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Rabies has been endemic to the eastern United States in raccoons (Procyon lotor) since 1960 and endemic to New York, USA, since the 1990s (1). The spread of rabies virus from raccoons in the mid-Atlantic states to species in New York has been reconstructed with spatiogenetic and phylogenic analyses (2). Despite this spread, a few locations in the region, including Suffolk and Nassau Counties on Long Island, New York, have been considered to be rabies free since 2011 (3). Maintaining these areas as low risk for rabies substantially decreases the likelihood of human and animal exposure to rabies virus and dramatically reduces the expenses paid for postexposure rabies virus treatments and rabies control (4).
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To identify any breaches in the elimination zone, Nassau and Suffolk County health departments, veterinarians, and wildlife control officers routinely submit animals with clinical signs compatible with rabies for rabies virus testing to the New York State Department of Health Rabies Laboratory (Slingerlands, New York, USA). Before 2016, rabies had not been reported in Suffolk County since 2009 or in Nassau County since 2007 (Figure 1) (5). During 2016–2017, rabies reappeared in Nassau and Suffolk Counties in 3 terrestrial animals: a raccoon (Procyon lotor), a river otter (Lontra canadensis), and a domestic cat (Felis catus). Here, we describe our efforts to identify the origins of these rabid animals and our contingency plans to eliminate further cases and restore the rabies virus–free zone status.
The Study
In March 2016, a rabid raccoon with neurologic signs was trapped in Hicksville in Nassau County. Real-time reverse transcription PCR (6) and Sanger sequencing demonstrated that the animal was infected with a raccoon rabies virus variant. A phylogenetic analysis of the full nucleoprotein and partial glycoprotein gene sequences did not provide us the resolution required for us to confidently identify where the virus had originated. At the time of this original analysis, whole-genome sequencing (WGS) was not available in our laboratory. We initiated enhanced rabies surveillance for ≈12 months in Babylon and Huntington of Nassau County to determine if rabies virus was circulating locally by increasing the number of wild animals submitted...