Analyses of drinking water quality during a protracted cholera epidemic in Malawi - a cross-sectional study of key physicochemical and microbiological parameters

Anecdotal evidence and available literature indicated that contaminated water played a major role in spreading the prolonged cholera epidemic in Malawi from 2022 to 2023. This study assessed drinking water quality in 17 cholera-affected Malawi districts from February to April 2023. Six hundred and thirty-three records were analysed. The median counts/100 ml for thermotolerant coliform was 98 (interquartile range (IQR): 4-100) and that for Escherichia coli was 0 (IQR: 0-9). The drinking water in all (except one) districts was contaminated by thermotolerant coliform, while six districts had their drinking water sources contaminated by E. coli. The percentage of contaminated drinking water sources was significantly higher in shallow unprotected wells (80.0% for E. coli and 95.0% for thermotolerant coliform) and in households (55.8% for E. coli and 86.0% for thermotolerant coliform). Logistic regression showed that household water has three times more risk of being contaminated by E. coli and two and a half times more risk of being contaminated by thermotolerant coliform compared to other water sources. This study demonstrated widespread contamination of drinking water sources during a cholera epidemic in Malawi, which may be the plausible reason for the protracted nature of the epidemic.

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 Chronic Cholera Situation in Africa: Why Are African Countries Unable to Tame the Well-Known Lion?

Seven years to the Global Taskforce on Cholera Control's target of reducing cholera cases and deaths by 90% by 2030, Africa continues to experience a high incidence of the disease. In the last 20 years, more than 2.6 million cases and 60 000 deaths of the disease have been recorded, mostly in sub-Saharan Africa. Case Fatality Ratio remains consistently above the WHO-recommended 1% with a yearly average of 2.2%. Between 1 January 2022 and 16 July 2023, fourteen African countries reported 213 443 cases and 3951 deaths (CFR, 1.9%) of the disease. In this perspective article, based on available literature and the authors' field experiences in Africa, we discuss the underlying reasons for the sustained transmission of the disease. We posit that in addition to the well-known risk factors for the disease, the chronic cholera situation in Africa is due to the poor socioeconomic development status, weak household and community resilience, low literacy levels, weak capacity of African countries to implement the 2005 International Health Regulation and the pervasively weak health system on the continent. Stemming this tide requires good leadership, partnership, political commitment, and equity in access to health services, water, and sanitation. Therefore, we recommend that African governments and stakeholders recognize and approach cholera prevention and control from the long-term development lens and leverage the current cholera emergency preparedness and response efforts on the continent to strengthen the affected countries' health, water, and sanitation systems. We call on international organizations such as WHO and the Africa Centres for Diseases Control to support African governments in scaling up research and innovations aimed at better characterizing the epidemiology of cholera and developing evidence-based, context-specific, and innovative strategies for its prevention and control. These recommendations require long-term multisectoral and multidisciplinary approaches.

Bridging the humanitarian-development divide in a protracted crisis: a case study of the use of a central plant to supply oxygen for COVID-19 case management in South Sudan

The rising demand for medicinal oxygen due to the COVID-19 pandemic exacerbated an underlying chronic shortage of the commodity in Africa. This situation is particularly dire in protracted crises where insecurity, dysfunctional health facilities, poor infrastructure and prohibitive costs hinder equitable access to the commodity. Against this backdrop, the Ministry of Health of South Sudan, with the guidance of its partners, procured and installed a pressure swing adsorption central oxygen supply plant to address the shortfall. The plant aimed to ensure a more sustainable and technologically appropriate medicinal oxygen supply system for the country and to bridge the humanitarian and development divide, which had always been challenging. This article discusses the key issues, challenges and lessons associated with the procurement and installation of this plant. The major challenges encountered during the procurement and installation of the plant were the time it took to procure and install in the face of urgent needs for medicinal oxygen and its short and long-term sustainability. Lessons learnt include the need for exhaustive and evidence-based considerations in deciding on which source of medicinal oxygen to deploy in protracted crisis settings. The successful installation and operationalization of the plant demonstrated that it is possible to bridge the humanitarian-development divide amidst the complexities of a protracted crisis and an ongoing pandemic. The Ministries of Health, with the support of its partners, should assess and document the impact of this and other similar central oxygen production plants in protracted crisis settings regarding their sustainability, cost, and effectiveness on medicinal oxygen supply. The Ministry of Health of South Sudan should expedite the finalization and operationalization of the longer-term public-private partnership and continue to monitor the quality of oxygen produced by this plant.

Transmissibility and severity of COVID-19 in a humanitarian setting: First few X investigation of cases and contacts in Juba, South Sudan, 2020

BACKGROUND

The first few 'X' (FFX) studies provide evidence to guide public health decision-making and resource allocation. The adapted WHO Unity FFX protocol for COVID-19 was implemented to gain an understanding of the clinical, epidemiological, virological and household transmission dynamics of the first cases of COVID-19 infection detected in Juba, South Sudan.

METHODS

Laboratory-confirmed COVID-19 cases were identified through the national surveillance system, and an initial visit was conducted with eligible cases to identify all close contacts. Consenting cases and close contacts were enrolled between June 2020 and December 2020. Demographic, clinical information and biological samples were taken at enrollment and 14-21 days post-enrollment for all participants.

RESULTS

Twenty-nine primary cases and 82 contacts were included in the analyses. Most primary cases (n = 23/29, 79.3%) and contacts (n = 61/82, 74.4%) were male. Many primary cases (n = 18/29, 62.1%) and contacts (n = 51/82, 62.2%) were seropositive for SARS-CoV-2 at baseline. The secondary attack rate among susceptible contacts was 12.9% (4/31; 95% CI: 4.9%-29.7%). All secondary cases and most (72%) primary cases were asymptomatic. Reported symptoms included coughing (n = 6/29, 20.7%), fever or history of fever (n = 4/29, 13.8%), headache (n = 3/29, 10.3%) and shortness of breath (n = 3/29, 10.3%). Of 38 cases, two were hospitalised (5.3%) and one died (2.6%).

CONCLUSIONS

These findings were used to develop the South Sudanese Ministry of Health surveillance and contract tracing protocols, informing local COVID-19 case definitions, follow-up protocols and data management systems. This investigation demonstrates that rapid FFX implementation is critical in understanding the emerging disease and informing response priorities.

Integrated approaches to COVID-19 emergency response in fragile, conflict-affected and vulnerable settings: a public health policy brief

In the absence of fully effective measures to prevent and treat COVID-19, the limited access to and hesitancy about vaccines, the prolongation of the on-going pandemic is likely. This underscores the need to continue to respond and maintain preparedness, preferably using a more sustainable approach. A sustainable management is particularly important in fragile, conflict-affected and vulnerable countries of sub-Saharan Africa given several peculiar challenges. This Viewpoint proposes policy options to guide transitioning from current COVID-19 emergency response interventions to longer-term and more sustainable responses in such settings. In the long term, a shift in policy from a vertical to a more effective approach should integrate response coordination, surveillance, case management, risk communication and operational support, among other elements, for better results. We call on public health policymakers, partners and donors to support full implementation of these policy options in a holistic manner to encompass all emerging public health threats.

Sustainable strategies for Ebola virus disease outbreak preparedness in Africa: a case study on lessons learnt in countries neighbouring the Democratic Republic of the Congo

BACKGROUND

From May 2018 to September 2022, the Democratic Republic of Congo (DRC) experienced seven Ebola virus disease (EVD) outbreaks within its borders. During the 10th EVD outbreak (2018-2020), the largest experienced in the DRC and the second largest and most prolonged EVD outbreak recorded globally, a WHO risk assessment identified nine countries bordering the DRC as moderate to high risk from cross border importation. These countries implemented varying levels of Ebola virus disease preparedness interventions. This case study highlights the gains and shortfalls with the Ebola virus disease preparedness interventions within the various contexts of these countries against the background of a renewed and growing commitment for global epidemic preparedness highlighted during recent World Health Assembly events.

MAIN TEXT

Several positive impacts from preparedness support to countries bordering the affected provinces in the DRC were identified, including development of sustained capacities which were leveraged upon to respond to the subsequent coronavirus disease 2019 (COVID-19) pandemic. Shortfalls such as lost opportunities for operationalizing cross-border regional preparedness collaboration and better integration of multidisciplinary perspectives, vertical approaches to response pillars such as surveillance, over dependence on external support and duplication of efforts especially in areas of capacity building were also identified. A recurrent theme that emerged from this case study is the propensity towards implementing short-term interventions during active Ebola virus disease outbreaks for preparedness rather than sustainable investment into strengthening systems for improved health security in alignment with IHR obligations, the Sustainable Development Goals and advocating global policy for addressing the larger structural determinants underscoring these outbreaks.

CONCLUSIONS

Despite several international frameworks established at the global level for emergency preparedness, a shortfall exists between global policy and practice in countries at high risk of cross border transmission from persistent Ebola virus disease outbreaks in the Democratic Republic of Congo. With renewed global health commitment for country emergency preparedness resulting from the COVID-19 pandemic and cumulating in a resolution for a pandemic preparedness treaty, the time to review and address these gaps and provide recommendations for more sustainable and integrative approaches to emergency preparedness towards achieving global health security is now.

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.

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.

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.

Assessment of infection prevention and control readiness for Ebola virus and other diseases outbreaks in a humanitarian crisis setting: a cross-sectional study of health facilities in six high-risk States of South Sudan

INTRODUCTION

the study was conducted to assess the readiness and capacity of the core components of infection prevention and control and water, sanitation and hygiene in health facilities to effectively contain potential outbreaks of Ebola virus and other diseases in South Sudan.

METHODS

it is a descriptive cross-sectional study which was conducted in health facilities in six high-risk States of the country from September 2020 to December 2021. Data was collected using a structured questionnaire and analyzed with Microsoft Excel software.

RESULTS

one hundred and fifty-one (151) health facilities with a total bed capacity of 3089 were enrolled into the study. Overall, the least prepared infection prevention and control, water and sanitation core components in ascending order were the coordination committee structure (13.19%), guidelines and SOPs (21.85%), vector control (22.02%), staff management (30.63%), and training received (33.64%). The best prepared components in descending order were integrated disease surveillance and response capacity (69.83%), medical waste management system (57.12%) and infrastructure compliance (54.69%).

CONCLUSION

the findings of this study which is comparable to those of other studies in similar settings validates the perception that Infection Prevention and Control/Water, Sanitation, and Hygiene (IPC/WASH) capacity and readiness is inadequate in South Sudan. To scale up these core components, we recommend development and implementation of a comprehensive and long-term infection prevention and control strategic plan as part of the country's broader health sector recovery planning.

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.

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.

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.

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.

Use of mobile medical teams to fill critical gaps in health service delivery in complex humanitarian settings, 2017-2020: a case study of South Sudan

The vulnerable populations in the protracted humanitarian crisis in South Sudan are faced with constrained access to health services and frequent disease outbreaks. Here, we describe the experiences of emergency mobile medical teams (eMMT) assembled by the World Health Organization (WHO) South Sudan to respond to public health emergencies. Interventions: the eMMTs, multidisciplinary teams based at national, state and county levels, are rapidly deployed to conduct rapid assessments, outbreak investigations, and initiate public health response during acute emergencies. The eMMTs were deployed to locations affected by flooding, conflicts, famine, and disease outbreaks. We reviewed records of deployment reports, outreach and campaign registers, and analyzed the key achievements of the eMMTs for 2017 through 2020. Achievements: the eMMTs investigated disease outbreaks including cholera, measles, Rift Valley fever and coronavirus disease (COVID-19) in 13 counties, conducted mobile outreaches in emergency locations in 38 counties (320,988 consultations conducted), trained 550 healthcare workers including rapid response teams, and supported reactive measles vaccination campaigns in seven counties [148,726, (72-125%) under-5-year-old children vaccinated] and reactive oral cholera vaccination campaigns in four counties (355,790 vaccinated). The eMMT is relevant in humanitarian settings and can reduce excess morbidity and mortality and fill gaps that routine health facilities and health partners could not bridge. However, the scope of the services offered needs to be broadened to include mental and psychosocial care and a strategy for ensuring continuity of vaccination services and management of chronic conditions after the mobile outreach is instituted.

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.

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.

Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 IgG in Juba, South Sudan, 20201

Relatively few coronavirus disease cases and deaths have been reported from sub-Saharan Africa, although the extent of its spread remains unclear. During August 10-September 11, 2020, we recruited 2,214 participants for a representative household-based cross-sectional serosurvey in Juba, South Sudan. We found 22.3% of participants had severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain IgG titers above prepandemic levels. After accounting for waning antibody levels, age, and sex, we estimated that 38.3% (95% credible interval 31.8%-46.5%) of the population had been infected with SARS-CoV-2. At this rate, for each PCR-confirmed SARS-CoV-2 infection reported by the Ministry of Health, 103 (95% credible interval 86-126) infections would have been unreported, meaning SARS-CoV-2 has likely spread extensively within Juba. We also found differences in background reactivity in Juba compared with Boston, Massachusetts, USA, where the immunoassay was validated. Our findings underscore the need to validate serologic tests in sub-Saharan Africa populations.

COVID-19 case management strategies: what are the options for Africa?

The ongoing coronavirus disease 2019 (COVID-19) pandemic has put a strain on health systems globally. Although Africa is the least affected region to date, it has the weakest health systems and an exponential rise in cases as has been observed in other regions, is bound to overwhelm its health systems. Early detection and isolation of suspected and confirmed COVID-19 cases are pivotal to the prevention and control of the pandemic. The World Health Organization (WHO) recommends that all laboratory-confirmed cases should be isolated and treated in a health care facility; however, where this is not possible due to the health system capacity, patients can be isolated in re-purposed facilities or at home. An already very apparent future challenge for Africa is facility-based isolation of COVID-19 cases, given the already limited health infrastructure and health workforce, and the risk of nosocomial transmission. Use of repurposed facilities requires additional resources, including health workers. Home isolation, on the other hand, would be a challenge given the poor housing, overcrowding, inadequate access to water and sanitation, and stigma related to infectious disease that is prevalent in many African societies. Conflict settings on the continent pose an additional challenge to the prevention and control of COVID-19 with the resultant population displacements in overcrowded camps where access to social services is limited. These unique cultural, social, economic and developmental differences on the continent, call for a tailored approach to COVID-19 case management strategies. This article proposes three broad case management strategies based on the transmission scenarios defined by WHO, and the criteria and package of care for each option, for consideration by policy makers and governments in African countries. Moving forward, African countries should generate local evidence to guide the development of realistic home-grown strategies, protocol and equipment for the management of COVID-19 cases on the continent .

Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Juba, South Sudan: a population-based study

BACKGROUND

Relatively few COVID-19 cases and deaths have been reported through much of sub-Saharan Africa, including South Sudan, although the extent of SARS-CoV-2 spread remains unclear due to weak surveillance systems and few population-representative serosurveys.

METHODS

We conducted a representative household-based cross-sectional serosurvey in Juba, South Sudan. We quantified IgG antibody responses to SARS-CoV-2 spike protein receptor-binding domain and estimated seroprevalence using a Bayesian regression model accounting for test performance.

RESULTS

We recruited 2,214 participants from August 10 to September 11, 2020 and 22.3% had anti-SARS-CoV-2 IgG titers above levels in pre-pandemic samples. After accounting for waning antibody levels, age, and sex, we estimated that 38.5% (32.1 - 46.8) of the population had been infected with SARS-CoV-2. For each RT-PCR confirmed COVID-19 case, 104 (87-126) infections were unreported. Background antibody reactivity was higher in pre-pandemic samples from Juba compared to Boston, where the serological test was validated. The estimated proportion of the population infected ranged from 30.1% to 60.6% depending on assumptions about test performance and prevalence of clinically severe infections.

CONCLUSIONS

SARS-CoV-2 has spread extensively within Juba. Validation of serological tests in sub-Saharan African populations is critical to improve our ability to use serosurveillance to understand and mitigate transmission.

The first sixty days of COVID-19 in a humanitarian response setting: a descriptive epidemiological analysis of the outbreak in South Sudan

Introduction

the coronavirus disease 2019 (COVID-19) was declared a pandemic on March 11, 2020. South Sudan, a low-income and humanitarian response setting, reported its first case of COVID-19 on April 5, 2020. We describe the socio-demographic and epidemiologic characteristics of COVID-19 cases in this setting.

Methods

we conducted a cross-sectional descriptive analysis of data for 1,330 confirmed COVID-19 cases from the first 60 days of the outbreak.

Results

among the 1,330 confirmed cases, the mean age was 37.1 years, 77% were male, 17% were symptomatic with 95% categorized as mild, and the case fatality rate was 1.1%. Only 24.7% of cases were detected through alerts and sentinel site surveillance, with 95% of the cases reported from the capital, Juba. Epidemic doubling time averaged 9.8 days (95% confidence interval [CI] 7.7 - 13.4), with an attack rate of 11.5 per 100,000 population. Test positivity rate was 18.2%, with test rate per 100,000 population of 53 and mean test turn-around time of 9 days. The case to contact ratio was 1: 2.2.

Conclusion

this 2-month initial period of COVID-19 in South Sudan demonstrated mostly young adults and men affected, with most cases reported as asymptomatic. Systems´ limitations highlighted included a small proportion of cases detected through surveillance, low testing rates, low contact elicitation, and long collection to test turn-around times limiting the country´s ability to effectively respond to the outbreak. A multi-pronged response including greater access to testing, scale-up of surveillance, contact tracing and community engagement, among other interventions are needed to improve the COVID-19 response in this setting.

Analyses of the performance of the Ebola virus disease alert management system in South Sudan: August 2018 to November 2019

South Sudan implemented Ebola virus disease preparedness interventions aiming at preventing and rapidly containing any importation of the virus from the Democratic Republic of Congo starting from August 2018. One of these interventions was a surveillance system which included an Ebola alert management system. This study analyzed the performance of this system. A descriptive cross-sectional study of the Ebola virus disease alerts which were reported in South Sudan from August 2018 to November 2019 was conducted using both quantitative and qualitative methods. As of 30 November 2019, a total of 107 alerts had been detected in the country out of which 51 (47.7%) met the case definition and were investigated with blood samples collected for laboratory confirmation. Most (81%) of the investigated alerts were South Sudanese nationals. The alerts were identified by health workers (53.1%) at health facilities, at the community (20.4%) and by screeners at the points of entry (12.2%). Most of the investigated alerts were detected from the high-risk states of Gbudwe (46.9%), Jubek (16.3%) and Torit (10.2%). The investigated alerts commonly presented with fever, bleeding, headache and vomiting. The median timeliness for deployment of Rapid Response Team was less than one day and significantly different between the 6-month time periods (K-W = 7.7567; df = 2; p = 0.0024) from 2018 to 2019. Strengths of the alert management system included existence of a dedicated national alert hotline, case definition for alerts and rapid response teams while the weaknesses were occasional inability to access the alert toll-free hotline and lack of transport for deployment of the rapid response teams which often constrain quick response. This study demonstrates that the Ebola virus disease alert management system in South Sudan was fully functional despite the associated challenges and provides evidence to further improve Ebola preparedness in the country.

The Democratic Republic of Congo announced its tenth outbreak of the Ebola virus disease on 1^st August 2018. As part of the preparedness measures to prevent and rapidly contain any importation of the virus, South Sudan, a neighbouring country to the Democratic Republic of Congo implemented a surveillance system which included an Ebola alert management system. We analyzed the performance of this system with a view to provide information to inform planning and allocation of resources to the other components of Ebola virus disease preparedness and to understand the key issues and challenges with the system. Our findings show that more than half of the reported alerts did not meet the case definition of the disease, alerts were mainly detected in the high-risk states, the commonest source of alert detection were from health facilities and the community and the most common symptoms presented by the alerts were fever, bleeding, headache, vomiting and weakness/fatigue. This study demonstrates that the Ebola virus disease alert management system in South Sudan was fully functional despite the associated challenges and provided evidence to further improve Ebola preparedness in the country. We recommend that the observed challenges should be urgently addressed.

Moving from rhetoric to action: how Africa can use scientific evidence to halt the COVID-19 pandemic

The ongoing pandemic of the coronavirus disease 2019 has spread rapidly to all countries of the world. Africa is particularly predisposed to an escalation of the pandemic and its negative impact given its weak economy and health systems. In addition, inadequate access to the social determinants of health such as water and sanitation and socio-cultural attributes may constrain the implementation of critical preventive measures such as hand washing and social distancing on the continent.Given these facts, the continent needs to focus on targeted and high impact prevention and control strategies and interventions which could break the chain of transmission quickly. We conclude that the available body of scientific evidence on the coronavirus disease 2019 holds the key to the development of such strategies and interventions.Going forward, we recommend that the African research community should scale up research to provide scientific evidence for a better characterization of the epidemiology, transmission dynamics, prevention and control of the virus on the continent.

What did we learn from preparing for cross-border transmission of Ebola virus disease into a complex humanitarian setting - The Republic of South Sudan?

Background

Following the West Africa Ebola virus disease (EVD) outbreak (2013–2016), WHO developed a preparedness checklist for its member states. This checklist is currently being applied for the first time on a large and systematic scale to prepare for the cross border importation of the ongoing EVD outbreak in the Democratic Republic of Congo hence the need to document the lessons learnt from this experience. This is more pertinent considering the complex humanitarian context and weak health system under which some of the countries such as the Republic of South Sudan are implementing their EVD preparedness interventions.

Main text

We identified four main lessons from the ongoing EVD preparedness efforts in the Republic South Sudan. First, EVD preparedness is possible in complex humanitarian settings such as the Republic of South Sudan by using a longer-term health system strengthening approach. Second, the Republic of South Sudan is at risk of both domestic and cross border transmission of EVD and several other infectious disease outbreaks hence the need for an integrated and sustainable approach to outbreak preparedness in the country. Third, a phased and well-prioritized approach is required for EVD preparedness in complex humanitarian settings given the costs associated with preparedness and the difficulties in the accurate prediction of outbreaks in such settings. Fourth, EVD preparedness in complex humanitarian settings is a massive undertaking that requires effective and decentralized coordination.

Conclusion

Despite a very challenging context, the Republic of South Sudan made significant progress in its EVD preparedness drive demonstrating that it is possible to rapidly scale up preparedness efforts in complex humanitarian contexts if appropriate and context-specific approaches are used. Further research, systematic reviews and evaluation of the ongoing preparedness efforts are required to ensure comprehensive documentation and application of the lessons learnt for future EVD outbreak preparedness and response efforts.

Epidemiology of Ebola Virus Disease in the Western Area Region of Sierra Leone, 2014-2015

Introduction

Western Area (WA) of Sierra Leone including the capital, Freetown, experienced an unprecedented outbreak of Ebola from 2014 to 2015. At the onset of the epidemic, there was little information about the epidemiology, transmission dynamics, and risk factors in urban settings as previous outbreaks were limited to rural/semi-rural settings. This study, therefore, aimed to describe the epidemiology of the outbreak and the factors which had most impact on the transmission of the epidemic and whether there were different drivers from those previously described in rural settings.

Methods

We conducted a descriptive epidemiology study in WA, Sierra Leone using secondary data from the National Ebola outbreak database. We also reviewed the Ebola situation reports, response strategy documents, and other useful documents.

Results

A total of 4,955 Ebola cases were identified between June 2014 and November 2015, although there were reports of cases occurring in WA toward end of May. All wards were affected, and Waterloo Area I (Ward 330), the capital city of Western Area Rural District, recorded the highest numbers of cases (580) and deaths (236). Majority of cases (63.4%) and deaths (66.8%) were in WA Urban District (WAU); 44 cases were imported from other provinces. Only 20% of cases had a history of contact with an Ebola case, and more than 30% were death alerts. Equal numbers of males and females were infected, and very few cases (3.2%) were health workers. Overall, transmission was through contact with infected individuals, and intense transmission occurred at the community level. In WAU, transmission was mostly between neighbors and among inhabitants of shared accommodations. The drivers of transmission included high population movement to and from WA, overcrowding, fear and lack of trust in the response, and negative community behaviors. Transmission was mostly through contact and with limited transmission through sex and breast milk.

Conclusion

The unprecedented outbreak in WA was attributed to delayed detection, inadequate preparedness and response, intense population movements, overcrowding, and unresponsive communities. Anticipation, strengthening preparedness for early detection, and swift and effective response remains critical in mitigating a potential urban explosion of similar future outbreaks.

Incident Management Systems Are Essential for Effective Coordination of Large Disease Outbreaks: Perspectives from the Coordination of the Ebola Outbreak Response in Sierra Leone

Background

Response to the 2014–2015 Ebola virus disease (EVD) outbreak in Sierra Leone overwhelmed the national capacity to contain it and necessitated a massive international response and strong coordination platform. Consequently, the Sierra Leone Government, with support of the international humanitarian community, established and implemented various models for national coordination of the outbreak. In this article, we review the strengths and limitations of the EVD outbreak response coordination systems in Sierra Leone and propose recommendations for improving coordination of similar outbreaks in the future.

Conclusion

There were two main frameworks used for the coordination of the outbreak; the Emergency Operation Center (EOC) and the National Ebola Response Center (NERC). We observed an improvement in outbreak coordination as the management mechanism evolved from the EOC to the NERC. Both coordination systems had their advantages and disadvantages; however, the NERC coordination mechanism appeared to be more robust. We identified challenges, such as competition and duplication of efforts between the numerous coordination groups, slow resource mobilization, inadequate capacity of NERC/EOC staff for health coordination, and an overtly centralized coordination and decision-making system as the main coordination challenges during the outbreak.

Recommendations

We recommend the establishment of EOCs with simple incident management system-based coordination prior to outbreaks, strong government leadership, decentralization of coordination systems, and functions to the epicenter of outbreaks, with clear demarcation of roles and responsibilities between different levels, regular training of key coordination leaders, and better community participation as methods to improve coordination of future disease outbreaks.

Epidemiological Data Management during an Outbreak of Ebola Virus Disease: Key Issues and Observations from Sierra Leone

Sierra Leone experienced intense transmission of Ebola virus disease (EVD) from May 2014 to November 2015 during which a total of 8,704 confirmed cases and over 3,589 confirmed deaths were reported. Our field observation showed many issues in the EVD data management system, which may have contributed to the magnitude and long duration of the outbreak. In this perspective article, we explain the key issues with EVD data management in the field, and the resulting obstacles in analyzing key epidemiological indicators during the outbreak response work. Our observation showed that, during the latter part of the EVD outbreak, surveillance and data management improved at all levels in the country as compared to the earlier stage. We identified incomplete filling and late arrival of the case investigation forms at data management centers, difficulties in detecting double entries and merging identified double entries in the database, and lack of clear process of how death of confirmed cases in holding, treatment, and community care centers are reported to the data centers as some of challenges to effective data management. Furthermore, there was no consolidated database that captured and linked all data sources in a structured way. We propose development of a new application tool easily adaptable to new occurrences, regular data harmonization meetings between national and district data management teams, and establishment of a data quality audit system to assure good quality data as ways to improve EVD data management during future outbreaks.

The Ebola Virus Disease Outbreak in West Africa: A Wake-up Call to Revitalize Implementation of the International Health Regulations

The 2014/15 Ebola virus disease (EVD) outbreak in West Africa has highlighted the inherent weaknesses associated with the implementation of the International Health Regulations (IHR). In this perspective article, the lessons learnt from the outbreak are used to review the challenges impeding effective implementation of the IHR and to propose policy and strategic options for enhancing its application. While some progress has been achieved in implementing the IHR in several countries, numerous challenges continue to impede its effectiveness, especially in developing countries, such as those affected by the West Africa EVD outbreak. Political and economic sensitivities associated with reporting public health emergencies of international concern (PHEIC), inadequate resources (human and financial), and lack of technical know-how required for implementation of the IHR are weaknesses that continue to constrain the implementation of the regulations. In view of the complex sociopolitical, cultural, and public health dimensions of PHEICs, frameworks, such as the IHR, which have legal backing, seem to be the most effective and sustainable option for assuring timely detection, notification, and response to such events. Renewed efforts to strengthen national and global institutional frameworks for implementation of the IHR are therefore required. Improvements in transparency, commitment, and accountability of parties to the IHR, mainstreaming of the IHR into national public health governance structures, use of multidisciplinary approaches, and mobilization of the required resources for the implementation of the IHR are imperative.

Contact Tracing during an Outbreak of Ebola Virus Disease in the Western Area Districts of Sierra Leone: Lessons for Future Ebola Outbreak Response

Introduction

Contact tracing is a critical strategy required for timely prevention and control of Ebola virus disease (EVD) outbreaks. Available evidence suggests that poor contact tracing was a driver of the EVD outbreak in West Africa, including Sierra Leone. In this article, we answered the question as to whether EVD contact tracing, as practiced in Western Area (WA) districts of Sierra Leone from 2014 to 2015, was effective. The goal is to describe contact tracing and identify obstacles to its effective implementation.

Methods

Mixed methods comprising secondary data analysis of the EVD case and contact tracing data sets collected from WA during the period from 2014 to 2015, key informant interviews of contact tracers and their supervisors, and a review of available reports on contact tracing were implemented to obtain data for this study.

Results

During the study period, 3,838 confirmed cases and 32,706 contacts were listed in the viral hemorrhagic fever and contact databases for the district (mean 8.5 contacts per case). Only 22.1% (852) of the confirmed cases in the study area were listed as contacts at the onset of their illness, which indicates incomplete identification and tracing of contacts. Challenges associated with effective contact tracing included lack of community trust, concealing of exposure information, political interference with recruitment of tracers, inadequate training of contact tracers, and incomplete EVD case and contact database. While the tracers noted the usefulness of community quarantine in facilitating their work, they also reported delayed or irregular supply of basic needs, such as food and water, which created resistance from the communities.

Conclusion

Multiple gaps in contact tracing attributed to a variety of factors associated with implementers, and communities were identified as obstacles that impeded timely control of the EVD outbreak in the WA of Sierra Leone. In future outbreaks, early community engagement and participation in contact tracing, establishment of appropriate mechanisms for selection, adequate training and supervision of qualified contact tracers, establishment of a well-managed and complete contact tracing database, and provision of basic needs to quarantined contacts are recommended as measures to enhance effective contact tracing.

The effect of food and frozen storage on the nutrient composition of some African fishes

Specimens of Tilapia zillii, Clarias lazera, Channa obscura, Synodontis schali, and Scomberomus tritor were collected between January and December 1990, covering the dry and rainy seasons. According to stomach analysis they were classified as either herbivorous, carnivorous, omnivorous, plankton consumers or invertebrate feeders. The crude protein, lipid and moisture contents were determined both for pre- and post frozen storage, with the exception of S. tritor (only post storage data). The percentage of total lipid and protein decreased significantly after each succeeding frozen storage, and the moisture content shows a trend similar to other parameters in all the species. Fresh fish is of the highest nutritional value. The feeding habit had some relationship with the muscle protein, fat and moisture content.