Mesocarnivores such as racoons, skunks, and foxes are widely distributed across the state of New York, including the five boroughs of New York City. These medium-sized carnivores play important ecosystem roles. However, they are also involved in the maintenance and spread of infectious diseases, including zoonotic diseases of public health importance such as rabies. These species are notable for their involvement in the multi-species “metareservoir” of interconnected carnivore populations maintaining canine distemper virus. Canine distemper virus (CDV), a single-stranded negative-sense RNA virus, is a morbillivirus in the family Paramyxoviridae. Unlike other viruses in its family, canine distemper virus can infect an astonishing variety of species with varying degrees of pathogenicity, complicating its epidemiology.

The purpose of this project is to analyze brain samples of wild mesocarnivore and domestic dogs and cats submitted to the Goodman Pathogen Genomics Laboratory by the New York City Department of Health and Mental Hygiene. The brain samples are from animals that were either found deceased or euthanized by the Department of Health between March 2023 and January 2024 because they were rabies suspects. All samples were screened and confirmed negative for rabies prior to their submission. No live animals will be utilized in this study. Using qRT-PCR, the brain samples will be screened for CDV. Following identification of a positive sample, full viral genome sequencing will be performed using the Nanopore MinION (Oxford Nanopore Technologies).