Epidemiology and genetic characterization of orphan polioviruses in Africa, 2022–2024: Unmasking silent transmission and implications for eradication

The continued detection of orphan polioviruses, defined by ≥ 1.5 % nucleotide divergence in the VP1-coding region of the virus compared with the VP1 of previous circulating isolates, presents a significant challenge to polio eradication efforts. Orphan polioviruses underscores the existence of undetected transmissions and surveillance blind spots. Understanding the epidemiology and genetic characteristics of these viruses is essential to accelerate eradication efforts. A retrospective analysis was conducted on orphan polioviruses detected in the WHO African region from 2022 to 2024, using WHO polio database. Descriptive statistics, spatial analysis, and phylogenetic methods were employed to assess virus transmission, genetic diversity, and surveillance system performance. A total of 130 orphan polioviruses were detected within the study period in 17 countries, with Nigeria and Chad accounting for 69 % of all reported orphan polioviruses. Circulating Vaccine-derived Poliovirus type 2 (cVDPV2) was the predominant serotype, accounting for 96 % of overall detections. The majority of the orphan polioviruses were among children under-five years, with 66 % having received the recommended 3 doses of Oral Polio Vaccine (OPV). The median time to detection was 54 days (IQR: 41–72), with significant delays observed in Chad and Democratic Republic of Congo (DRC). Phylogenetic analysis revealed independent emergences and prolonged circulation. Nigeria showed high genetic diversity with at least 6 distinct sub-lineages, the predominant emergence being NIE-ZAS-1. Closely related chains of transmission were identified in Nigeria, Chad, Niger, and Cameroon, highlighting sustained cross-border transmission within the Lake Chad Basin region. Also, the detection of orphan poliovirus in Angola genetically traced to Nigeria demonstrates the risk of an even wider geographic spread. The detection of orphan polioviruses and demonstration of viral genetic linkages highlights persistent surveillance and immunity gaps in the WHO African region. Improving the sensitivity of surveillance systems, expanding regional sequencing capacity, and intensifying cross-border synchronization of surveillance and immunization activities are important in the timely detection of silent transmissions and advancing eradication goals. • Assess epidemiological patterns, genetic characteristics of Orphan polioviruses • Spatial analysis for temporal and geographic distribution • Phylogenetic analyses to investigate viral evolution and transmission patterns • Discusses programmatic and policy implications • Impacts of various polio vaccines in eradication efforts