Phylogeographic analysis of Influenza D virus evolution

Influenza D virus (IDV), first identified in 2011 and primarily affecting cattle, has since been detected in a wide range of mammalian hosts and geographic regions. Despite widespread circulation in domestic cattle, the virus’s evolutionary history and global migration dynamics remain poorly understood. This study presents the first comprehensive phylogeographic analysis of IDV using segment 4 (HEF gene) sequences. A time-calibrated Bayesian phylogeographic reconstruction suggests a most recent common ancestor around 1998, with the root most likely in the USA or Japan, although data biases limit definitive conclusions. Generalized linear models (GLMs) were used to assess potential drivers of viral spread, revealing strong associations with cattle trade and shared land borders. However, sequencing efforts heavily influence inferred migration patterns, emphasizing the role of sampling bias in such reconstructions. These findings highlight the mobility of IDV and the critical need for expanded genomic surveillance in underrepresented regions to better detect similar pathogens and understand their transmission dynamics.