Epidemiology and phylodynamic analysis of canine distemper virus circulating in Michigan, USA

Canine distemper virus (CDV) is a highly contagious generalist pathogen that can cause significant mortality in domestic dogs and wild mammals. Due to the fast-evolving nature of CDV and its global spread, epizootic events and the emergence of new strains have been frequently reported. In Michigan, CDV surveillance from 2008 to 2018 was previously reported. Here, we combine and extend these data through 2023 to bring together 16 years of CDV surveillance in wild mammals in Michigan. We also sequenced CDV strains originating from both wildlife and domestic dogs to examine viral evolution across host populations. To facilitate interpretation of these data in both local and global contexts, we developed a Nextstrain workflow for CDV, enabling interactive visualization of viral evolution over time and geographic space. Our data show persistence of CDV in Michigan mammals during the study period and point to temporal, geographic, and host factors associated with CDV occurrence. Phylogenetic analysis using the newly built Nextstrain workflow showed that three CDV lineages--America-3, America-5, and Canada-1--are currently circulating in both wild and domestic animals in Michigan. The Nextstrain workflow enables reproducible, scalable integration of genomic sequencing into local surveillance and provides an updateable platform for ongoing and future surveillance efforts. This study demonstrates the value of coupling wildlife surveillance and diagnostic testing with genomic sequencing to identify lineage turnover and anticipate changes in viral behavior.