Shelina Moonsamy

Background: Sustaining progress toward polio eradication requires not only effective vaccination but also a resilient laboratory network capable of timely poliovirus detection, confirmation, and genetic characterization. In the WHO African region, the African polio laboratory network provides essential virological support for eradication efforts; however, persistent circulating Vaccine-derived Polioviruses (cVDPVs) outbreaks and increasing demands of genomic surveillance continue to challenge laboratory capacity. Despite its critical role, evidence describing the operational performance, adaptive capacity, and evolution of regional polio laboratory network remains limited. This study evaluates the performance and operational experience of the African polio laboratory network in 2025, highlighting contributions to poliovirus detection, genomic surveillance, quality assurance, and outbreak response, while sharing lessons to inform regional public health systems. Methods: A retrospective secondary data analysis was conducted using laboratory surveillance and outbreak databases, supplemented by reviews of programmatic reports. Data were cleaned and harmonized prior to analysis. Descriptive analyses were performed to assess laboratory workload, timeliness indicators, genomic capacity, quality assurance performance, and operational challenges. Qualitative review of programmatic documents was conducted to identify contextual factors influencing performance. Results: In 2025, 77,230 Acute Flaccid Paralysis (AFP) specimens were analyzed across 16 laboratories. Ninety-two percent of specimens met the timeliness target for virus isolation, and 94% met the target for PCR-ITD. Genomic sequencing confirmed 20 cVDPV outbreaks in 10 countries. The establishment of new sequencing laboratories in Uganda and Nigeria reduced turnaround times, and a 2025 expansion plan aimed to build sequencing capacity in 12 additional countries. All laboratories assessed in 2024 for virus isolation, PCR-ITD, and environmental surveillance exceeded quality assurance accreditation thresholds and were rated “Pass”. The pilot implementation of Direct Detection Nanopore Sequencing (DDNS) techniques is expected to further strengthen genomic surveillance. Challenges remain, including stock out of essential supplies, uneven workloads, and infrastructure gaps. Conclusions: The African polio laboratory network has demonstrated sustained capacity, adaptability, and innovation in supporting polio eradication activities in the WHO African region. This study provides evidence on the importance of strengthening laboratory systems, expanding genomic capacity, and maintaining quality assurance mechanisms to support the final phase of polio eradication and broader public health surveillance.

The manuscript provides a comprehensive synthesis of determinants of persistent WPV1 transmission in Pakistan and Afghanistan and is relevant to global eradication efforts. It is a strong manuscript overall, and I enjoyed reading it. Below are sugge...

Eight years after WHO adopted a resolution to eliminate hepatitis B by the year 2030, the disease remains a global public health concern, with vertical transmission of HBV being a major obstacle to this goal. Our study aimed to determine the HBV infection status of pregnant women in South Africa at a national level to evaluate the risk of vertical transmission and provide evidence for public health decision-making. We conducted HBsAg testing on 1,942 HIV-uninfected and 2,312 HIV-infected pregnant women from South Africa’s public health sector in 2017, followed by HBeAg testing on HBsAg-positive samples. Our data were stratified by five-year age groups and province. The overall HBV prevalence was 11.24% (478/4,254), significantly higher among HIV-infected women (15.83%) compared to HIV-uninfected women (5.77%, p = 0.007). HBV prevalence was highest among women 40–44 years (14.00%) and in Limpopo Province (19.35%). Coinfection rates of HIV-HBV ranged from 14.00% to 17.00% among women 15–44 years, and provincially, rates were highest in Limpopo, North West, and Western Cape Provinces (>20%). HBeAg prevalence among HBsAg positive women was 9.48%, with higher rates among HIV infected women (11.29%) compared to HIV-uninfected women (7.34%, p = 0.7931). HBeAg prevalence was highest among women 15–19 (10.81%), 20–24 (11.88%) and 40–44 years (25.00%), and provincially, highest in North West (26.67%). Our findings highlight the significant prevalence of HBV infection among pregnant women in 2017, emphasising concerns about vertical transmission, particularly given the high prevalence of HBeAg among HBsAg-positive women. We advocate for the prompt implementation of a universal birth dose of the HBV vaccine in South Africa to augment existing vaccination schedules and mitigate the risk of vertical transmission, thereby advancing progress towards WHO elimination targets.

In 2016, WHO adopted a resolution to eliminate hepatitis B by 2030, targeted at reducing disease burden. In South Africa, HBV disease burden has largely been estimated from community-based or sentinel studies, thereby limiting its accuracy. Since 2009, the WHO recommended the addition of a birth dose of the HBV vaccine to current vaccine schedules to mitigate the risks of vertical transmission. This intervention is crucial to reduce disease burden, given the increased risks of developing chronic disease if contracted at birth or infancy. Despite the introduction of the HBV vaccine into their EPI schedule in 1995, South Africa is yet to fulfil this recommendation. In this study, our objective was to assess HBV disease burden in the public health sector of South Africa through meticulous analyses of an extensive national dataset spanning 2015 to 2019. Additionally, we aimed to model the potential impact of a birth dose of the HBV vaccine using country-specific HBV prevalence data obtained from our own testing conducted on women attending antenatal care in 2017. Over the five years, the national HBV prevalence was 9.02%, declining gradually each year. Overall, males had consistently higher prevalence rates than females. The observed lower infection and higher immunity rates among vaccine-eligible individuals clearly demonstrated the positive impact of the HBV vaccine. Nevertheless, HBV infection among these individuals was quite concerning, highlighting the roll-over effects of suboptimal vaccine coverage rates. The prevalence of HBsAg among pregnant women was alarmingly high at 11.24%, further compounded by the high HBeAg prevalence among these women. These findings alerted us to the increased probability of vertical transmission, representing a concerning source of disease burden in the country. Among vaccine-eligible women under 19 years old, HBsAg prevalence was surprisingly high at 8.08%, noting that these women still had approximately 30 more years of potential child-bearing. These findings pose a serious threat to achieving, or even nearing, WHO elimination goals. Using a deterministic HBV transmission model to simulate the impact of a birth dose of the HBV vaccine, we estimated more than a three-fold reduction in chronic HBV infections and HBV-related deaths, specifically when considering new cases from initiation of our model. In essence, this represents a greater than three-fold reduction in HBV disease burden. Our findings are unique for South Africa given their national representation and country-specific model inputs. Despite the introduction of the HBV vaccine in 1995, hepatitis B remained highly endemic in South Africa. Adding a birth dose to the current HBV vaccination schedule and achieving optimal vaccine coverage rates will markedly reduce country HBV burden. We therefore recommend prompt implementation of a birth dose of the HBV vaccine, together with increased efforts aimed at improving HBV vaccine coverage rates to optimal levels.

As global SARS-CoV-2 burden and testing frequency have decreased, wastewater surveillance has emerged as a key tool to support clinical surveillance efforts. The aims of this study were to identify and characterize SARS-CoV-2 variants in wastewater samples collected from urban centers across South Africa. Here we show that wastewater sequencing analyses are temporally concordant with clinical genomic surveillance and reveal the presence of multiple lineages not detected by clinical surveillance. We show that wastewater genomics can support SARS-CoV-2 epidemiological investigations by reliably recovering the prevalence of local circulating variants, even when clinical samples are not available. Further, we find that analysis of mutations observed in wastewater can provide a signal of upcoming lineage transitions. Our study demonstrates the utility of wastewater genomics to monitor evolution and spread of endemic viruses.

Hepatitis B, a potentially life-threatening viral infection of the liver, remains a global public health concern despite the availability of effective vaccines for over three decades. The aim of our study was to provide national data on active hepatitis B infections in the public health sector of South Africa. We conducted retrospective analyses on national laboratory data over the period 2015 to 2019. We identified 176,530 cases who tested positive for HBsAg (active infection) with a test positivity rate of 9.02%. Of these active infections, 11,355 (6.43%) were found to be chronically infected. We linked 24,839 (14.07%) and 2,461 (21.67%) HBeAg positive results to all active HBV infections and identified chronic infections respectively. Clearance of HBsAg was observed in 5,569 cases, inclusive of clearance in 135 chronic cases. Active HBV infections were significantly higher in men than women over the five years (p < 0.0001). Among individuals who were vaccine-eligible as infants (0 to 19 years old), we observed 4,981 active HBV infections, including 1,131 infections under five years old, majority of which (65.78%) were under one year old. In the under five-year age group, the HBsAg population positivity rate was 0.02% and test positivity rate was 4.83%. Among all women with active HBV infections (78,935), 85.17% were of reproductive age and of these, 13.73% were HBeAg positive. Without a birth dose of the HBV vaccine, lack of routine HBsAg screening at antenatal care, and HBsAg and HBeAg prevalence among women of reproductive age, it is likely that the majority of cases under five years old were vertically infected. Optimal HBV vaccine coverage, inclusive of a birth dose, is key to eliminating horizontal and vertical transmission of HBV. Early identification of HBV chronicity through real time data analysis is fundamental in reducing the risk of liver cirrhosis and hepatocellular carcinoma.

The use of wastewater for SARS-CoV-2 surveillance is a useful complementary tool to clinical surveillance. The aims of this study were to characterize SARS-CoV-2 from wastewater samples, and to identify variants of concern present in samples collected from wastewater treatment plants in South African urban metros from April 2021 to January 2022. A total of 325 samples were collected from 15 wastewater treatment plants. Nucleic acids were extracted from concentrated samples, and subjected to amplicon-based whole genome sequencing. To identify variants of concerns and lineages, we used the Freyja tool ( https://github.com/andersen-lab/Freyja ), which assigns each sample with the prevalence of each variant present. We also used signature mutation analysis to identify variants in each wastewater treatment site. A heatmap was generated to identify patterns of emerging mutations in the spike gene using Excel conditional formatting. Using the Freyja tool, the Beta variant was detected and became predominate from April to June 2021 followed by the Delta variant and lastly the Omicron variant. Our heatmap approach was able to identify a pattern during the changes of predominate variant in wastewater with the emergence of mutations and the loss of others. In conclusion, sequencing of SARS-CoV-2 from wastewater largely corresponded with sequencing from clinical specimens. Our heatmap has the potential to detect new variants prior to emergence in clinical samples and this may be particularly useful during times of low disease incidence between waves, when few numbers of positive clinical samples are collected and submitted for testing. A limitation of wastewater sequencing is that it is not possible to identify new variants, as variants are classified based on known mutations in clinical strains.

Hepatitis B, a potentially life-threatening viral infection of the liver, remains a global public health concern despite the availability of effective vaccines for over three decades. Given that most HBsAg studies targeted distinct cohorts, we aimed to provide HBsAg data nationally in the public health sector of South Africa. We conducted a cross-sectional study on HBsAg tests obtained from the National Health Laboratory Service Central Data Warehouse for tests performed nationally during the period 2015 to 2019. Annual data were cleaned and appended prior to data interrogation to determine and analyse the total number of cases who tested positive for HBsAg and the number of chronic HBV infections. We identified 176,530 cases who tested positive for HBsAg at least once during the 5-year period, with a test positivity rate of 9%. Chronic infections were identified in 6.4% of HBsAg positive cases. Clearance of HBsAg was observed in 5,571 cases, inclusive of clearance in 135 chronic cases. Significantly more males tested positive for HBsAg and were chronically infected (p < 0.0001). Amongst individuals who were vaccine-eligible as infants (0 to 19 years old), 4,980 tested HBsAg positive, of which 22.7% (1,131) were under 5 years old, with a HBsAg population positivity rate of 0.02% and test positivity rate of 4.83%. HBsAg positivity amongst vaccine-eligible individuals is likely due to suboptimal vaccine coverage rates reported for South Africa. Without a birth dose of the HBV vaccine and lack of routine HBsAg screening at antenatal care, it is likely that the majority of HBsAg positive cases under 5 years old were vertically infected. Optimal HBV vaccine coverage, inclusive of a birth dose, is key to eliminating horizontal and vertical transmission of HBV. Early identification of HBV chronicity is fundamental in reducing the risk of liver cirrhosis and hepatocellular carcinoma.

Background: Hepatitis B virus (HBV), a global public health threat, is targeted for elimination by 2030. As national HBV prevalence and incidence is lacking for South Africa, our study aimed to provide such data in the public health sector. Methods: We analysed laboratory-confirmed HBV data from 2015 to 2019 to determine annual prevalence and incidence rates of HBV infection per 100,000 population, HBsAg and anti-HBc IgM test positivity rates, and HBsAg and anti-HBc IgM testing rates per 100,000 population. Time trend and statistical analyses were performed on HBsAg and anti-HBc IgM test positivity rates. Results: The national prevalence rate of HBV infection per 100,000 population increased from 56.14 in 2015 to 67.76 in 2019. Over the five years, the prevalence rate was higher in males than females, highest amongst individuals 25 to 49 years old and highest in Gauteng province. The HBsAg test positivity rate dropped from 9.77% in 2015 to 8.09% in 2019. Over the five years, the HBsAg test positivity rate was higher in males than females, amongst individuals 25 to 49 years old and amongst individuals of Limpopo province. Amongst HBsAg positive children under 5 years old, the majority (65.7%) were less than a year old. HBsAg testing rates per 100,000 population were higher in females under 45 years of age and in males 45 years and above. The national incidence rate of acute HBV infection per 100,000 population dropped from 3.17 in 2015 to 1.69 in 2019. Over the five-year period, incidence rates were similar between males and females, highest amongst individuals 20 to 39 years old and highest in Mpumalanga province. Amongst individuals 20 to 24 years old, there was a substantial decline in the incidence and anti-HBc IgM test positivity rates over time. Anti-HBc IgM testing rates per 100,000 population were higher in females under 40 years of age and in males 40 years and above. Conclusion: Critical to hepatitis B elimination is strengthened infant vaccination coverage and interruption of vertical transmission. Transmission of HBV infection in adults may be reduced through heightened awareness of transmission routes and prevention measures.