African Viral Dark Matter: From Viral Discovery to Anticipatory Surveillance

Global genomic surveillance has transformed pathogen detection, but most diagnostic assays and reference databases remain optimized for known targets. Divergent, low-abundance, and uncharacterized viruses can therefore remain undetected or biologically unresolved. This limitation is particularly relevant in Africa, where complex ecosystems and rapidly changing human–animal interfaces coexist with historically uneven sampling and reference-data coverage. Here, we define African Viral Dark Matter as viral diversity that remains undetected, unresolved, or biologically uninterpretable within current surveillance systems. We distinguish three epistemic states evidence, Plausibility, and Unknowns (EPU) to separate demonstrated viral signals from ecological inferences and unresolved biological questions. We then propose an African Viral Dark Matter Atlas (AVDMA) that links viral genomes to hosts, environments, geography, and time, together with a five-dimensional Viral Relevance and Priority Score (VRPS) integrating novelty, evidentiary strength, host connectivity, geographical trajectory, and public-health relevance. The framework shifts surveillance from static viral cataloguing towards longitudinal, context-rich viral intelligence. Its objective is not to predict the next pandemic virus, but to reduce uncertainty, identify changing viral systems, and support earlier, evidence-based surveillance decisions. Successful implementation will require African leadership in sampling, sequencing, analytics, data governance, and interpretation.