Wild Polio Is Gone, but Vaccine-Derived Outbreaks Are Testing Africa’s Defences

Africa's fight against polio is increasingly being decided not only by how quickly vaccines reach communities, but by how fast laboratories can detect, sequence and trace the virus before transmission spreads.

The study "The African Polio Laboratory Network: Advancing Regional Poliovirus Detection, Genomic Surveillance, and Eradication," by Brook Tesfaye, Terna Nomhwange, Shelina Moonsamy, Julius E. Chia, Maryceline M. Baba, Adedayo Omotayo Fanaye, Mesfin Tefera, Yogolelo Riziki, Peter Borus, Josephine Bwogi, Marie-Claire Endegue, Mariette Glitho, Idah Ndumba, Priscilla Mosoke, Ousmane M. Diop, John Kofi Odoom, Martin Faye, Gedi Mohamed and Anfumbom Kfutwah, published in Vaccines, evaluates how Africa's polio laboratory system performed during 2025.

The assessment shows a network that is technically strong but operating under mounting pressure. Across 16 WHO-accredited laboratories, 77,230 acute flaccid paralysis specimens were processed during 2025, while 92% of specimens met the target for virus-isolation timeliness and 94% met the target for PCR-based intratypic differentiation. Additionally, persistent vaccine-derived poliovirus transmission, sequencing bottlenecks, uneven laboratory workloads and supply shortages show why the final stage of eradication may be harder than the progress already achieved.

Polio Eradication Now Depends on Speed as Much as Coverage

The WHO African Region was certified free of indigenous wild poliovirus in 2020, a landmark public-health achievement. But that milestone did not eliminate the threat. Circulating vaccine-derived polioviruses continue to emerge where immunization gaps allow weakened vaccine viruses to circulate long enough to evolve and regain the ability to cause paralysis.

Vaccination remains fundamental, but eradication also depends on detecting transmission early enough for immunization campaigns to contain it. Laboratory delays therefore translate directly into lost response time, particularly when transmission crosses borders or continues silently before the first cases are confirmed.

The study reports 22 distinct poliovirus outbreaks across 10 countries during 2025, with type 2 vaccine-derived poliovirus responsible for 19 of them. Angola recorded the largest number of distinct outbreak clusters, followed by Nigeria and Ethiopia, while some genetic lineages showed evidence of substantial viral evolution.

The laboratory network sits at the centre of this response chain. Once poliovirus is confirmed, results feed into national and regional coordination mechanisms, triggering emergency structures, risk assessment and response planning. The authors note that laboratory confirmation can activate emergency operations within 72 hours, illustrating how diagnostics function not simply as scientific evidence but as an operational trigger.

Performance on early diagnostic stages was generally strong. Most laboratories met WHO targets for virus isolation, and all except the Democratic Republic of Congo met the PCR-ITD timeliness target. Those results indicate a surveillance system capable of producing rapid initial confirmation across very different national and resource settings.

Genomic Sequencing Is Emerging as the Critical Bottleneck

The more difficult challenge lies further downstream. Genomic sequencing allows health authorities to establish whether detected viruses are related, determine how long transmission may have been occurring and identify chains that cross administrative or national borders. For eradication programmes, that intelligence determines where vaccination campaigns must go next.

Until early 2025, only South Africa and Ghana had poliovirus sequencing capacity within the African network. New facilities in Uganda and at the University of Ibadan in Nigeria began operating during the year, reducing reliance on distant regional and international centres and improving the geographic distribution of sequencing capacity.

During the study period, 1,726 poliovirus samples were sequenced. Ibadan processed 751 samples, South Africa 545, Ghana 258 and Uganda 115, while another 57 were handled in France. Yet only 67% of sequencing results were reported within the expected turnaround target, considerably weaker than performance for earlier stages of detection.

Genomic information becomes less useful as an outbreak accelerates. Ghana reported a median sequencing turnaround of four days and Uganda five days, while South Africa recorded seven days. Ibadan, despite carrying the largest sequencing workload, had a median turnaround of 11 days and much wider variation, suggesting that expanding capacity without matching investment in staff, equipment and logistics can simply relocate the bottleneck.

The regional response is increasingly focused on decentralization. The study describes plans to expand sequencing capacity across 12 additional countries, including Cameroon, the Democratic Republic of Congo, Kenya, Senegal, Algeria, Ethiopia, Madagascar, Zambia and Zimbabwe.

Portable nanopore platforms and Direct Detection and Nanopore Sequencing could further change the surveillance model. By reducing dependence on traditional virus-isolation steps, these technologies could shorten the interval between receiving a specimen and identifying transmission, bringing genomic epidemiology closer to real-time outbreak intelligence.

A Strong Network Is Still Vulnerable to Uneven Capacity

The study also exposes an important structural weakness: workloads are distributed extremely unevenly. Nigeria's Ibadan laboratory processed 18,929 AFP specimens, Maiduguri handled 12,878 and the Democratic Republic of Congo processed 9,239. Together, laboratories in Nigeria and the DRC accounted for 53% of the entire regional workload.

Such concentration makes sense in countries with large populations and heavier surveillance burdens, but it also creates operational risk. A shortage of reagents, equipment failure or staffing pressure at a small number of high-volume laboratories could disrupt surveillance across multiple countries and delay outbreak confirmation.

Supply chains are already a recurring concern. Laboratories reported shortages of critical reagents and other materials that interrupted processing and delayed results. The network sometimes compensated by transferring supplies from laboratories with surplus stocks, demonstrating useful regional solidarity but also revealing how fragile routine operations can become when procurement systems fail.

Quality assurance, however, remains a major strength. The network operates within a structured WHO accreditation system covering virus isolation, PCR-based differentiation and environmental surveillance. By the end of 2024, all regional polio laboratories were accredited for processing AFP and environmental-surveillance samples, while more than 190 laboratory personnel participated in targeted technical training.

This combination of standardized procedures, peer review and workforce development helps explain why most laboratories maintained strong performance despite resource constraints. But sustaining that performance will require more than periodic training. Reliable procurement, workforce retention, maintenance budgets and workload redistribution will become increasingly important as genomic surveillance expands.

Africa's Polio Labs Could Become a Wider Health-Security Asset

The strategic significance of this network extends beyond polio. Polio eradication has created laboratory infrastructure, quality systems, trained personnel, data-management capabilities and cross-border coordination mechanisms that can potentially support surveillance for other infectious diseases.

The authors explicitly argue that policymakers should integrate the network into broader regional health-security frameworks rather than allowing laboratory capacity to contract once eradication goals are reached. The same sequencing technologies and diagnostic expertise being developed for poliovirus could strengthen responses to emerging and epidemic-prone pathogens.

For African governments and development partners, that raises a financing question. Disease-specific programmes have historically attracted resources because they offer measurable targets, but the infrastructure they create can have much wider value. Preserving polio laboratories as multi-pathogen surveillance assets could turn decades of eradication investment into long-term health-system capacity.

The study is descriptive rather than causal, and its limitations matter. It relies mainly on AFP stool specimens and routine surveillance data, meaning the workload captured does not represent every activity undertaken by participating laboratories. Sequencing results also reflect the samples available at the time of extraction and may change as additional data become available.

Having said that, the evidence highlights an important shift in Africa's eradication challenge. The continent has already demonstrated that vaccination campaigns and surveillance can eliminate indigenous wild poliovirus. The remaining fight is increasingly about making detection faster, sequencing more local, supply chains more resilient and laboratory capacity less uneven.