Data and code from: Viral outbreak dynamics and evolution in wildlife at the interface with humans

In this study, we used a multi-faceted approach to understand patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and persistence in a wild white-tailed deer population. Serology data indicated transmission of SARS-CoV-2 and persistence during the seven-month sampling period. Traditional disease modeling based on deer-to-deer transmission indicated relatively low prevalence with an R 0 of 1.2 and recovery period of 5 days; however, individual-based modeling informed by GPS tracked-movement data captured a potential transmission event. Phylogenetic analyses revealed a recurring pattern of divergent groups of deer-derived sequences with human-derived sequences falling close to each deer-derived cluster.Further, human-derived sequences were frequently sampled months prior to the deer-derived sequences, indicating repeated human to deer spillover. Using multiple types of data as well as both fine and broad scale analyses, we have characterized a pattern of ..., , # Data and code from: Viral outbreak dynamics and evolution in wildlife at the interface with humans

Dataset DOI: [10.5061/dryad.fbg79cp81](10.5061/dryad.fbg79cp81)

## Description of the data and file structure

We captured 39 white-tailed deer (31 females and 8 males) via chemical immobilization in winter (January-March) and summer (June-August) of 2024 (Supplementary Info). Biological samples, including serum isolated by centrifuging blood drawn by jugular venipuncture, as well as nasal and oral swabs, were gathered at capture for SARS-CoV-2 testing and shipped to the USDA National Wildlife Research Center (Fort Collins, CO) for diagnostic testing. This information was used to classify the disease status of each animal.

We conducted phylogenetic analyses using complete SARS-CoV-2 collected from both humans and white-tailed deer. Of the sampled individuals, 3 were SARS-CoV-2 positive, and we were able to sequence full viral genomes from samples. These 3 viral genomes and all other g...,