Five decades of progress in vaccine-preventable disease surveillance and immunization coverage in East and Southern Africa: focus on polio and measles

¹World Health Organization, Inter-Country Support Team office for East and Southern Africa, Harare, Zimbabwe, ²World Health Organization, Kenya Country Office, United Nations Office in Nairobi UN Avenue Gigiri, Nairobi, Kenya

^&Corresponding author
Daudi Manyanga, World Health Organization, Inter-Country Support Team Office for East and Southern Africa, Harare, Zimbabwe

Introduction    

Over the past fifty years, East and Southern Africa (ESA) sub-region has witnessed remarkable advancements in the surveillance of vaccine-preventable diseases, particularly polio and measles and mainly contributed by the global polio eradication initiative [1,2]. Launched in 1988, Global Polio Eradication Initiative (GPEI) led to a dramatic reduction in polio cases and introduced Acute Flaccid Paralysis (AFP) surveillance, which became the cornerstone of broader VPD surveillance systems in the region. Its infrastructure was integrated into WHO-AFRO's Integrated Disease Surveillance and Response (IDSR) strategy, enabling expansion to other epidemic-prone diseases, strengthening data systems, training health workers, and laying a foundation for sustained public health improvements. These efforts have been instrumental in reducing the burden of these diseases and improving public health outcomes across the region. This was witnessed by the declined of measles disease burden mostly from 2000 as well as polio from 1990s in most of the ESA countries [3,4]. The journey began with the establishment of the Expanded Programme on Immunization (EPI) by the World Health Organization (WHO) in 1974, which aimed to provide equitable access to vaccines for all children [5]. This initiative laid the foundation for robust surveillance systems that have evolved significantly over the decades.

The Expanded Programme on Immunization (EPI) across the ESA subregion has made significant strides in data collection and surveillance systems, particularly for polio eradication and vaccination coverage. Since 1997, the Polio Eradication Initiative (PEI) has driven the transition from paper-based records and typewritten data to computerized systems such as Lotus, Excel templates, Microsoft Access, and Epi Info, which were standardized and deployed at district levels. These innovations greatly enhanced data quality, accessibility, and reporting completeness. Over time, the PEI infrastructure expanded to support surveillance for routine immunization, measles, yellow fever, maternal and neonatal tetanus, and new vaccines. Today, web-based platforms and real-time data sharing mechanisms enable timely access to immunization and disease surveillance data, facilitating rapid public health responses and informed decision-making [6-8]. Vaccine-preventable disease (VPD) surveillance in the region has also evolved. While earlier analyses relied on EPI Info and various versions of ArcGIS, many countries now leverage advanced data visualization tools such as Power BI to present real-time surveillance insights [9]. This transformation has strengthened regional collaboration, improved outbreak detection, and enhanced immunization coverage monitoring across countries. As technological innovations continue to shape public health response, strengthening digital data systems across East and Southern Africa remains essential for effective immunization and disease surveillance efforts.

Polio surveillance in the region has been a cornerstone of the Global Polio Eradication Initiative (GPEI) since the WHO resolution to eradicate polio in 1988 [10]. The implementation of Acute Flaccid Paralysis (AFP) surveillance, community-based reporting, wastewater surveillance and laboratory testing has enabled the detection and rapid response to polio cases. Despite challenges such as political instability, COVID-19 pandemic and logistical barriers, the region has made substantial progress towards polio eradication [11-15].

Similarly, since the adoption of the measles elimination goal in 2011, countries in the WHO African Region have leveraged polio surveillance infrastructure to implement case-based measles surveillance, conduct wide-age-range SIAs, and strengthen routine immunization coverage, resulting in a decline in measles burden and increased reporting of suspected cases. However, notable gaps persist in surveillance performance, with fewer than two-thirds of countries consistently meeting both principal monitoring indicators, and a decline in sample timeliness from 72% in 2012 to 67% in 2016 [16]. The introduction of case-based surveillance, outbreak investigation protocols, and supplementary immunization activities (SIAs) has strengthened the region's ability to prevent, detect, monitor and control measles outbreaks, and the recovery from the outbreaks [17]. Efforts to integrate measles and rubella surveillance have further enhanced the effectiveness of these programs towards elimination of measles and rubella in the African Region [18,19].

Recent studies have shown that outbreaks of Corynebacterium diphtheriae in Nigeria and South Africa are closely associated with gaps in routine immunization and weaknesses in disease surveillance systems [20,21]. These immunization shortfalls have been exacerbated by insecurity and limited access to healthcare services in certain regions. Furthermore, inadequate surveillance has led to delayed case detection and underreporting, which in turn has hindered timely public health responses and containment efforts, allowing the disease to spread among vulnerable populations. Also, Bordetella pertussis has re-emerged in a few ESA countries, highlighting ongoing challenges related to routine immunization and disease surveillance [22-24]. Disruptions to immunization services, particularly during the COVID-19 pandemic, have resulted in decreased coverage of the DTP3 vaccine, leaving many children vulnerable to infection [25]. Additionally, weak surveillance systems in several ESA countries have contributed to underreporting and delayed detection of cases, which limits timely public health responses. These gaps in both vaccination and surveillance infrastructure have created conditions that allow pertussis to persist and occasionally resurge in the region.

As of 2024, most countries in the ESA subregion have successfully achieved Maternal and Neonatal Tetanus Elimination, as reflected in various studies and reports [26]. However, South Sudan has not yet reached this important milestone. The main obstacles to elimination in these countries stem from gaps in routine immunization and weak surveillance systems [27]. Low coverage of tetanus toxoid-containing vaccines among women of reproductive age, limited access to skilled birth attendants, and disruptions to maternal health services, particularly during conflicts or public health emergencies, have all hindered progress [28]. Furthermore, inadequate surveillance and underreporting of neonatal tetanus cases have complicated efforts to monitor progress and effectively target interventions.

The advancements in surveillance have not only contributed to the near elimination of polio and significant reductions in measles morbidity and mortality but have also built a resilient health infrastructure capable of addressing other emerging infectious diseases [29]. As we look to the future, continued investment in surveillance systems, research, and capacity building will be crucial to sustaining these gains and achieving the targets set by the Immunization Agenda 2030 [30].

Recognizing the need for additional documentation on the evolution of vaccine-preventable disease surveillance, particularly for measles and polio in the ESA subregion, we initiated a focused effort to address this gap. Our goal was to systematically record and publish the key milestones and long-term progress of VPD surveillance over the past fifty years, tracing developments since the program's inception. This initiative was driven by the need to provide a detailed historical account that highlights the critical developments, challenges, and successes encountered throughout the decades. By doing so, we aim to offer valuable insights and lessons learned that can inform future public health strategies and policies. Our documentation will serve as a vital resource for health professionals, researchers, and policymakers, ensuring that the legacy of VPD surveillance in the ESA sub-region is preserved and utilized to enhance ongoing and future efforts in disease prevention and control.

Methods     

Study design: we conducted a descriptive mixed-methods secondary data analysis using both quantitative and qualitative data from 20 East and Southern African countries: Botswana, Comoros, Eritrea, Eswatini, Ethiopia, Lesotho, Kenya, Madagascar, Malawi, Mauritius, Mozambique, Namibia, Rwanda, Seychelles, South Africa, South Sudan, Tanzania, Uganda, Zambia, and Zimbabwe. The study utilized data submitted to WHO by these countries between January 1980 and December 2024. Quantitative data sources included the weekly field acute flaccid paralysis and measles case-based surveillance database, as well as the electronic WHO-UNICEF Joint Reporting Forms (eJRF). Qualitative data were obtained from surveys, comprehensive Expanded Programme on Immunization (EPI) reviews, and external surveillance assessment reports. These qualitative sources were analyzed thematically to complement and contextualize the quantitative findings. Most of the data sources are publicly available through WHO platforms. The analysis and discussion explore the progression of VPD surveillance in the ESA subregion, focusing on trends in measles, rubella, and polio incidence over time. By applying WHO-standard performance indicators for polio and measles surveillance, the study provides insights into the impact of immunization and surveillance efforts on disease reduction, highlighting both achievements and persistent gaps in elimination and eradication outcomes.

Variables: the variables used in this study included reported cases of measles, rubella, polio, diphtheria, pertussis, and neonatal tetanus by country. Vaccination coverage indicators were derived from the WHO-UNICEF Estimates of National Immunization Coverage (WUENIC), specifically for the first dose of measles-containing vaccine, the third dose of diphtheria-tetanus-pertussis (DTP3), and the third dose of oral polio vaccine (OPV3). Additional variables included the number of reported poliovirus cases (wild or vaccine-derived), acute flaccid paralysis (AFP) cases, non-polio AFP (NP-AFP) rate, and stool adequacy percentage. Measles and rubella indicators comprised reported and confirmed cases, as well as incidence per 1,000,000 population. Laboratory workload indicators for measles and rubella included the number of samples received in ESA laboratories, samples tested for measles and rubella, measles IgM-positive cases, rubella IgM-positive cases, and their respective positivity rates. Data also included congenital rubella syndrome (CRS) cases and environmental surveillance indicators for polio. Data analysis was conducted using CDC Epi Info version 3.5.4, supplemented by Microsoft Excel and SPSS version 22 for inferential statistics. Trend analysis was performed on reported vaccine-preventable diseases to observe changes over time and triangulate findings with vaccination coverage trends.

Data source: we gathered vaccine-preventable disease (VPD) data and routine immunization data through the electronic WHO-UNICEF Joint Reporting Form (eJRF), weekly measles and AFP case-based surveillance data, and laboratory data from 20 ESA countries: Botswana, Comoros, Eritrea, Eswatini, Ethiopia, Kenya, Lesotho, Madagascar, Malawi, Mauritius, Mozambique, Namibia, Rwanda, Seychelles, South Africa, South Sudan, Uganda, Tanzania, Zambia, and Zimbabwe. The dataset spans the period from 1980 to 2024, with data for South Sudan available from 2012 to 2024. The eJRF data are publicly accessible and are routinely validated by the WHO and UNICEF secretariats. Polio surveillance data are stored in the POLIS database, which is overseen by the Global Polio Eradication Initiative along with the Global Polio Laboratory Network. Measles surveillance is supported by the Global Measles and Rubella Laboratory Network. Data reported through the eJRF include all suspected cases before the year 2000 and confirmed cases from most countries thereafter; however, in some instances, the data may still reflect suspected cases and may not completely align with case-based surveillance records, which include laboratory confirmation, epidemiological linkage, and clinical compatibility. For polio, all cases reported since 2000 have been classified using a virological classification, which replaces earlier clinical classifications. Although the Expanded Programme on Immunization was established in some countries, such as South Africa, before 1975, consistent and comprehensive VPD data have only been available from 1980 onward. Polio, measles, yellow fever, and rotavirus can be confirmed through specific laboratory tests. Polio is diagnosed using virological testing, while measles and yellow fever are confirmed through serological tests that detect IgM antibodies. For rotavirus, an Enzyme Immunoassay (EIA) is used to identify rotavirus antigens in stool specimens. Pediatric bacterial meningitis is diagnosed through the analysis of cerebrospinal fluid. Although surveillance for maternal and neonatal tetanus primarily relies on clinical observations, laboratory confirmation may be selectively employed for differential diagnosis. The analysis of laboratory data focused on the period from 2016 to 2024 due to incomplete or missing records before that time. This study relied exclusively on secondary data obtained from the WHO-UNICEF Joint Reporting Form repository and other official WHO databases; no primary data were collected, and any information outside the defined study period or from unofficial sources was excluded from the analysis.

Results     

Epidemiological trends of measles, polio, neonatal tetanus, and other vaccine-preventable diseases in East and Southern Africa (1980-2024)

In our study, a total of 8,188,202 measles cases were reported across the ESA subregion. Kenya accounted for 20.4% of these cases, followed by Malawi with 15.8% and Madagascar with 14.4%. In contrast, Mauritius and Seychelles reported the lowest proportions, at 0.01% and 0.02%, respectively. A significant majority of measles cases, over 5.48 million (67%), occurred between 1980 and 1989. This period was followed by a 49.6% decline in cases during the 1990-1999 period (p < 0.0001; 95% CI: 49.526-49.674), and a further reduction of 9.7% in the 2000-2009 period (p < 0.0001; 95% CI: 9.609-9.791). The highest incidence of measles was recorded in 1981, with 6,403.2 cases per 1,000,000 population, primarily contributed by Zambia, Kenya, Madagascar, Rwanda, and Malawi. Conversely, the lowest incidence was observed in 2016 at 10.8 cases per 1,000,000, while the incidence rose again to 87.3 in 2023. Countries with the highest average incidence over the study period included Malawi (3,752.9), Zambia (2,485.5), Madagascar (2,129.2), and Kenya (1,994.7), with Mauritius reporting the lowest average at 23.2. In 2024, Mauritius and Eswatini reported zero incidence, while Lesotho and Rwanda reported 0.9 and 5 cases per 1,000,000 population, respectively.

In addition, a total of 19,207 polio cases were reported, with 96.8% occurring between 1980 and 1999. Most of these cases were recorded in the 1980-1989 (71.1%) and 1990-1999 (25.7%) periods, mirroring the trends observed in measles cases. Kenya reported the highest proportion of polio cases at 36.6%, followed by Ethiopia (16.6%), Zambia (11.9%), Tanzania (8.7%), South Africa (6.9%), and Uganda (5.6%). Notably, Mauritius and Seychelles did not report any polio cases. The proportion of polio cases in the periods 2000-2009 and 2020-2024 was only 1.4% for each period, with the earlier cases involving wild poliovirus and the later cases attributed to circulating vaccine-derived poliovirus (cVDPV). The leading countries reporting cVDPV cases included Ethiopia, South Sudan, Madagascar, and Mozambique, while Eritrea, Uganda, and Zambia, prominent in earlier data, have been less notable in recent years. Since 2007, data from the POLIS system indicate that 84,807 AFP cases have been reported in the ESA subregion. Of these, 56 cases (0.066%) were confirmed as wild poliovirus, and 329 cases (0.38%) as cVDPV.

Regarding neonatal tetanus (NNT), a total of 36,124 cases were identified. Uganda accounted for 25.9%, Kenya for 16.1%, Tanzania for 10.2%, Mozambique for 8.7% and Ethiopia for 7.1% of the total reported cases. Seychelles did not report any cases of NNT, while Mauritius and Lesotho collectively recorded 16 cases (Table 1). Over the years in the subregion, most cases were reported between 1980 and 1989 (38.4%), followed by 1990 to 1999 (21.4%). The lowest number of cases was recorded between 2010 and 2019 (9.5%), while a resurgence occurred during the 2020 to 2024 period (13.1%). Nevertheless, there was a 4.5% decline compared to the figures reported during the 2000-2009 period. This difference is statistically significant, with a p-value of <0.0001 and a 95% confidence interval ranging from 3.151 to 5.834. In this recent period, the countries reporting the most cases were Uganda (52%), Kenya (21%), Mozambique (12%), Ethiopia (5%), Madagascar (4%), Zambia (2%), and South Sudan and Tanzania (1% each) of the total cases reported.

The review showed a total of 102,490 rubella cases reported between 1999 and 2024, with no data available before 1999. Countries contributing the highest proportion of reported cases during this period were South Africa (35%), Uganda (17.7%), Kenya (9.1%), and Ethiopia (7.8%). Seychelles and Comoros documented only four and 93 cases respectively, all reported from 1999 onward. The highest number of rubella cases was recorded in 2024, with 16,779 cases accounting for 16.4% of all cases during the study period. In that year, South Africa contributed 90% of the total cases, followed by Tanzania (2.3%), Kenya (2.2%), and Ethiopia (1.7%).

We also noted that a total of 49,495 diphtheria cases were reported during the review period from 1980 to 2024. Most cases originated from Ethiopia (47.8%), Madagascar (33.7%), and Kenya (13.1%), while Comoros and Seychelles reported zero cases, and Mauritius recorded only nine cases throughout the entire period. In 1980, the ESA sub-region reported 7,068 cases accounting for 14.3% of the total. Subsequently, the number of cases declined sharply, reaching a low of five cases (0.01%) in 1992, and remained relatively stable in the following years. However, in 2019, a resurgence was observed with 9,000 cases (18.2% of the total), primarily reported from Ethiopia and Madagascar.

A total of 1,228,670 cases of pertussis (whooping cough) were documented in the study period for the ESA countries. Kenya had the highest proportion of cases, accounting for 38%, followed by Malawi at 15.9% and Madagascar at 15.8%. The lowest case counts were reported in Comoros (3 cases), Mauritius (19 cases), and Seychelles (58 cases). Most cases (82.8%) occurred between 1980 and 1989, with the highest annual count 209,000 (17%) reported in 1982, primarily from Kenya, Madagascar, Zambia, and Malawi. In recent years, only 3,575 of cases were reported in 2018, and just 2,073 in 2023, with cases limited to Ethiopia, South Africa, South Sudan, and Zimbabwe.

Surveillance data for Congenital Rubella Syndrome (CRS) in ESA countries were unavailable until 2003. Throughout the entire study period, a total of 310 CRS cases were reported in the subregion. Most cases were reported from South Africa (70 cases), Uganda and Zimbabwe (69 cases each), and Tanzania (47 cases). Eritrea was the first country to report CRS cases, with 9 cases in 2003 and 3 additional cases in 2005. In 2006, Mauritius reported 3 cases, followed by Zimbabwe, which reported 1 case in 2007. No further reports were recorded until 2012, when Zimbabwe reported 63 cases, along with Rwanda (5 cases) and Mauritius (1 case). The highest number of CRS cases during the study period was recorded in 2015, with a total of 78 cases reported from Tanzania (41 cases), South Africa (32 cases), and Mauritius (2 cases). The most recent reports came from South Africa, Mauritius, and Namibia. Throughout the study period, the following countries did not report any CRS cases: Comoros, Kenya, Lesotho, Madagascar, Malawi, Mozambique, Seychelles, and South Sudan.

Performance of AFP, measles, and environmental surveillance systems in East and Southern Africa: achievements and gaps (2000-2024)

Reliable AFP surveillance data for the ESA subregion have been available since 2000. During this period, the non-polio AFP (NPAFP) rate was recorded at 1.19 per 100,000 population under 15 years of age. This rate surpassed the threshold of 2.0 in 2005, reaching 2.20 per 100,000, and continued to increase, exceeding 3.0 in 2016 (Table 2). The most recent data from 2023 indicate an NPAFP rate of 4.62 per 100,000. Countries with the highest average NPAFP rates during the study period included South Sudan (7.33), Eritrea (4.4), and Madagascar (4.27), whereas Seychelles recorded the lowest average rate (0.26 per 100,000 population).

The percentage of stool adequacy, a key indicator of AFP surveillance quality, improved significantly over time. The lowest regional average was recorded at 46% in 2000, increasing to 80% in 2005 and reaching a peak of 91% in 2015 (Table 3). Countries with consistently lower stool adequacy percentages included Seychelles (11%), South Sudan (45%), Comoros (68%), Mauritius (77%), and Mozambique (78%). In contrast, Lesotho (93%), Rwanda (93%), and Tanzania (93%) reported the highest average stool adequacy rates in the subregion. The overall ESA subregion average for stool adequacy during the study period was 79%.

Environmental surveillance (ES) for poliovirus was first introduced in the ESA subregion in October 2013, with Kenya leading the initiative, supplementing acute flaccid paralysis surveillance. However, detailed performance data for ES sites was not publicly available until 2016. At that time, there were 20 ES sites 3 in Kenya and 17 in Madagascar, all of which reported enterovirus (EV) isolation rates above 50%. In 2017, the number of countries implementing environmental surveillance increased from 2 to 6, with Ethiopia, South Sudan, Uganda, and Mozambique joining Kenya and Madagascar. The total number of ES sites also rose to 29.

By 2024, the number of ES sites had significantly expanded to 194 across 19 countries. Comoros remained the only country in the subregion not participating in environmental surveillance. Despite the expansion, the proportion of ES sites isolating EV declined from 85% in 2016 to 78.35% in 2024. This decline was largely attributed to low EV isolation rates in Eswatini, Lesotho, Madagascar, Malawi, Mauritius, Mozambique, Rwanda, South Africa, and South Sudan. During the same period, the workload of polio laboratories increased substantially, with the number of ES samples received rising from 353 in 2016 to 2,582 in 2024. Although there were challenges in sample shipment, the condition of the received samples slightly declined from 93.2% in 2016 to 93.0% in 2024. However, the proportion of samples yielding results improved from 93.2% in 2016 to 100% in 2024.

Concerning measles surveillance in the ESA subregion, we accessed data from 2012 onwards for 19 ESA countries using the eJRF platform. However, data for Mauritius were missing, Seychelles had incomplete data (only available for 4 years), South Sudan provided 10 years of data, and Comoros had data for 12 out of the 13-year study period (Table 4). The average rate of discarded non-measles, non-rubella cases per 100,000 population across the ESA subregion was 4.87. The lowest rate was recorded in 2021 at 2.21, while the highest was noted in 2023 at 9.64. There was significant variation at the country level, with higher rates observed in Namibia, Lesotho, and Botswana. In contrast, countries such as Malawi, Kenya, South Sudan, Zambia, and Ethiopia showed suboptimal performance, falling below the target rate of =2 cases per 100,000 population.

Regarding the annual achievement of the target rate (=2 per 100,000 population), Eritrea, Eswatini, Lesotho, Mozambique, Namibia, and Rwanda consistently met this target across all 13 years, showing 100% performance. On the other hand, countries with low annual performance included Malawi (8%), Kenya (15%), Ethiopia (23%), and both South Sudan and Zambia (31%). For laboratory-confirmed measles cases, we evaluated data from 2015 to 2024. The lowest proportion of laboratory confirmation occurred in 2021 and 2023, where it was 32% for the ESA subregion. Countries with the highest proportions of laboratory-confirmed cases included Rwanda, Eritrea, Seychelles, and South Africa, while the lowest proportions were reported by Namibia and South Sudan.

Immunization coverage trends in East and Southern Africa (1980-2024): progress, persistent gaps, and implications for VPD surveillance

During the first decade of the study (1980-1989), vaccination coverage for key antigens was notably low, with arithmetic mean coverage rates of 59.8% for DTP3, 58.2% for OPV3, and 57.7% for MCV1. However, substantial improvements were observed in subsequent decades. By 2000-2009, mean coverage exceeded 80%, marking significant progress in immunization efforts (Table 5). The highest recorded mean vaccination coverage occurred during 2010-2019, reaching 85.9% for DTP3, 85.6% for OPV3, and 84.7% for MCV1. Several countries exhibited persistently low vaccination coverage throughout the study period. Ethiopia recorded the lowest averages, with 44% for DTP3, 51.1% for OPV3, and 40.9% for MCV1. Other countries with relatively low coverage included Madagascar (DTP3: 57.7%, OPV3: 56.5%, MCV1: 50.7%), South Sudan (DTP3: 62.5%, OPV3: 63.6%, MCV1: 64.6%), Uganda (DTP3: 63.2%, OPV3: 61.8%, MCV1: 64.7%), Mozambique (DTP3: 63.5%, OPV3: 63.3%, MCV1: 66.7%), and Comoros (DTP3: 70.6%, OPV3: 69.7%, MCV1: 66.7%). Conversely, Mauritius and Seychelles consistently demonstrated high vaccination coverage throughout the study period, achieving rates exceeding 90% for all three antigens, underscoring their strong immunization programs and effective healthcare policies.

Laboratory surveillance of measles and rubella in East and Southern Africa: IgM positivity rates and testing workload (2016-2024)

In our study, we examined annual laboratory testing data for measles and rubella from 2016 to 2024, focusing on IgM immunological tests for both virus infections (Table 6). A total of 205,915 samples were collected from ESA countries, with 94.3% tested for measles IgM and 86.1% for rubella IgM. Some samples were tested for both viruses according to the testing protocol. Among the tested samples, 16.8% were positive for rubella IgM, while 14.8% were positive for measles IgM. We noticed substantial changes in laboratory workload over the years. In 2020, only 4.2% of the total samples were received, but this figure increased sharply to 23.6% in 2024. This marks a decline of 5.6 percentage points from 2019 (which was 9.8%) to 2020. By 2024, the workload had grown to nearly six times higher than that of 2020.

By year, the highest measles IgM positivity rate was recorded in 2023 at 21%, whereas the lowest was in 2017 at 6.1%. For rubella IgM, the highest positivity rate was observed in 2024 at 30.9%, and the lowest occurred in 2021 at 6.4%. When comparing the pre-COVID-19, COVID-19, and post-COVID-19 periods, we found that the highest seropositivity rates were seen in the post-COVID-19 period: 16.6% for measles and 23% for rubella. In contrast, during the COVID-19 period, the rates were 14.4% for measles and 7.8% for rubella.

Discussion     

The surveillance of vaccine-preventable diseases (VPDs) in the ESA subregion has significantly evolved over the past four decades. Initially, surveillance systems depended on clinical diagnoses and aggregate data collected through paper-based tools. Prior to 2000, most polio cases were diagnosed clinically, which often led to overestimations due to the overlap in symptoms with other febrile illnesses [31]. The shift to laboratory-supported, case-based surveillance marked a turning point by improving diagnostic accuracy and enabling more precise outbreak detection and response. The introduction of real-time electronic data collection systems and geospatial technologies has further enhanced surveillance capabilities, improving the geographical localization of cases and facilitating timely public health interventions [9]. These advancements have coincided with a notable decline in measles, polio, and other VPDs, largely attributed to increased routine immunization coverage and supplementary immunization activities (SIAs), which have strengthened population immunity [32].

Interestingly, countries reporting higher measles case counts also tended to report more polio cases, reflecting both gaps in population immunity and the robustness of surveillance systems. In contrast, Mauritius and Seychelles consistently reported fewer cases, mainly due to reporting challenges and relatively small population sizes. Despite achieving coverage rates exceeding 90% for DTP3, OPV3, and MCV1, these countries have demonstrated suboptimal performance in VPD surveillance indicators, likely due to limited case detection opportunities and underreporting [33] rubella surveillance was formally introduced in the ESA subregion around 2000, coinciding with the gradual rollout of rubella-containing vaccines. Countries with established laboratory capacity were key contributors to rubella case reporting, underscoring the importance of diagnostic infrastructure in supporting case-based surveillance [34]. Between 2016 and 2024, ESA countries tested over 205,000 samples for measles and rubella IgM, yielding positivity rates of 14.8% and 16.8%, respectively. A systematic review and meta-analysis confirmed the high diagnostic accuracy of IgM testing, with pooled sensitivity and specificity of 94% for measles and 97% for rubella [35]. These findings validate the use of IgM serology as the gold standard for laboratory confirmation in VPD surveillance.

The COVID-19 pandemic had a profound impact on surveillance systems. In 2020, only 4.2% of total samples were received, a sharp decline from 9.8% in 2019, due to lockdowns, disruptions in specimen transport, and the reallocation of health resources [36]. WHO's analysis of measles surveillance in Africa during the pandemic documented similar trends, noting reduced case detection and laboratory submissions [37]. By 2024, sample volumes had surged to 23.6% of the total, indicating a recovery in surveillance activities and increased efforts to detect and respond to outbreaks. The resurgence of measles outbreaks in 2023 underscores the lingering impact of the pandemic on immunization services. The growing number of zero-dose children, those who have not received any vaccines, poses a significant threat to regional health security [38]. This situation highlights the need for sustained investment in both field and laboratory surveillance, including reagents, supplies, and trained personnel.

Addressing outbreaks of diphtheria and pertussis requires a dual approach: closing immunity gaps and reinforcing surveillance systems. Laboratory capacity remains a cornerstone of this effort. Continued support from WHO and partners is essential to ensure that countries have access to the necessary reagents, equipment, and human resources [39]. The Immunization Agenda 2030, endorsed by the World Health Assembly, provides a strategic framework to guide global efforts in immunization and VPD surveillance. This agenda emphasizes the importance of resilient surveillance systems, equitable access to vaccines, and data-driven decision-making to achieve disease elimination and control goals [39].

The surveillance of acute flaccid paralysis (AFP) in the ESA subregion has demonstrated significant progress since 2000, particularly in the detection of non-polio AFP (NPAFP) cases and the quality of stool specimen collection. Initially, the NPAFP rate stood at 1.19 per 100,000 children under 15 years, below the WHO-recommended threshold of 2.0. However, by 2005, the region had surpassed this benchmark, reaching 2.20, and continued to improve, peaking at 4.62 in 2023. This upward trend reflects enhanced surveillance sensitivity and aligns with findings from the Global Polio Surveillance Action Plan (GPSAP), which reported similar improvements across most ESA countries during 2022-2023.

Countries such as South Sudan (7.33), Eritrea (4.4), and Madagascar (4.27) consistently recorded the highest NPAFP rates, indicating robust surveillance systems. In contrast, Seychelles reported the lowest average rate (0.26), and notably, did not report any AFP cases during the 2022-2023 period, leading to its exclusion from regional analyses. These disparities underscore the influence of population size, surveillance infrastructure, and health system capacity on AFP detection. Stool adequacy, defined by WHO as the collection of two stool specimens within 14 days of paralysis onset, 24 hours apart, and arriving in good condition at a WHO-accredited laboratory is a critical indicator of AFP surveillance quality. The ESA region improved markedly in this area, rising from 46% in 2000 to 91% in 2015, with an overall average of 79% during the study period. High performers included Lesotho, Rwanda, and Tanzania, each with average adequacy rates of 93%, while Seychelles (11%), South Sudan (45%), and Comoros (68%) lagged. These findings are consistent with WHO surveillance guidelines, which emphasize that =80% stool adequacy is essential for reliable AFP surveillance and timely outbreak response. Environmental surveillance (ES) for poliovirus was introduced in the ESA region in 2013, beginning with Kenya and later expanding to 19 countries by 2024. Initially, ES sites showed strong performance, with enterovirus (EV) isolation rates above 50%. However, by 2024, the proportion of sites isolating EV declined to 78.35%, attributed to underperformance in countries such as Eswatini, Lesotho, Madagascar, Malawi, Mauritius, Mozambique, Rwanda, South Africa, and South Sudan 3. Despite this decline, ES remains a vital supplement to AFP surveillance, particularly in detecting silent transmission in areas without reported cases. WHO's first quarter in 2025 bulletin highlighted that ES detections preceded 50% of recorded outbreaks in the African region, reinforcing its role as an early warning system. The expansion of ES has also placed increased demands on polio laboratories. Sample volumes rose from 353 in 2016 to 2,582 in 2024, with a slight decline in sample condition (from 93.2% to 93.0%) but an improvement in result reporting, reaching 100% in 2024 3. These trends reflect both the growing reliance on ES and the need for sustained investment in laboratory capacity and logistics.

In summary, the ESA subregion has made notable progress in immunization coverage and surveillance of vaccine-preventable diseases. This progress has been particularly enhanced by the transition from clinical diagnosis and paper-based reporting to laboratory-confirmed, real-time electronic systems. These advancements have significantly improved the accuracy and effectiveness of outbreak detection and response. However, persistent disparities in performance especially in countries with lower immunization coverage and weaker surveillance infrastructure highlight the need for targeted investments, capacity building, and innovative approaches to strengthen surveillance systems. The COVID-19 pandemic further exposed vulnerabilities, disrupting specimen collection and laboratory testing and contributing to a resurgence of measles and rubella outbreaks in the post-pandemic period.

Notably, the region has also achieved substantial improvements in acute flaccid paralysis and environmental surveillance, including better specimen quality and the expansion of surveillance sites. Yet, gaps remain in certain countries and surveillance components, which threaten the sustainability of polio eradication efforts. Achieving the goals of measles and rubella elimination, as well as broader VPD control under the Immunization Agenda 2030, requires resilient, integrated, and high-quality surveillance systems. Continued support from WHO and partners is crucial to ensure access to essential resources, including reagents, equipment, and trained personnel, and to maintain momentum toward regional and global public health targets.

While the structural integrity, sensitivity, data transmission, and technological innovations in surveillance systems have improved over time enhancing early detection, case and outbreak confirmation, geographical localization in cases of importation, and facilitating timely response and recovery efforts the surveillance systems in the ESA subregion continue to face significant challenges. These include issues related to data quality, delays in specimen shipment and outbreak confirmation, as well as diminished resources to support essential surveillance activities (including commodities for laboratories), infrastructure, and human capacity. Addressing these persistent challenges requires innovative solutions to ensure the sustained effectiveness of VPD detection and response, particularly considering evolving disease patterns and the potential for future resurgences.

Study limitations: the following outlines the limitations of our study. First, the use of secondary data sources, such as the WHO-UNICEF Joint Reporting Forms and program review reports, raised potential concerns about data completeness, accuracy, and consistency. Prior to 2000, surveillance systems relied heavily on paper-based tools and clinical diagnoses, which may have led to overreporting, particularly for diseases with similar symptoms, such as measles and polio. Although the transition to electronic systems has improved data quality, inconsistencies in historical case definitions and reporting standards may still affect the reliability of trend analyses. Additionally, data for South Sudan has been limited up to 2012, data for congenital rubella syndrome became available only in 2018, measles surveillance data has been available only since 2012, and environmental surveillance data have been available only since 2016. Moreover, the study did not fully account for confounding factors such as population changes, migration, health system disruptions, and variations in laboratory capacity across countries. These variables may have influenced disease patterns and reporting rates. The descriptive and retrospective nature of the study also limits its ability to establish causal relationships between technological advancements and public health outcomes. Furthermore, the lack of standardized outbreak response metrics across countries affects the comparability of surveillance effectiveness. These limitations highlight the need for continued investment in surveillance infrastructure, improvements in data quality, and more rigorous analytical approaches in future research.

Conclusion     

Over time, the ESA subregion has made significant progress in surveillance and immunization coverage for vaccine-preventable diseases. Surveillance systems have evolved from relying on clinical diagnoses and paper-based reporting to utilizing laboratory-confirmed, real-time electronic platforms. This evolution has enhanced the sensitivity, specificity, and timeliness of outbreak detection. These advancements, combined with increased routine immunization especially for DTP3, OPV3, and MCV1 have led to a notable decline in cases of measles, polio, and rubella. However, disparities remain, with countries like Ethiopia, Madagascar, and South Sudan consistently reporting lower vaccination coverage and weaker surveillance indicators. The COVID-19 pandemic further highlighted vulnerabilities in surveillance infrastructures, resulting in disruptions to specimen collection and laboratory testing, as well as a resurgence of measles and rubella outbreaks in the post-pandemic period. Despite these challenges, the growth of environmental surveillance and recovery in laboratory testing volumes reflects resilience and a renewed commitment to disease control. Countries with strong health systems, such as Mauritius and Seychelles, continue to show high immunization performance, though concerns about VPD surveillance sensitivity persist in low-incidence settings. To ensure timely detection and response to outbreaks of measles, rubella, diphtheria, neonatal tetanus, and pertussis, it is crucial to strengthen surveillance and laboratory capacity. This effort needs sustained investment and technical assistance from the World Health Organization. Ongoing challenges including data quality issues, shipment delays, and resource limitations demand innovative strategies to maintain effective VPD surveillance, particularly given the evolving epidemiological patterns and the risk of future outbreaks. Achieving the objectives of the Immunization Agenda 2030 will rely on resilient systems, equitable access, and coordinated regional efforts.

Competing interests     

The authors declare no competing interests.

Authors' contributions     

Daudi Manyanga, Sarah Wanyoike and Charles Teboh conceptualized and designed the study, and constructed the background information, study analysis, interpretation, discussion, and organization of the manuscript. Charles Byabamazima and Charles Muitherero participated in the study analysis of both field and laboratory data, interpretation, discussion, and critical review of the manuscript for publication. Weldegebriel Goitom participated in the review and discussion of the manuscript. Brine Masvikeni and Maryanna Ochieng compiled the data and participated in the data analysis.

Acknowledgments     

We acknowledge efforts made by all Surveillance Officers, Laboratory technicians and Data Managers from Ministries of Health, WHO and other partners in the ESA countries for their tireless efforts till polio is eradicated.

Tables     

Table 1: trends in reported measles, polio, and neonatal tetanus (NNT) cases by Country in the ESA subregion (1980-2024)

Table 2: trends in non-polio acute flaccid paralysis rates per 100,000 populations under 15 years by country in the East and Southern Africa sub-region from 2000 to 2024

Table 3: trends in stool adequacy percentage by country in the East and Southern Africa Sub-Region (2000-2024)

Table 4: reported discarded non-measles, non-rubella cases per 100,000 populations (2012-2024) and proportion of laboratory-confirmed measles cases (2015-2024), by country in the ESA sub-region

Table 5: historical trends in measles first-dose, DTP third-dose, and polio third-dose vaccination coverage (WUENIC) across ESA subregion countries (1980-2024)

Table 6: annual measles and rubella testing workload and IgM seropositivity in ESA Region (2016-2024)

References