Bacteriology testing and antimicrobial resistance detection capacity of national tiered laboratory networks in sub-Saharan Africa: an analysis from 14 countries.

Background: Accurate detection of antimicrobial resistance (AMR) depends on adequate laboratory capacity. We aimed to document key weaknesses hindering AMR detection at various tiers of laboratory networks in 14 countries in sub-Saharan Africa, and analyse their significance in AMR surveillance and policies.

Methods: In this analysis, we obtained retrospective data on AMR and antimicrobial consumption from 14 countries participating in the Mapping Antimicrobial Resistance and Antimicrobial Use Partnership between May 1, 2019, and June 30, 2020.

Longitudinal wastewater-based surveillance of SARS-CoV-2 during 2023 in Ethiopia.

Introduction: Although 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.

Methods: A 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 Looming Threat of Dengue Fever: The Africa Context.

In Africa, compared to 2019, dengue infections have surged ninefold by December 2023, with over 270 000 cases and 753 deaths reported across 18 African Union (AU) Member States. This commentary synthesises the context of dengue outbreaks in Africa and provides recommendations for sustainable control. In 2023, 18 African Union Member States reported outbreaks of dengue, among which seven had ongoing armed conflicts.

Establishing an early warning event management system at Africa CDC.

Africa is home to hotspots of disease emergence and re-emergence. To adequately detect and respond to these health threats, early warning systems inclusive of event-based surveillance (EBS) are needed. However, data systems to manage these events are not readily available.

Predictors of neonatal mortality among neonates admitted to the neonatal intensive care unit at Hawassa University Comprehensive Specialized Hospital, Sidama regional state, Ethiopia.

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.

Boosting pathogen genomics and bioinformatics workforce in Africa.

Next-generation sequencing (NGS) of genomic data has established its fundamental value in public health surveillance, research and development, and precision medicine. In Africa, severe shortages of competent experts in genomics and bioinformatics, few opportunities for research, and inadequate genomic infrastructure have had a knock-on effect on the use of NGS technologies for research and public health practice. Several reasons-ranging from poor funding, inadequate infrastructure for training and practice, to brain drain-might partly account for the scarcity of genomics and bioinformatics expertise in the region.

Insights into SARS-CoV-2 in Angola during the COVID-19 peak: Molecular epidemiology and genome surveillance.

Background: In Angola, COVID-19 cases have been reported in all provinces, resulting in >105,000 cases and >1900 deaths. However, no detailed genomic surveillance into the introduction and spread of the SARS-CoV-2 virus has been conducted in Angola. We aimed to investigate the emergence and epidemic progression during the peak of the COVID-19 pandemic in Angola.

Evaluating event-based surveillance capacity in Africa: Use of the Africa CDC scorecard, 2022-2023.

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).

Building Integrated Testing Programs for Infectious Diseases.

In the past 2 decades, testing services for diseases such as human immunodeficiency virus (HIV), tuberculosis, and malaria have expanded dramatically. Investments in testing capacity and supportive health systems have often been disease specific, resulting in siloed testing programs with suboptimal capacity, reduced efficiency, and limited ability to introduce additional tests or respond to new outbreaks. Emergency demand for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing overcame these silos and demonstrated the feasibility of integrated testing.

Examining 7 years of implementing quality management systems in medical laboratories in sub-Saharan Africa.

Background: Achievement of ISO15189 accreditation demonstrates competency of a laboratory to conduct testing. Three programmes were developed to facilitate achievement of accreditation in low- and middle-income countries: Strengthening Laboratory Management Towards Accreditation (SLMTA), Stepwise Laboratory Improvement Process Towards Accreditation (SLIPTA) and Laboratory Quality Stepwise Implementation (LQSI).

Objective: To determine the level of accreditation and associated barriers and facilitators among medical laboratories in the WHO-AFRO region by 2020.

Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus.

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.

Implementation of COVID-19 Laboratory Testing Certification Program (CoLTeP) in African Region.

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.

Molecular Epidemiology and Transmission Dynamics of the HIV-1 Epidemic in Ethiopia: Epidemic Decline Coincided With Behavioral Interventions Before ART Scale-Up.

Background: Ethiopia 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.

High Level of HIV Drug Resistance and Virologic Nonsuppression Among Female Sex Workers in Ethiopia: A Nationwide Cross-Sectional Study.

Objective: To determine viral load (VL) nonsuppression (VLN) rates, HIV drug resistance (HIVDR) prevalence, and associated factors among female sex workers (FSWs) in Ethiopia.

Methods: A cross-sectional biobehavioral survey was conducted among FSWs in 11 cities in Ethiopia in 2014. Whole blood was collected, and HIVDR genotyping was performed.

The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study.

Background: Although the first wave of the COVID-19 pandemic progressed more slowly in Africa than the rest of the world, by December, 2020, the second wave appeared to be much more aggressive with many more cases. To date, the pandemic situation in all 55 African Union (AU) Member States has not been comprehensively reviewed. We aimed to evaluate reported COVID-19 epidemiology data to better understand the pandemic's progression in Africa.

Genomic-informed pathogen surveillance in Africa: opportunities and challenges.

The ongoing COVID-19 pandemic has highlighted the need to incorporate pathogen genomics for enhanced disease surveillance and outbreak management in Africa. The genomics of SARS-CoV-2 has been instrumental to the timely development of diagnostics and vaccines and in elucidating transmission dynamics. Global disease control programmes, including those for tuberculosis, malaria, HIV, foodborne pathogens, and antimicrobial resistance, also recommend genomics-based surveillance as an integral strategy towards control and elimination of these diseases.

Role of public-private partnerships in achieving UNAIDS HIV treatment targets.

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.