Patterns of Animal Rabies Prevalence in Northern South Africa between 1998 and 2022.

Rabies is endemic in South Africa and rabies cycles are maintained in both domestic and wildlife species. The significant number of canine rabies cases reported by the World Organization for Animal Health Reference Laboratory for Rabies at Onderstepoort suggests the need for increased research and mass dog vaccinations on specific targeted foci in the country. This study aimed to investigate the spatiotemporal distribution of animal rabies cases from 1998 to 2017 in northern South Africa and environmental factors associated with highly enzootic municipalities. A descriptive analysis was used to investigate temporal patterns. The Getis-Ord Gi statistical tool was used to exhibit low and high clusters. Logistic regression was used to examine the association between the predictor variables and highly enzootic municipalities. A total of 9580 specimens were submitted for rabies diagnosis between 1998 and 2022. The highest positive case rates were from companion animals (1733 cases, 59.71%), followed by livestock (635 cases, 21.88%) and wildlife (621 cases, 21.39%). Rabies cases were reported throughout the year, with the majority occurring in the mid-dry season. Hot spots were frequently in the northern and eastern parts of Limpopo and Mpumalanga. Thicket bush and grassland were associated with rabies between 1998 and 2002. However, between 2008 and 2012, cultivated commercial crops and waterbodies were associated with rabies occurrence. In the last period, plantations and woodlands were associated with animal rabies. Of the total number of municipalities, five consistently and repeatedly had the highest rabies prevalence rates. These findings suggest that authorities should prioritize resources for those municipalities for rabies elimination and management.

Spatio-temporal epidemiology of animal and human rabies in northern South Africa between 1998 and 2017.

BACKGROUND: Rabies is a fatal zoonotic disease that is maintained in domestic dogs and wildlife populations in the Republic of South Africa. A retrospective study was conducted to improve understanding of the dynamics of rabies in humans, domestic dogs, and wildlife species, in relation to the ecology for three northern provinces of South Africa (Limpopo, Mpumalanga, and North-West) between 1998 and 2017. METHODS: A descriptive epidemiology study was conducted for human and animal rabies. Dog rabies cases were analyzed using spatio-temporal scan statistics. The reproductive number (Rt) was estimated for the identified disease clusters. A phylogenetic tree was constructed based on the genome sequences of rabies viruses isolated from dogs, jackals, and an African civet, and Bayesian evolutionary analysis using a strict time clock model. Several ecological and socio-economic variables associated with dog rabies were modeled using univariate analyses with zero-inflated negative binomial regression and multivariable spatial analyses using the integrated nested Laplace approximation for two time periods: 1998-2002 and 2008-2012. RESULTS: Human rabies cases increased in 2006 following an increase in dog rabies cases; however, the human cases declined in the next year while dog rabies cases fluctuated. Ten disease clusters of dog rabies were identified, and utilizing the phylogenetic tree, the dynamics of animal rabies over 20 years was elucidated. In 2006, a virus strain that re-emerged in eastern Limpopo Province caused the large and persistent dog rabies outbreaks in Limpopo and Mpumalanga Provinces. Several clusters included a rabies virus variant maintained in jackals in Limpopo Province, and the other variant in dogs widely distributed. The widely distributed variant maintained in jackal populations in North-West Province caused an outbreak in dogs in 2014. The Rt was high when the disease clusters were associated with either multiple virus strains or multiple animal species. High-risk areas included Limpopo and Mpumalanga Provinces characterized by woodlands and high temperatures and precipitation. CONCLUSION: Canine rabies was maintained mainly in dog populations but was also associated with jackal species. Rural communities in Limpopo and Mpumalanga Provinces were at high risk of canine rabies originating from dogs.

Complete Coding Sequences of 23 South African Domestic and Wildlife Rabies Viruses.

South African rabies viruses originating from dogs and jackals (canid viruses) are closely related and highlight cross-species transmission events between the two canine species. Rabies due to the canid lyssavirus variant is a significant public health matter in this country. The complete coding sequences of 23 canid lyssaviruses from South Africa are reported here.