The evolutionary relationships among pathogen lineages in multi-host systems are often the only observable signature of unobserved ecological and epidemiological processes. The evolution of viruses infecting humans, particularly, is of interest because of the public health importance of understanding the relationship of virus exposure to disease risk. Here I report results of two analyses of the evolutionary relationships among West Nile viruses in North America. These analyses suggest that (1) assortative mixing occurs between virus groups and human vs. non-human hosts and (2) human-derived isolates are related to each other. The ecological processes generating these viruses and the epidemiological consequences of West Nile virus host preference are unknown.