Rabies virus (RABV), a member of the Lyssavirus genus, was diagnosed in Cape fur seals (Arctocephalus pusillus pusillus) in South Africa using direct fluorescent antibody testing (dFAT). Following initial confirmation in May 2024, an investigation sought to determine the origin and geographic extent of RABV infection in this pinniped species. The study combined retrospective testing of frozen samples with targeted prospective sampling of marine mammals showing neurologic signs and opportunistic carcass sampling along the South African coast.
From March 2023 through November 2025, investigators collected 216 brain tissue samples from Cape fur seals across the Northern and Western Cape provinces, including six retrospective specimens. Of these, 85 (39%) tested positive for lyssavirus antigen by dFAT and 131 (61%) tested negative. Positive animals were found at multiple coastal locations; the earliest confirmed positive sample was a retrospective specimen from Cape Town collected in September 2023.
Positive animals included those found dead (n = 45) and animals euthanized or shot due to neurologic signs or aggression (n = 40). After confirmation of RABV in a seal, health authorities considered all marine mammals with neurologic signs as suspect rabies cases and collected brain samples from deceased or captured animals euthanized by pentobarbital or gunshot. Only one other marine mammal—a dead orca found in St. Helena Bay in October 2024—was tested and was negative for RABV antigen.
A case of human interest involved an unvaccinated domestic dog (sample 170/24WC) from Cape Town, confirmed rabid by dFAT on May 20, 2024. The dog’s owner reported that the dog had been bitten by a Cape fur seal during an off-leash encounter about two weeks before onset of clinical signs; subsequent epidemiologic investigation identified a seal that had been injured in a fight with dogs and died after capture, and that seal tested positive for RABV (sample 186/24WC).
Researchers sequenced 51 RABV genomes from Cape fur seals and the genome from dog 170/24WC. Generated sequences were deposited in GenBank. Phylogenetic analysis resolved four strongly supported clusters (A–D) with posterior probabilities of 1. Cluster A included all 51 seal-derived sequences plus the dog sequence; pairwise comparisons within cluster A showed 99.79% nucleotide sequence identity, indicating very close relatedness among the seal viruses and the dog virus.
Cluster B comprised sequences from black-backed jackals and a bat-eared fox. Clusters A and B shared a common ancestor and had approximately 98% nucleotide identity between them. Clusters C and D contained RABVs from other wildlife (bat-eared foxes and aardwolves) and domestic dogs retrieved from GenBank, respectively.
Bayesian evolutionary analysis (BEAST) estimated the mean substitution rate for the included RABV sequences at 3.7838 × 10−4 substitutions/site/year (95% highest posterior density 2.0322–5.6575 × 10−4). The estimated time to the most recent common ancestor (tMRCA) for clusters A and B was 1998. The tMRCA for cluster A was estimated at 2015, with subcluster A1 dated to 2020. These dates suggest viral divergence and establishment in seals preceded laboratory confirmation by several years.
All sequenced seal viruses were highly similar (99.79% identity), consistent with a single introduction event into the seal population followed by sustained within-species transmission. The phylogenetic proximity between cluster A (seals) and cluster B (black-backed jackals and a bat-eared fox), together with tMRCA estimates, supports the black-backed jackal as the most likely source of the initial introduction into Cape fur seals.
The genomic clustering of the domestic dog isolate (170/24WC) with seal-derived viruses indicates a seal-to-dog spillover event, consistent with the owner’s report of the dog being bitten by a seal. The authors note that RABV typically circulates within reservoir species but that direct contact between a susceptible mammal and a reservoir host can produce cross-species transmission; in rare instances such events enable adaptation and establishment in a new host species. In this investigation, evidence points to sustained transmission among seals across much of their South African range, likely aided by the species’ extensive marine movements and intercolonial contact.
This investigation documents emergence of rabies in Cape fur seals, with phylogenetic evidence indicating introduction from terrestrial reservoirs—most likely the black-backed jackal—followed by sustained seal-to-seal transmission and at least one seal-to-dog spillover. The genetic homogeneity of seal-derived RABVs supports a single-source introduction rather than multiple independent introductions.
The study is limited in its ability to estimate true prevalence of RABV in the overall Cape fur seal population because sampling focused on animals with neurologic signs, mortalities, opportunistic carcasses, and available retrospective specimens. Only one non-seal marine mammal was tested and found negative. Results underscore the capacity of RABV to infect new host species and maintain transmission cycles once established. Continued surveillance and targeted sampling are implied by the findings, though specific public health or wildlife management recommendations were not detailed in the source article.