A circulating vaccine-derived poliovirus type 2 outbreak in a chronic conflict setting: a descriptive epidemiological study in South Sudan - 2020 to 2021.

BACKGROUND: In this study, we describe the epidemiological profile of an outbreak of the circulating Vaccine Derived Polio Virus type 2 in South Sudan from 2020 to 2021. METHOD: We conducted a retrospective descriptive epidemiological study using data from the national polio/AFP surveillance database, the outbreak investigation reports, and the vaccination coverage survey databases stored at the national level. RESULTS: Between September 2020 and April 2021, 59 cases of the circulating virus were confirmed in the country, with 50 cases in 2020 and 9 cases in 2021. More cases were males (56%) under five (93%). The median age of the cases was 23.4 ± 11.9 months, ranging from 1 to 84 months. All states, with 28 out of the 80 counties, reported at least one case. Most of the cases (44, 75%) were reported from five states, namely Warrap (31%), Western Bahr el Ghazal (12%), Unity (12%), Central Equatoria (10%), and Jonglei (10%). Four counties accounted for 45.8% of the cases; these are Gogrial West with 12 (20%), Jur River with 5 (8.5%), Tonj North with 5 (8.5%), and Juba with 5 (8.5%) cases. The immunization history of the confirmed cases indicated that 14 (24%) of the affected children had never received any doses of oral polio or injectable vaccines either from routine or during supplemental immunization before the onset of paralysis, 17 (28.8%) had received 1 to 2 doses, while 28 (47.5%) had received 3 or more doses (Fig. 4). Two immunization campaigns and a mop-up were conducted with monovalent Oral Polio Vaccine type 2 in response to the outbreak, with administrative coverage of 91.1%, 99.1%, and 97% for the first, second, and mop-up rounds, respectively. CONCLUSION: The emergence of the circulating vaccine-derived poliovirus outbreak in South Sudan was due to low population immunity, highlighting the need to improve the country's routine and polio immunization campaign coverage.

The sensitivity of acute flaccid paralysis surveillance - the case of South Sudan: retrospective secondary analysis of AFP surveillance data 2014-2019.

Introduction: South Sudan has made quite impressive progress in interrupting wild poliovirus and maintaining a polio-free status since the last case was reported in 2009. South Sudan introduced different complementary strategies to enhance acute flaccid paralysis (AFP) surveillance. Hence, the objective of this study is to evaluate the sensitivity of the surveillance system using the WHO recommended surveillance standard and highlight the progress and challenges over the years. Methods: we conducted a retrospective, descriptive, quantitative study design and used the available secondary AFP surveillance database. Results: the overall non-polio AFP rate was 6.2/100,000 children under 15 years old in the study period. The stool adequacy was maintained well above the certification level of surveillance. The two main surveillance performance indicators were met at the national level throughout the study period. In contrast, only five out of ten states persistently attained and maintained the two main surveillance performance indicators throughout the study period, while in 2019 all states achieved except for Jonglei state. During the analysis period, no wild poliovirus was isolated except two circulating Vaccine Derived Poliovirus Type 2 (cVDPV2) cases in 2014 and one Immunodeficiency Vaccine Derived Poliovirus Type 2 (iVDPV2) case in 2015. However, on average, three cases were classified as polio compatible with each year of the study. Conclusion: South Sudan met the two key surveillance performance indicators and had a sensitive AFP surveillance system during the period studied. We recommend intensifying surveillance activities in the former conflict-affected states and counties to maintain polio-free status.

South Sudan's road to universal health coverage: a slow but steady journey.

Amidst the myriad of challenges that constrain good quality health care services delivery in the World's youngest nation, South Sudan, there is a beacon of hope. The country's revitalized peace agreement offers a new impetus for rebuilding the country, including its health system. Key achievements in the health care sector of the country such as development and implementation of a health sector strategic and health sector stabilization and recovery plans and implementation of a Boma Health Initiative programme which aims to scale up health services delivery at the community level provide a foundation on which acceleration of universal health coverage could rest. Other key achievements include polio-free certification of the country, significant reductions in the prevalence of Guinea Worm and other neglected tropical diseases and timely detection and response to the ongoing COVID-19 outbreak. Moving forward, attainment of universal health coverage in the country requires a strong and people-centred primary healthcare approach which will ensure that services reach the last mile. Bridging the humanitarian-development nexus is required to ensure accelerated recovery of the country's health system. Furthermore, scaling up of community-based health initiatives such as the Boma Health Initiative as platforms for taking good quality health services to the hard-to-reach areas is imperative. This Journal Supplement highlights the key achievements and challenges on the road to universal health coverage in South Sudan and provides evidence-based information for rapidly scaling up health services provision.

Epidemiological characterization of COVID-19 in displaced populations of South Sudan.

Introduction: South Sudan is facing a protracted humanitarian crisis with increasing population vulnerability. The study aimed to describe the epidemiology of COVID-19 in displaced populations in South Sudan. Methods: the study involved the internally displaced populations (IDP) in Bentiu IDP camp, South Sudan. This was a descriptive cross-sectional study involving individuals that met the COVID-19 probable and confirmed case definitions from May 2020 to November 2021. Case data were managed using Microsoft Excel databases. Results: the initial COVID-19 case in Bentiu IDP camp was reported on 2 May 2020. The overall cumulative attack rate (cases per million) was 3,230 for Bentiu IDP and 1,038 at the national level. The COVID-19 Case Fatality Ratio (CFR) among the IDPs was 19.08% among confirmed and 1.06% at the national level. There was one wave of COVID-19 transmission in the IDPs that coincided with the second COVID-19 wave in South Sudan for the period May 2020 to November 2021. Adult males aged 20-49 years were the most affected and constituted 47.1% of COVID-19 cases. Most severe cases were reported among adults 60-69 years (53%) and ≥ 70 years (80%). The risk of COVID-19 death (deaths per 10,000) increased with age and was highest in patients aged ≥ 60 years at 64.1. The commonest underlying illnesses among COVID-19 deaths was HIV-related illness, heart disease, and tuberculosis. Conclusion: COVID-19 constitutes a significant impact on internally displaced populations of South Sudan. The COVID-19 response in displaced populations and the high-risk groups therein should be optimized.

Evaluation of integrated disease surveillance and response (IDSR) and early warning and response network (EWARN) in South Sudan 2021.

Introduction: South Sudan has been implementing the Integrated Disease Surveillance and Response (IDSR) strategy since 2006, along with Early Warning and Alert Response and Network (EWARN). The IDSR/EWARN stakeholders commissioned an independent evaluation to establish performance at national, state, county, health facility, and community levels in the first half of 2021. Methods: the evaluation was conducted between June and September 2021 (during the COVID-19 pandemic) and was based on the World Health Organization (WHO) protocols for monitoring and evaluating communicable disease surveillance and response systems and the guidelines for evaluating EWARN. Results: integrated disease surveillance and response/early warning and alert response and network indicator data showed improving timeliness and completeness from the beginning of 2021 to week 16 and then a slight depression of timeliness by week 32, while completeness remained high. Event-based surveillance was active at the beginning of 2021 and in week 32. However, there was inadequate sample collection to investigate acute watery diarrhea, bloody diarrhea, and acute jaundice syndrome alerts. Respondents in all cadres had substantial experience working in IDSR/EWARN. All respondents performed the various IDSR/EWARN tasks and duties as expected, but needed more resources and training. Conclusion: while IDSR/EWARN is performing relatively well, confirmation of priority diseases by the laboratories needs to be strengthened. Health facilities need more regular supervision from the higher levels. Community health workers need more training on IDSR/EWARN. The whole IDSR/EWARN system needs more resources, particularly for communication and transport and to confirm priority diseases. Staff at all levels requested more training in IDSR/EWARN.

Integrated disease surveillance and response in humanitarian context: South Sudan experience.

Introduction: decades of instability continue to impact the implementation of the Integrated Disease Surveillance and Response (IDSR) strategy. The study reviewed the progress and outcomes of rolling out IDSR in South Sudan. Methods: this descriptive cross-sectional study used epidemiological data for 2019, 2020, and other program data to assess indicators for the five surveillance components including surveillance priorities, core and support functions, and surveillance system structure and quality. Results: South Sudan expanded the priority disease scope from 26 to 59 to align with national and regional epidemiological trends and the International Health Regulations (IHR) 2005. Completing the countrywide rollout of electronic Early Warning Alert and Response (EWARS) reporting has improved both the timeliness and completeness of weekly reporting to 78% and 90%, respectively, by week 39 of 2020 in comparison to a baseline of 54% on both timeliness and completeness of reporting in 2019. The National Public Health Laboratory confirmatory testing capacities have been expanded to include cholera, measles, HIV, tuberculosis (TB), influenza, Ebola, yellow fever, and Severe Acute Respiratory Syndrome 2 (SARS-COV-2). Rapid response teams have been established to respond to epidemics and pandemics. Conclusion: since 2006, South Sudan has registered progress towards using indicator and event-based surveillance and continues to strengthen IHR (2005) capacities. Following the adoption of third edition IDSR guidelines, the current emphasis entails maintaining earlier gains and strengthening community and event-based surveillance, formalizing cross-sectoral one-health engagement, optimal EWARS and District Health Information Systems (DHIS2) use, and strengthening cross-border surveillance. It is also critical that optimal government, and donors' resources are dedicated to supporting health system strengthening and disease surveillance.

Joint external evaluation of the international health regulations (2005) capacity in South Sudan: assessing the country´s capacity for health security.

Introduction: joint external evaluation is a voluntary and collaborative process to assess a country´s capacity under International Health Regulations (2005) to prevent, detect, and respond to public health threats. The main objective is to measure a country´s status in building the necessary capacities to prevent, detect, and respond to infectious disease threats and establish a baseline measurement of capacities and capabilities. The Republic of South Sudan conducted the Joint External Evaluation from 16-20 October 2017, where its capacities were assessed to public health threats per the International Health Regulation (2005). Methods: cross-sectional descriptive study of the Joint External Evaluation process and the findings are described along with major findings and recommendations for the country. Results: South Sudan's overall mean score across 48 indicators was 1.5 (min= 1, max= 4) and 42/48 indicators (87.5%) scored < 2 on a 1 to 5 scale. Technical areas in the prevent category with the lowest score were antimicrobial resistance, biosafety and biosecurity, and National legislation, policy, and financing. In the detect category, the mean score was 2. Technical areas with the lowest mean scores were workforce development and the National Laboratory System. Preparedness, medical countermeasures, personnel deployment, linking public health, and security authorities had the lowest scores in the respond category. Chemical events, radiation emergencies, and points of entry had a score of 1 in the other IHR-related hazards and points of entry category. Conclusion: South Sudan's mean score of 1.5 can be attributed to several civil conflicts experienced, which have impacted negatively on the health system. Recommendations from the Joint External Evaluation need to be implemented and these must be aligned with the costed National Action Plan for Health Security.

Analysis of the 2017-2018 Rift valley fever outbreak in Yirol East County, South Sudan: a one health perspective.

Introduction: the emergence and re-emergence of zoonotic diseases have threatened both human and animal health globally since their identification in the 20th century. Rift Valley fever (RVF) virus is a recurrent zoonotic disease in South Sudan, with the earliest RVF cases confirmed in 2007 in Kapoeta North County, Eastern Equatoria state. Methods: we analyzed national RVF outbreak data to describe the epidemiological pattern of the RVF outbreak in Yirol East county in Lakes State. The line list of cases (confirmed, probable, suspected, and non-cases) was used to describe the pattern and risk factors associated with the outbreak. The animal and human blood samples were tested using Enzyme-Linked Immunosorbent Assay (ELISA) (Immunoglobulin IgG and IgM) and Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR). Qualitative data were collected from weekly RVF situation reports, and national guidelines and policies. Results: between December 2017 and December 2018, 58 suspected human RVF cases were reported. The cases were reclassified based on laboratory and investigations results, such that as of 16th December 2018, there were a total of six (10.3%) laboratory-confirmed, three (5.2%) probable, one (1.7%) suspected, and 48 (82.8%) non-cases were reported. A total of four deaths were reported during the outbreak (case fatality rate (CFR) 6.8% (4/58). A total of 28 samples were collected from animals; of these, six tested positives for RVF (positivity rate of 32.1% (9/28). The outbreak was announced in March 2018, after four months of the first reported suspected RVF case. Several factors were attributed to the delayed notification and outbreak announcement such as lack of multi-sectorial coordination at the state and county level, multi-sectoral coordination at national level mostly attended by public health experts from human health, inadequate animal health surveillance, poor coordination between livestock disease surveillance and public health surveillance, limited in-country laboratory diagnostic capacity, the laboratory results for the animal health took longer than expected, and lack of a national One Health approach strategy. Conclusion: the outbreak demonstrated gaps to investigate and respond to zoonotic disease outbreaks in South Sudan.

Prevalence and factors associated with transmission of schistosomiasis in school-aged children in South Sudan: a cross-sectional study.

Introduction: South Sudan is affected by a high burden of Neglected Tropical Diseases (NTDs). The country is very vulnerable to NTDs due to its favourable tropical climate and multiple risk factors. However, the distribution of the diseases and the populations at risk for the various NTDs is unknown. This paper described the distribution of schistosomiasis in 58 counties and 261 schools in South Sudan. Methods: a descriptive quantitative cross-sectional study of schistosomiasis in 58 counties in 8 states of South Sudan recruited school-aged children. Using different laboratory techniques, the children were tested for Schistosoma mansoni (S. mansoni) and Schistosoma haematobium (S. haematobium). A quantitative descriptive statistical was performed to determine the prevalence rates and the endemicity of schistosomiasis among 13,286 school-aged children. Results: the overall prevalence of S. mansoni and S. haematobium were 6.1% and 3.7% using Kato Katz and urine filtration concentration testing techniques. The highest state prevalence was reported in Western Equatoria for both S. mansoni (14.7%) and S. haematobium (7.3%). The age of the participants varied from 4 to 18 years; of these, children 10 to 12 years old had the highest prevalence of S. mansoni (6.8%) and S. haematobium (3.7%). The prevalence of S. mansoni (7% male vs 5% female) and S. haematobium (3.6% male vs 3.1% female) were higher in males than females. The likelihood of the prevalence of S. mansoni in males was 1.42 (95% CI:1.23, 1.64) higher than in females, while for S. haematobium, 1.36 (95% CI:1.12, 1.65) higher than in females. The prevalence of S. mansoni and S. haematobium showed a statistically significant gender difference (P< 0.05). Conclusion: the study had provided evidence of the distribution of schistosomiasis in South Sudan for policy direction and recommended annual preventive chemotherapy with praziquantel in all endemic areas.

Contribution of Auto-Visual AFP Detection and Reporting (AVADAR) on polio surveillance in South Sudan.

Introduction: the last wild polio virus in South Sudan was documented in 2009. Nonetheless, it was one of the last four countries in the WHO African region to be accepted as a polio-free country in June 2020. In line with this, to accelerate the polio-free documentation process, the country has piloted Auto Visual AFP Detection and Reporting (AVADAR) in three counties. This study examined the contribution of the AVADAR surveillance system to the traditional Acute Flaccid Paralysis (AFP) surveillance system to document lessons learnt and best practices. Methods: we performed a retrospective descriptive quantitative study design to analyze secondary AVADAR surveillance data collected from June 2018 to December 2019 and stored at the WHO AVADAR server. Results: the AVADAR community surveillance system has improved the two main AFP surveillance indicators in the piloted counties and made up 86% of the total number of true AFP cases detected in these counties. The completeness and timeliness of weekly zero reporting were 97% and 94%, respectively and maintained above the standard throughout the study, while the two main surveillance indicators in the project area were improved progressively except for the Gogrial West County. In contrast, main surveillance indicators declined in some of the none-AVADAR implementing counties. Conclusion: the AVADAR surveillance system can overcome the logistical and remoteness barriers that can hinder the early detection and reporting of cases due to insecurity, topographical, and communication barrier in rural and hard-to-reach areas to accomplish and sustain the two main surveillance indicators, along with the completeness and timeliness of weekly zero reporting. We recommend extending this application-based surveillance system to other areas with limited resources and similar challenges by incorporating other diseases of public health concern.

Polio eradication in a chronic conflict setting lessons from the Republic of South Sudan, 2010-2020.

Introduction: in 1988 the World Health Assembly set an ambitious target to eradicate Wild Polio Virus (WPV) by 2000, following the successful eradication of the smallpox virus in 1980. South Sudan and the entire African region were certified WPV free on August 25, 2020. South Sudan has maintained its WPV free status since 2010, and this paper reviewed the country's progress, outlined lessons learned, and describes the remaining challenges in polio eradication. Methods: secondary data analysis was conducted using the Ministry of Health and WHO polio surveillance datasets, routine immunisation coverage, polio campaign data, and surveys from 2010 to 2020. Relevant technical documents and reports on polio immunisation and surveillance were also reviewed. Data analysis was conducted using EPI Info 7 software. Results: administrative routine immunisation coverage for bivalent Oral Polio Vaccine (OPV) 3rd dose declined from 77% in 2010 to 56% in 2020. In contrast, the administrative and post-campaign evaluation coverage recorded for the nationwide supplemental polio campaigns since 2011 was consistently above 85%; however, campaigns declined in number from four in 2011 to zero in 2020. Overall, 76% of notified cases of Acute Flaccid Paralysis (AFP) received three or more doses of the oral polio vaccine. The Annualized Non-AFP rate ranged between 4.0 to 5.4 per 100,000 under 15 years populations, and stool adequacy ranged from 83% to 94%. Conclusion: South Sudan's polio-free status documentation was accepted by the ARCC in 2020, thereby enabling the African Region to be certified WPV free on August 25, 2020. However, there are concerns as the country continues to report low routine immunisation coverage and a reduction in the number of polio campaigns conducted each year. It is recommended that the country conduct high-quality nationwide supplemental polio campaigns yearly to achieve and maintain the required herd immunity. It invests in its routine immunisation program while ensuring optimal AFP surveillance performance indicators.

Prevalence and factors associated with transmission of lymphatic filariasis in South Sudan: a cross-sectional quantitative study.

Introduction: South Sudan is affected by a high burden of Neglected Tropical Diseases (NTDs). The country is very vulnerable to NTDs due to its favourable tropical climate and multiple risk factors. However, the distribution of the diseases and the populations at risk for the various NTDs is unknown. This paper describes the distribution of lymphatic filariasis (LF) in 58 counties of South Sudan. Methods: a descriptive quantitative cross-sectional study of LF in 58 counties in 8 states of South Sudan recruited adult volunteers aged ≥ 15 years tested for circulating filarial antigens (CFA). A quantitative descriptive statistical was performed to determine the prevalence rates and the endemicity (CFA positivity rate ≥1%) of lymphatic filariasis in 9213 adult individuals from 101 villages. Results: the overall prevalence of positive CFA was 1.6%, and the highest state prevalence was reported in the Upper Nile state at 3.4%. Based on the prevalence of positive CFA 64% of the surveyed counties are endemic to lymphatic filariasis. The endemicity ranged from 1-11.1% positive CFA. The highest prevalence of positive CAF was observed in the >50 years old age group (2.7%), followed by the 46-50 age group (2.3%). Males tested more positive than females (52.4% Vs 47.6%). Participants were three times more likely to test positive for CFA on filarial test strips (FTS) compared to immunochromatographic test (ICT). There was a statistically significant difference in the prevalence of positive CFA among the two tests (P=.002). Conclusion: the distribution of LF is widespread, with varying transmission risks. The produced prevalence maps of infection provided evidence on the areas for targeted interventions in the national NTD program in South Sudan. An increased number of positive CFA were identified using FTS than ICT; hence, it is advisable to use FTS in the future transmission survey.

Systematic review: Safety of surgical male circumcision in context of HIV prevention public health programmes.

Background: Since the recommendation of voluntary medical male circumcision (VMMC) to reduce the risk of heterosexually acquired HIV, a number of adolescent boys and men in 15 priority countries in Africa have been circumcised. Our primary goal was to identify the incidence of adverse events (AEs) associated with VMMC and to assess the safety profile among adolescent boys 10 - 14 years. Methods: We searched the databases MEDLINE and Embase, WHO, and conference abstracts from 2005 to 2019. The incidence of AEs was estimated by type of AE, size of study and age. Results: We retained 40 studies. Severe and moderate AEs overall were estimated at 0.30 per 100 VMMC clients with wide variability per study type. A higher rate was noted in small and moderate scale programmes and device method research studies compared with larger scale programmes. There was a limited number of studies reporting AEs among younger adolescent boys and they had higher infection-related AEs than those aged 20 years and older. Case studies noted rare AEs such as necrotizing fasciitis, tetanus, and glans injury. Conclusions: AE rates were comparable to those from the randomized controlled trials (RCTs) that led to recommendations and implementation of VMMC in high HIV burden countries, despite being implemented in low resource settings. Clients over time have increasingly included adolescents under the age of 15 years. Studies suggest potentially higher risks in this age group. As VMMC services are sustained, patient safety surveillance systems and promoting a patient safety culture are crucial to identify and mitigate potential harms from medical male circumcision.

Experience in piloting HIV drug resistance early warning indicators to improve the antiretroviral program in Papua New Guinea.

In 2009, World Health Organization human immunodeficiency virus drug resistance early warning indicator monitoring was piloted at 2 large antiretroviral therapy (ART) clinics in Papua New Guinea: Heduru Clinic in Port Moresby and Tininga Clinic in Mount Hagen. Results demonstrated that both Heduru and Tininga clinics met internationally suggested targets for prescribing appropriate first-line ART regimens in accordance with national ART guidelines, retention on first-line ART at 12 months, and drug supply continuity. However, both clinics failed to achieve suggested targets for rates of loss to follow-up and on-time pill pickup. Reasons for poor clinic performance on loss to follow-up and on-time pill pickup were explored, and appropriate corrective actions were implemented.