public health response to COVID-19. The focus group participants identified key areas for improvement of existing and future phylogenetic and data visualization platforms for monitoring SARS-CoV-2 genomic epidemiology. This information is critical to both policymakers and developers as they consider how to handle existing and emerging SARS-CoV-2 variants during the ongoing crisis. 

Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alters pathogen spread is poorly understood. Here, we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma (Puma concolor) from two contrasting regions: one bounded by the wildland urban interface (WUI) and one unbounded with minimal anthropogenic development (UB). We found landscape variables and host gene flow explained significant amounts of variation of feline immunodeficiency virus (FIV) spread in the WUI, but not in the unbounded region. The most important predictors of viral spread also differed; host spatial proximity, host relatedness, and mountain ranges played a role in FIV spread in the WUI, whereas roads might have facilitated viral spread in the unbounded region. Our research demonstrates how anthropogenic landscapes can alter pathogen spread, providing a more nuanced understanding of host-pathogen relationships to inform disease ecology in free-ranging species.