Co-circulation of two rabies virus clades among domestic and wildlife species in Zimbabwe

Rabies virus (RABV) exhibits genetic diversity closely linked to its geographical origins and its animal reservoirs. ln Southern Africa, several lineages and reservoirs have been identified. ln Zimbabwe, the latest studies on RABV reported the circulation of AF1 b sub-lineage (Cosmopolitan clade) in domestic dogs and livestock in 2014 and the detection of AF1b in the Harare outbreak (2010-2017). However, no wildlife rabies data has been published in the last decade. More information about current epidemiology and genetic diversity of RABV in wildlife and domestic animais are needed. To address this gap, a retrospective study analysed 74 brain samples from 50 domestic and 24 wild animais submitted for rabies diagnosis between 2014 and 2020. As part of the surveillance, the Central Veterinary Laboratory (DVS) confirmed rabies through direct immunofluorescence. Samples were then tested by RT-PCR and sequencing. Available metadata comprised only the location and species of each sample. Samples in domestic animais were mainly submitted in the districts around Harare and Bulawayo while the wildlife samples mostly came from the Hwange district (including Hwange National Park). Phylogenetic analyses showed that AF1 b sublineage was dominant, but not exclusive with AF3 clade (mongoose reservoir) also present. The two AF1 b subclades were both found in the Harare reg ion. ln the province, SC2 was detected in the North-West (near Zambia and Botswana) and SC1 in the South-East (near South-Africa and Mozambique). The two AF3 positive samples came from a dog from Harare region in 2018 and a common slender mongoose in the Hwange national park in 2020. Ali samples were genetically related to strains found in neighbouring countries with no evidence of spatial or temporal clustering. This study indicates the circulation of 2 clades in both wildlife and domestic animais, underscoring the presence of several transmission cycles of RABV at the wildlife-domestic interface. Strengthening surveillance efforts, including comprehensive data collection on positive cases, is essential to characterize these cycles and inform control strategies.