Epidemics and epizootics of eastern equine encephalitis virus (EEEV) occur sporadically in temperate regions where transmission is seasonal from late summer to early fall. These outbreaks may derive from virus that overwinters locally or perhaps results from reintroduction of virus from other sites. To evaluate these possibilities, we compared the phylogenetic relationships of EEEV isolates obtained from mosquitoes collected during statewide arbovirus surveillance in Connecticut, in addition to isolates from concurrent outbreaks in southern New Hampshire and upstate New York. In Connecticut, viral isolates grouped into temporally discrete clades by year of isolation or over 2 years of sampling. Two or more clades arose in 2000, 2001, 2003, 2004, and 2006, possibly the result of separate introduction events into the state, whereas viruses from upstate New York and New Hampshire segregated into single clades that persisted for 2 or more years. New Hampshire viruses shared recent common ancestry to those isolated in Connecticut suggesting viral dispersal among these regions. These results provide additional evidence for independent episodes of EEEV overwintering in northern foci.
