Alternatives to central nervous system samples for enhanced rabies surveillance: Exploring natural infections of Lyssavirus rabies in striped skunks (Mephitis mephitis) in Northern Colorado

Enhanced rabies surveillance (ERS) of wildlife populations complements passive public health surveillance through active field-based sampling. The combined data augment rabies management decision-making through tracking virus distribution and movement, rapidly identifying potential outbreaks, and informing containment and elimination strategies at regional and landscape scales. Laboratory diagnostic methods are critical to ERS and several gold standard methods are recommended for detection of Lyssavirus rabies (RV); each validated using central nervous system (CNS) tissue which requires necropsy and cold storage, posing challenges and risks in remote field settings. Alternative sample types to CNS tissue may improve ERS efficiency and field personnel safety, provided they offer robust diagnostic specificity and sensitivity. We evaluated multiple sample types opportunistically collected postmortem from naturally infected striped skunks (Mephitis mephitis) and used real-time reverse transcriptase PCR (rtRT-PCR) to evaluate diagnostic sensitivity and specificity of each sample type compared to CNS tissue. The detection rate of RV RNA was 97 % (95 % CI 81-100) for oral swabs and 96 % (95 % CI 80-100) for eye swabs; when swab types were combined, the detection rate was 100 % (95 % CI 85-100) and comparable to detection from CNS. Other sample types demonstrated compromised diagnostic sensitivities (33-76 %). All sample types were 100 % specific for RV diagnosis. The combination of eye and oral swabs as ERS samples may expand sampling opportunities that improve efficiency, mitigate sample collection and storage challenges, and decrease RV exposure risk among field staff while enhancing the information provided to estimate impacts of RV management on target wildlife populations.