Viral surveillance at the human-animal interface: Molecular detection, characterisation, and pathogen discovery in Namibia

Viral pathogens circulating among wildlife, livestock and companion animals in southern Africa remain poorly characterised, despite their potential to affect conservation outcomes, animal health and public health systems. Namibia provides a unique setting for investigating these dynamics, particularly in species such as the African penguin (Spheniscus demersus), which has previously been detected with highly pathogenic avian influenza linked to domestic poultry outbreaks. This detection highlights the permeability of boundaries between wildlife and human-associated systems and underscores the need for sustained monitoring of vulnerable species. This thesis applies targeted molecular diagnostics alongside integrated metagenomic sequencing across multiple studies to identify, describe and interpret viral diversity at key human-animal interfaces in Namibia. The work reveals previously unrecognised viral circulation, documents outbreak-associated events and highlights potential cross-species transmission pathways. By demonstrating the complementary strengths of focused molecular diagnostics and unbiased genomic approaches, this thesis generates essential baseline data for Namibia and emphasises the importance of strengthening One Health surveillance in regions where pathogen circulation remains under-documented. Overall, this work provides a multi-species perspective on viral ecology relevant to southern Africa and offers insights of value to the international scientific community through collaborative research networks between Namibia and Italy.