South Africa’s next viral emergence may already be here: under-recognized zoonotic and arboviral transmission as a surveillance blind spot

Abstract

South Africa has demonstrated exceptional capacity for viral detection and genomic analysis, most visibly through severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomics and wastewater-based monitoring. Yet outside respiratory virus programmes, the country’s approach to emerging viral infections remains comparatively reactive, pathogen-specific, and biased toward high-visibility events. This Perspective argues that South Africa’s most actionable surveillance blind spot is not only the importation of novel pathogens, but the delayed recognition of transmission already underway within endemic and re-emerging zoonotic and arboviral systems. Using illustrative exemplars-mpox, Crimean–Congo haemorrhagic fever virus, Rift Valley fever virus, and neglected neuroinvasive arboviruses- we propose that “emergence” in South Africa often takes the form of under-diagnosed local amplification rather than dramatic first appearance. We advocate a syndrome-based, diagnostically guided strategy coupled to an integrated One Health “signal-to-action” framework that links clinical syndromes with veterinary events, vector and environmental monitoring, and proportionate laboratory escalation (targeted molecular/serology testing, confirmatory assays, and sequencing when indicated). The objective is not indiscriminate multiplexing, but earlier alignment between ecological risk, clinical suspicion, and test availability- so that outbreak response begins despite tentative early signals and before widespread human infection or the acceleration of the outbreak.