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IntroductionAlthough wastewater-based epidemiology (WBE) successfully functioned as a tool for monitoring the coronavirus disease 2019 (COVID-19) pandemic globally, relatively little is known about its utility in low-income countries. This study aimed to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater, estimate the number of infected individuals in the catchment areas, and correlate the results with the clinically reported COVID-19 cases in Addis Ababa, Ethiopia.MethodsA total of 323 influent and 33 effluent wastewater samples were collected from three Wastewater Treatment Plants (WWTPs) using a 24-h composite Moore swab sampling method from February to November 2023. The virus was captured using Ceres Nanotrap® Enhancement Reagent 2 and Nanotrap® Microbiome A Particles, and then nucleic acids were extracted using the Qiagen QIAamp Viral RNA Mini Kit. The ThermoFisher TaqPath™ COVID-19 kit was applied to perform real-time reverse transcriptase polymerase chain reaction (qRT-PCR) to quantify the SARS-CoV-2 RNA. Wastewater viral concentrations were normalized using flow rate and number of people served. In the sampling period, spearman correlation was used to compare the SARS-CoV-2 target gene concentration to the reported COVID-19 cases. The numbers of infected individuals under each treatment plant were calculated considering the target genes’ concentration, the flow rate of treatment plants, a gram of feces per person-day, and RNA copies per gram of feces.ResultsSARS-CoV-2 was detected in 94% of untreated wastewater samples. All effluent wastewater samples (n = 22) from the upflow anaerobic sludge blanket (UASB) reactor and membrane bioreactor (MBR) technology were SARS-COV-2 RNA negative. In contrast, two out of 11 effluents from Waste Stabilization Pond were found positive. Positive correlations were observed between the weekly average SARS-CoV-2 concentration and the cumulative weekly reported COVID-19 cases in Addis Ababa. The estimated number of infected people in the Kality Treatment catchment area was 330 times the number of COVID-19 cases reported during the study period in Addis Ababa.DiscussionThis study revealed that SARS-CoV-2 was circulating in the community and confirmed previous reports of more asymptomatic COVID-19 cases in Ethiopia. Additionally, this study provides further evidence of the importance of wastewater-based surveillance in general to monitor infectious diseases in low-income settings.ConclusionWastewater-based surveillance of SARS-CoV-2 can be a useful method for tracking the increment of COVID-19 cases before it spreads widely throughout the community.

In 2023, Africa experienced 180 public health emergencies, of which 90% were infectious diseases and 75% were related to zoonotic diseases. Testing capacity for epidemic-prone diseases is essential to enable rapid and accurate identification of causative agents, and for action to prevent disease spread. Moreover, testing is pivotal in monitoring disease transmission, evaluating public health interventions and informing targeted resource allocation during outbreaks. An online, self-assessment survey was conducted in African Union Member States to identify major challenges in testing for epidemic-prone diseases. The survey assessed current capacity for diagnosing priority epidemic-prone diseases at different laboratory levels. It explored challenges in establishing and maintaining testing capacity to improve outbreak response and mitigate public health impact. Survey data analysed diagnostic capacity for priority infectious diseases, diagnostic technologies in use, existing surveillance programmes and challenges limiting diagnostic capacity, by country. The survey result from 15 Member States who responded to the survey, showed high variability in testing capacity and technologies across countries and diverse factors limiting testing capacity for certain priority diseases like dengue and Crimean-Congo haemorrhagic fever. At the same time diagnostic capacity is better for coronavirus disease 2019 (COVID-19), polio, and measles due to previous investments. Unfortunately, many countries are not utilizing multiplex testing, despite its potential to improve diagnostic access. The challenges of limited laboratory capacity for testing future outbreaks are indeed significant. Recent disease outbreaks in Africa have underscored the urgent need to strengthen diagnostic capacity and introduce cost-effective technologies. Small sample sizes and differing disease prioritisation within each country limited the analysis. These findings suggest the benefits of evaluating laboratory testing capacity for epidemic-prone diseases and highlight the importance of effectively addressing challenges to detect diseases and prevent future pandemics.

Abstract Background Despite promising efforts, substantial deaths occurred during the neonatal period. According to estimates from the World Health Organization (WHO), Ethiopia is among the top 10 nations with the highest number of neonatal deaths in 2020 alone. This staggering amount makes it difficult to achieve the SDG (Sustainable Development Goals) target that calls for all nations to work hard to meet a neonatal mortality rate target of ≤ 12 deaths per 1,000 live births by 2030. We evaluated neonatal mortality and it’s contributing factors among newborns admitted to the Neonatal Intensive Care Unit (NICU) at Hawassa University Comprehensive Specialized Hospital (HUCSH). Methods A hospital-based retrospective cross-sectional study on neonates admitted to the NICU from May 2021 to April 2022 was carried out at Hawassa University Comprehensive Specialized Hospital. From the admitted 1044 cases over the study period, 225 babies were sampled using a systematic random sampling procedure. The relationship between variables was determined using bivariate and multivariable analyses, and statistically significant relations were indicated at p-values less than 0.05. Results The magnitude of neonatal death was 14.2% (95% CI: 0.099–0.195). The most common causes of neonatal death were prematurity 14 (43.8%), sepsis 9 (28.1%), Perinatal asphyxia 6 (18.8%), and congenital malformations 3 (9.4%). The overall neonatal mortality rate was 28 per 1000 neonate days. Neonates who had birth asphyxia were 7.28 times more probable (AOR = 7.28; 95% CI: 2.367, 9.02) to die. Newborns who encountered infection within the NICU were 8.17 times more likely (AOR = 8.17; 95% CI: 1.84, 36.23) to die. Conclusion The prevalence of newborn death is excessively high. The most common causes of mortality identified were prematurity, sepsis, perinatal asphyxia and congenital anomalies. To avert these causes, we demand that antenatal care services be implemented appropriately, delivery care quality be improved, and appropriate neonatal care and treatment be made available.

ABSTRACTThe Africa Centres for Disease Control and Prevention Biosafety and Biosecurity Initiative being implemented across the 55 African Union Member States is presented. Based on consultations with Member States between 2019 and 2021, national-level capacity gaps were identified which informed the biosafety and biosecurity 5-year (2021–2025) strategic plan. The process of identifying national gaps, development, implementation and monitoring of the 5-year strategic plan is described. Notable achievements include development of a regional biosafety and biosecurity legislative framework now approved by African Union structures and process of domestication that has started in some countries; establishment and operationalisation of multi-sectoral regional biosafety and biosecurity technical working groups tasked with coordinating and monitoring implementation of the initiative, development and implementation of an accessible and regionally endorsed Regional Training and Certification Program for Biosafety and Biosecurity Professionals; establishment of a Regional Centre of Excellence for biosafety and biosecurity from where two cohorts of students in the two areas of biorisk management (16 students from 8 countries) and biological waste management (19 students from 10 countries) have been trained and development of a Regulatory and Certification Framework for Institutions Handling High-Risk Pathogens with three components of minimum standards of biosafety and biosecurity for high-containment facilities, a standard evaluation checklist for checking compliance and a certification framework for authorising performance of tasks related to dangerous pathogens. A guidance document with step-by-step process on how to translate regional successes to national implementation was developed and published. Based on notable regional successes of the initiative, Africa CDC co-chaired the Global Health Security Agenda Action Package 3 on Prevention and the Africa Signature Initiative Biosafety and Biosecurity Working Group. Challenges of delayed implementation due to the COVID-19 pandemic, limited resources to implement all planned activities and limited staff dedicated to biosafety and biosecuruty at Africa CDC.

Introduction: Event-based surveillance (EBS) is a critical component of Early Warning, Alert and Response (EWAR) capacity needed for outbreak prevention and control. To better understand existing EBS and monitor the progress of capacity-building efforts over time, Africa CDC developed an EBS scorecard as part of a revision to the EBS Framework. Methods: We distributed the scorecard to African Union (AU) Member States (MSs). Survey responses from the MSs’ human health sector were aggregated, cleaned, and analysed. MS, regional, and continental EBS capacity was assessed. Results: Between 21 July 2022 and 4 April 2023, a total of 63 respondents representing 49 (89%) of 55 MSs completed the survey. Given Africa CDC’s public health mandate, we acknowledged the importance of One Health collaboration in MSs but focused on and analysed only the human health sector responses. Thirty-four (71%) MSs stated having EBS in place; hotline was the most common type of EBS implemented (76%). Seventeen (50%) MSs reported multisectoral, One Health collaboration as part of EBS implementation. Scorecard outcomes showed a minimal (score of

No abstract available.

Event-based surveillance (EBS) is a core component of early warning surveillance. In 2018, Africa CDC developed the first edition of an event-based surveillance framework to guide African Union Member States in implementing EBS. Country experiences during the COVID-19 pandemic demonstrated the value of data from non-traditional sources for real time situational awareness; at the same time revealed the huge gaps in strengthening this arm of surveillance. Learning from these lessons and to begin to close those gaps, Africa CDC convened subject matter experts from African Union Member States and technical partners to develop the second edition of the EBS framework, 2023 and its training materials. The revised version includes additional sections such as, the multi-sectoral one health collaboration in EBS, monitoring and evaluation, cross border EBS, and use of event management systems. The current manuscript provides an overview of the 2023 Africa CDC EBS framework and highlights experience in two countries that have successfully employed this resource in their implementation efforts.

National laboratories are a fundamental capacity for public health, contributing to disease surveillance and outbreak response. The establishment of regional laboratory networks has been posited as a means of improving health security across multiple countries. Our study objective was to assess whether membership in regional laboratory networks in Africa has an effect on national health security capacities and outbreak response. We conducted a literature review to select regional laboratory networks in the Eastern and Western African regions. We examined data from the World Health Organization Joint External Evaluation (JEE) mission reports, the 2018 WHO States Parties Annual Report (SPAR), and the 2019 Global Health Security Index (GHS). We compared the average scores of countries that are members of a regional laboratory network to those that are not. We also assessed country-level diagnostic and testing indicators during the COVID-19 pandemic. We found no significant differences in any of the selected health security metrics for member versus non-member countries of the either the East Africa Public Health Laboratory Networking Project (EAPHLNP) in the Eastern Africa region, nor for the West African Network of Clinical Laboratories (RESAOLAB) in the Western Africa region. No statistically significant differences were observed in COVID-19 testing rates in either region. Small sample sizes and the inherent heterogeneities in governance, health, and other factors between countries within and between regions limited all analyses. These results suggest potential benefit in setting baseline capacity for network inclusion and developing regional metrics for measuring network impact, but also beyond national health security capacities, other effects that may be required to justify continued support for regional laboratory networks.

We propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order of detection. Within IIb, the cause of the current global outbreak, we identified multiple lineages (A.1, A.2, A.1.1 and B.1) to support real-time genomic surveillance.

Objectives:Coronavirus disease 2019 was declared a global pandemic in March 2020 with correct and early detection of cases using laboratory testing central to the response. Hence, the establishment of quality management systems and monitoring their implementation are critical. This study describes the experience of implementing the COVID-19 Laboratory Testing and Certification Program (CoLTeP) in Africa.MethodsPrivate and public laboratories conducting SARS-CoV-2 testing using polymerase chain reaction were enrolled and assessed for quality and safety using the CoLTeP checklists.ResultsA total of 84 laboratories from 7 countries were assessed between April 2021 to December 2021 with 52% of these from the private sector. Among them, 64% attained 5 stars and were certified. Section 4 had the highest average score of 92% and the lowest of 78% in Section 3. Also, 82% of non-conformities (NCs) were related to sample collection, transportation, and risk assessments. Non-availability, inconsistency in performing, recording, instituting corrective actions for failed internal and external quality controls were among major NCs reported.ConclusionsLaboratories identified for SARS-CoV-2 testing by public and private institutions mostly met the requirements for quality and safe testing as measured by the CoLTeP checklist.

Abstract Objective The COVID-19 pandemic is a biosecurity threat, and many resource-rich countries are stockpiling and/or making plans to secure supplies of vaccine, therapeutics, and diagnostics for their citizens. We review the products that are being investigated for the prevention, diagnosis, and treatment of COVID-19; discuss the challenges that countries in sub-Saharan Africa may face with access to COVID-19 vaccine, therapeutics, and diagnostics due to the limited capacity to manufacture them in Africa; and make recommendations on actions to mitigate these challenges and ensure health security in sub-Saharan Africa during this unprecedented pandemic and future public-health crises. Main body Sub-Saharan Africa will not be self-reliant for COVID-19 vaccines when they are developed. It can, however, take advantage of existing initiatives aimed at supporting COVID-19 vaccine access to resource-limited settings such as partnership with AstraZeneca, the Coalition for Epidemic Preparedness and Innovation, the Global Alliance for Vaccine and Immunisation, the Serum Institute of India, and the World Health Organization’s COVID-19 Technology Access Pool. Accessing effective COVID-19 therapeutics will also be a major challenge for countries in sub-Saharan Africa, as production of therapeutics is frequently geared towards profitable Western markets and is ill-adapted to sub-Saharan Africa realities. The region can benefit from pooled procurement of COVID-19 therapy by the Africa Centres for Disease Control and Prevention in partnership with the African Union. If the use of convalescent plasma for the treatment of patients who are severely ill is found to be effective, access to the product will be minimally challenging since the region has a pool of recovered patients and human resources that can man supportive laboratories. The region also needs to drive the local development of rapid-test kits and other diagnostics for COVID-19. Conclusion Access to vaccines, therapeutics, and diagnostics for COVID-19 will be a challenge for sub-Saharan Africans. This challenge should be confronted by collaborating with vaccine developers; pooled procurement of COVID-19 therapeutics; and local development of testing and diagnostic materials. The COVID-19 pandemic should be a wake-up call for sub-Saharan Africa to build vaccines, therapeutics, and diagnostics manufacturing capacity as one of the resources needed to address public-health crises.

BackgroundEthiopia is one of the sub-Saharan countries hit hard by the HIV epidemic. Previous studies have shown that subtype C dominates the Ethiopian HIV-1 epidemic, but the evolutionary and temporal dynamics of HIV-1 in Ethiopia have not been closely scrutinized. Understanding the evolutionary and epidemiological pattern of HIV is vital to monitor the spread, evaluate and implement HIV prevention strategies.MethodsWe analyzed 1,276 Ethiopian HIV-1 subtype C polymerase (pol sequences), including 144 newly generated sequences, collected from different parts of the country from 1986 to 2017. We employed state-of-art maximum likelihood and Bayesian phylodynamic analyses to comprehensively describe the evolutionary dynamics of the HIV-1 epidemic in Ethiopia. We used Bayesian phylodynamic models to estimate the dynamics of the effective population size (Ne) and reproductive numbers (Re) through time for the HIV epidemic in Ethiopia.ResultsOur analysis revealed that the Ethiopian HIV-1 epidemic originated from two independent introductions at the beginning of the 1970s and 1980s from eastern and southern African countries, respectively, followed by epidemic growth reaching its maximum in the early 1990s. We identified three large clusters with a majority of Ethiopian sequences. Phylodynamic analyses revealed that all three clusters were characterized by high transmission rates during the early epidemic, followed by a decline in HIV-1 transmissions after 1990. Re was high (4–6) during the earlier time of the epidemic but dropped significantly and remained low (Re

Seth Inzaule and co-authors discuss implications of the COVID-19 pandemic for health in African countries.

Abstract Background Despite progress towards achieving UNAIDS 90–90-90 goals, barriers persist in laboratory systems in sub-Saharan Africa (SSA) restricting scale up of early infant diagnosis (EID) and viral load (VL) test monitoring of patients on antiretroviral therapy. If these facilities and system challenges persist, they may undermine recorded gains and appropriate management of patients. The aim of this review is to identify Public Private Partnerships (PPP) in SSA that have resolved systemic barriers within the VL and EID treatment cascade and demonstrated impact in the scale up of VL and EID. Methods We queried five HIV and TB laboratory databases from 2007 to 2017 for studies related to laboratory system strengthening and PPP. We identified, screened and included PPPs that demonstrated evidence in alleviating known system level barriers to scale up national VL and EID testing programs. PPPs that improved associated systems from the point of viral load test request to the use of the test result for patient management were deemed eligible. Results We identified six PPPs collaborations with multiple activities in select countries that are contributing to address challenges to scale up national viral load programs. One of the six PPPs reached 14.5 million patients in remote communities and transported up to 400,000 specimens in a year. Another PPP enabled an unprecedented 94% of specimens to reach national laboratory through improved sample referral network and enabled a cost savings of 62%. Also PPPs reduced cost of reagents and enabled 300,000 tested infants to be enrolled in care as well as reduced turnaround time of reporting results by 50%. Conclusions Our review identified the benefits, enabling factors, and associated challenges for public and private sectors to engage in PPPs. PPP contributions to laboratory systems strengthening are a model and present opportunities that can be leveraged to strengthen systems to achieve the UNAIDS 90–90-90 treatment targets for HIV/AIDS. Despite growing emphasis on engaging the private sector as a critical partner to address global disease burden, PPPs that specifically strengthen laboratories, the cornerstone of public health programs, remain largely untapped.

Coronavirus disease 2019 (COVID 19) has had serious social, economic, and health effects globally. The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV- 2), which was first announced in December 2019 has resulted in more than 24 million infections. There is paucity of knowledge on the role of risk perception in the adoption of public health interventions needed to control the spread of COVID 19 infections within communities. This was a scoping review and documents how risk perception may be a major challenge for populations to adopt and implement different behavioral changes recommended to curtail the spread COVID- 19 pandemic in sub-Saharan Africa; and seeks to proffer solutions on how the identified challenges can be addressed drawing from lessons learnt from previous epidemics within the region. Database search of Google Scholar, PubMed, Research Gate among others were performed using related keywords to identify relevant journals and lists of primary articles. Culture, religious beliefs and poverty may influence how populations respond to infectious disease outbreaks. Risk strategies that focus only on biomedical approaches to control the COVID-19 pandemic may not mobilize the needed behavioral change. Lessons learnt from HIV and Ebola epidemics showed that involvement of communities could help transform weak adoption of public health measures when measures were framed in the relevant cultural context. An understanding of the factors influencing risk perception is needed to design appropriate risk communication strategies. Community engagement and reliance on local communication networks could promote mutual trust and increase the uptake of public-health interventions.

No abstract available.

BACKGROUND:The HIV-1 epidemic in Ethiopia has been shown to be dominated by two phylogenetically distinct subtype C clades, the Ethiopian (C'-ET) and East African (C-EA) clades, however, little is known about the temporal dynamics of the HIV epidemic with respect to subtypes and distinct clades. Moreover, there is only limited information concerning transmission of HIV-1 drug resistance (TDR) in the country. METHODS:A cross-sectional survey was conducted among young antiretroviral therapy (ART)-naïve individuals recently diagnosed with HIV infection, in Gondar, Ethiopia, 2011-2013 using the WHO recommended threshold survey. A total of 84 study participants with a median age of 22 years were enrolled. HIV-1 genotyping was performed and investigated for drug resistance in 67 individuals. Phylogenetic analyses were performed on all available HIV sequences obtained from Gondar (n = 301) which were used to define subtype C clades, temporal trends and local transmission clusters. Dating of transmission clusters was performed using BEAST. RESULT:Four of 67 individuals (6.0%) carried a HIV drug resistance mutation strain, all associated with non-nucleoside reverse transcriptase inhibitors (NNRTI). Strains of the C-EA clade were most prevalent as we found no evidence of temporal changes during this time period. However, strains of the C-SA clade, prevalent in Southern Africa, have been introduced in Ethiopia, and became more abundant during the study period. The oldest Gondar transmission clusters dated back to 1980 (C-EA), 1983 (C-SA) and 1990 (C'-ET) indicating the presence of strains of different subtype C clades at about the same time point in Gondar. Moreover, some of the larger clusters dated back to the 1980s but transmissions within clusters have been ongoing up till end of the study period. Besides being associated with more sequences and larger clusters, the C-EA clade sequences were also associated with clustering of HIVDR sequences. One cluster was associated with the G190A mutation and showed onward transmissions at high rate. CONCLUSION:TDR was detected in 6.0% of the sequenced samples and confirmed pervious reports that the two subtype C clades, C-EA and C'-ET, are common in Ethiopia. Moreover, the findings indicated an increased diversity in the epidemic as well as differences in transmission clusters sizes of the different clades and association with resistance mutations. These findings provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.

No abstract available.

Background: In 2010, a National Laboratory Strategic Plan was set forth in Ethiopia to strengthen laboratory quality systems and set the stage for laboratory accreditation. As a result, the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme was initiated in 45 Ethiopian laboratories. Objectives: This article discusses the implementation of the programme, the findings from the evaluation process and key challenges. Methods: The 45 laboratories were divided into two consecutive cohorts and staff from each laboratory participated in SLMTA training and improvement projects. The average amount of supportive supervision conducted in the laboratories was 68 hours for cohort I and two hoursfor cohort II. Baseline and exit audits were conducted in 44 of the laboratories and percent compliance was determined using a checklist with scores divided into zero- to five-star ratinglevels. Results: Improvements, ranging from < 1 to 51 percentage points, were noted in 42 laboratories, whilst decreases were recorded in two. The average scores at the baseline and exit audits were 40% and 58% for cohort I (p < 0.01); and 42% and 53% for cohort II (p < 0.01),respectively. The p-value for difference between cohorts was 0.07. At the exit audit, 61% ofthe first and 48% of the second cohort laboratories achieved an increase in star rating. Poor awareness, lack of harmonisation with other facility activities and the absence of a quality manual were challenges identified. Conclusion: Improvements resulting from SLMTA implementation are encouraging. Continuous advocacy at all levels of the health system is needed to ensure involvement of stakeholders and integration with other improvement initiatives and routine activities.

Background: Early diagnosis of infants infected with HIV (EID) and early initiation of treatment significantly reduces the rate of disease progression and mortality. One of the challengesto identification of HIV-1-infected infants is availability and/or access to quality molecular laboratory facilities which perform molecular virologic assays suitable for accurate identificationof the HIV status of infants. Method: We conducted a joint site assessment and designed laboratories for the expansion of DNA polymerase chain reaction (PCR) testing based on dried blood spot (DBS) for EID insix regions of Ethiopia. Training of appropriate laboratory technologists and development of required documentation including standard operating procedures (SOPs) was carried out. The impact of the expansion of EID laboratories was assessed by the number of tests performed as well as the turn-around time. Results: DNA PCR for EID was introduced in 2008 in six regions. From April 2006 to April 2008, a total of 2848 infants had been tested centrally at the Ethiopian Health and Nutrition Research Institute (EHNRI) in Addis Ababa, and which was then the only laboratory with the capability to perform EID; 546 (19.2%) of the samples were positive. By November 2010, EHNRI and the six laboratories had tested an additional 16 985 HIV-exposed infants, of which 1915 (11.3%) were positive. The median turn-around time for test results was 14 days (range 14−21 days). Conclusion: Expansion of HIV DNA PCR testing facilities that can provide quality and reliable results is feasible in resource-limited settings. Regular supervision and monitoring for quality assurance of these laboratories is essential to maintain accuracy of testing.

Author(s): Seth C. Inzaule 1, Pascale Ondoa 2, Marguerite Massinga Loembe 1, Yenew Kebede Tebeje 1, Ahmed E Ogwell Ouma 1, John N. Nkengasong 1,* Summary points Coronavirus Disease 2019 [...]