Evaluating the accuracy of multiple rapid diagnostic tests for HIV detection in serum samples analysed during point-of-care proficiency testing assessments.

Background: HIV rapid diagnostic tests are crucial for timely diagnosis, especially in resource-limited settings. The World Health Organization recommends sensitivity ≥99 % and specificity ≥98 %. This study assessed RDT performance across South Africa's provinces using a proficiency testing program.

Comprehensive profiling and risk assessment of antibiotic resistomes in surface water and plastisphere by integrated shotgun metagenomics.

The ever-increasing microplastics (MPs) and antibiotic-resistance genes (ARGs) in aquatic ecosystems has become a serious global challenging issue. However, the impact of different pollution sources on microbiome and antibiotic resistome in surface water (SW) and plastisphere (PS) remains largely elusive. Here, shotgun metagenomics was used to analyze microbiome structure and antibiotic resistome in SW and PS under the influence of different pollution sources.

Empowering African Expertise: Enhancing Safety Data Integration and Signal Detection for COVID-19 Vaccines Through the African Union Smart Safety Surveillance Joint Signal Management Group.

Introduction: The COVID-19 pandemic accelerated new vaccine development. Limited safety data necessitated robust global safety surveillance to accurately identify and promptly communicate potential safety issues. The African Union Smart Safety Surveillance (AU-3S) program established the Joint Signal Management (JSM) group to support identification of potential vaccine safety concerns in five pilot countries (Ethiopia, Ghana, Kenya, Nigeria, South Africa), accounting for approximately 35% of the African population.

Migrant Health Country Profile tool (MHCP-t) for transforming health data collection and surveillance in the Middle East and North African (MENA) region: tool development protocol with embedded process evaluation.

Introduction: The Middle East and North Africa (MENA) region is characterised by major health disparities and complex migration flows. Yet, because of a lack of epidemiological data, there is an urgent need to strengthen routine data collection around migrant health and to define key indicators towards migrant health monitoring. To address this problem, we aim to design and pilot test the Migrant Health Country Profile tool (MHCP-t) which can collate country-level data collection around migration health data, policies and healthcare provision.

Hepatitis B infection (HBsAg and HBeAg) status among women attending antenatal care at public healthcare facilities of South Africa, 2017.

Eight years after WHO adopted a resolution to eliminate hepatitis B by the year 2030, the disease remains a global public health concern, with vertical transmission of HBV being a major obstacle to this goal. Our study aimed to determine the HBV infection status of pregnant women in South Africa at a national level to evaluate the risk of vertical transmission and provide evidence for public health decision-making. We conducted HBsAg testing on 1,942 HIV-uninfected and 2,312 HIV-infected pregnant women from South Africa's public health sector in 2017, followed by HBeAg testing on HBsAg-positive samples.

Characterization of NAT, GST, and CYP2E1 Genetic Variation in Sub-Saharan African Populations: Implications for Treatment of Tuberculosis and Other Diseases.

Tuberculosis (TB) is a major health burden in Africa. Although TB is treatable, anti-TB drugs are associated with adverse drug reactions (ADRs), which are partly attributed to pharmacogenetic variation. The distribution of star alleles (haplotypes) influencing anti-TB drug metabolism is unknown in many African populations.

Enhanced pathogen identification among patients with clinically suspected meningitis.

Background: Delayed or incorrect treatment of meningitis may result in adverse patient outcomes. However, laboratory testing in resource-limited settings is often limited to conventional diagnostic methods. We explored the utility of syndromic molecular assays for diagnosis.

Resistance mutations that distinguish HIV-1 envelopes with discordant VRC01 phenotypes from multi-lineage infections in the HVTN703/HPTN081 trial: implications for cross-resistance.

The Antibody Mediated Prevention (AMP) trials showed that passively infused VRC01, a broadly neutralizing antibody (bNAb) targeting the CD4 binding site (CD4bs) on the HIV-1 envelope protein (Env), protected against neutralization-sensitive viruses. We identified six individuals from the VRC01 treatment arm with multi-lineage breakthrough HIV-1 infections from HVTN703, where one variant was sensitive to VRC01 (IC < 25 ug/mL) but another was resistant. By comparing Env sequences of resistant and sensitive clones from each participant, we identified sites predicted to affect VRC01 neutralization and assessed the effect of their reversion in the VRC01-resistant clone on neutralization sensitivity.

Cohort profile: the potentially preventable burden of community-acquired pneumonia in South African adults in the era of widespread PCV13 immunisation and antiretroviral therapy roll-out, before and during the COVID-19 pandemic - the multicentre, multimethod PotPrev Study.

Purpose: In the setting of an established childhood pneumococcal vaccination programme with immediate initiation and treatment of antiretroviral therapy (ART) for people living with HIV (PLWH), the risk of adult pneumococcal community-acquired pneumonia (CAP) is not recently described. We aimed to investigate CAP incidence, recurrence, mortality, risk factors and microbiology before and during the COVID-19 pandemic.

Participants: Adults aged ≥18 years were enrolled in three South African provinces from March 2019 to October 2021, with a brief halt during the initial COVID-19 lockdown.

Genomic analysis of virulent, multidrug resistant Klebsiella pneumoniae and Klebsiella oxytoca from bloodstream infections, South Africa.

Unlabelled: The study investigated the resistome, virulome and mobilome of multidrug resistant (MDR) Klebsiella pneumoniae and Klebsiella oxytoca clinical isolates.

Methods: A total of 46 suspected Klebsiella species (spp.) were collected from blood cultures within the uMgungundlovu District in the KwaZulu-Natal Province.

Costs of Influenza Illness and Acute Respiratory Infections by Household Income Level: Catastrophic Health Expenditures and Implications for Health Equity.

Background: Seasonal influenza illness and acute respiratory infections can impose a substantial economic burden in low- and middle-income countries (LMICs). We assessed the cost of influenza illness and acute respiratory infections across household income strata.

Methods: We conducted a secondary analysis of data from a prior systematic review of costs of influenza and other respiratory illnesses in LMICs and contacted authors to obtain data on cost of illness (COI) for laboratory-confirmed influenza-like illness and acute respiratory infection.

A Global Collaborative Comparison of SARS-CoV-2 Antigenicity Across 15 Laboratories.

Setting up a global SARS-CoV-2 surveillance system requires an understanding of how virus isolation and propagation practices, use of animal or human sera, and different neutralisation assay platforms influence assessment of SARS-CoV-2 antigenicity. In this study, with the contribution of 15 independent laboratories across all WHO regions, we carried out a controlled analysis of neutralisation assay platforms using the first WHO International Standard for antibodies to SARS-CoV-2 variants of concern (source: NIBSC). Live virus isolates (source: WHO BioHub or individual labs) or spike plasmids (individual labs) for pseudovirus production were used to perform neutralisation assays using the same serum panels.

A generalised catalytic model to assess changes in risk for multiple reinfections with SARS-CoV-2.

Background: Monitoring trends in multiple infections with SARS-CoV-2, following several pandemic waves, provides insight into the biological characteristics of new variants, but also necessitates methods to understand the risk of multiple reinfections.

Objectives: We generalised a catalytic model designed to detect increases in the risk of SARS-CoV-2 reinfection, to assess the population-level risk of multiple reinfections.

Methods: The catalytic model assumes the risk of reinfection is proportional to observed infections and uses a Bayesian approach to fit model parameters to the number of nth infections among individuals that occur at least 90 days after a previous infection.

Molecular epidemiology of invasive group B Streptococcus in South Africa, 2019-2020.

Background: Group B Streptococcus (GBS) is a leading cause of neonatal meningitis and sepsis and an important cause of disease in adults. Capsular polysaccharide and protein-based GBS vaccines are currently under development.

Methods: Through national laboratory-based surveillance, invasive GBS isolates were collected from patients of all ages between 2019 and 2020.

Development of a luminex-based assay for the detection of anti-capripoxvirus and rift valley fever virus antibodies in domestic ruminants.

The three members of the genus capripoxvirus (CaPV), lumpy skin disease virus (LSDV), sheeppox virus (SPPV), and goatpox virus (GTPV) have common hosts and areas of overlapping geographical distribution with Rift Valley fever virus (RVFV). Hence, to ensure more cost-effective disease surveillance we developed and evaluated a Luminex assay for the simultaneous detection of antibodies against CaPV and RVFV in domestic ruminants. In cattle, the assay had a sensitivity (Se) of 98.

The importance of microbiology reference laboratories and adequate funding for infectious disease surveillance.

Microbiology reference laboratories perform a crucial role within public health systems. This role was especially evident during the COVID-19 pandemic. In this Viewpoint, we emphasise the importance of microbiology reference laboratories and highlight the types of digital data and expertise they provide, which benefit national and international public health.

Global impact of ten-valent and 13-valent pneumococcal conjugate vaccines on invasive pneumococcal disease in all ages (the PSERENADE project): a global surveillance analysis.

Background: Pneumococcal conjugate vaccines (PCVs) that are ten-valent (PCV10) and 13-valent (PCV13) became available in 2010. We evaluated their global impact on invasive pneumococcal disease (IPD) incidence in all ages.

Methods: Serotype-specific IPD cases and population denominators were obtained directly from surveillance sites using PCV10 or PCV13 in their national immunisation programmes and with a primary series uptake of at least 50%.

Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa.

The role of genomics in public health surveillance has been accentuated by its crucial contributions during the COVID-19 pandemic, demonstrating its potential in addressing global disease outbreaks. While Africa has made strides in expanding multi-pathogen genomic surveillance, the integration into foodborne disease (FBD) surveillance remains nascent. Here we highlight the critical components to strengthen and scale-up the integration of whole genome sequencing (WGS) in foodborne disease surveillance across the continent.

SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study.

Background: In low- and middle-income countries (LMICs) such as South Africa, there is paucity of data on SARS-CoV-2 infections among children attending school, including seroprevalence and transmission dynamics.

Objective: This pilot study aims to assess (1) the prevalence of self-reported or confirmed SARS-CoV-2 prior infections, COVID-19 symptoms (including long COVID), seroprevalence of SARS-CoV-2 antibodies, and general/mental health, (2) longitudinal changes in SARS-CoV-2 seroprevalence, and (3) SARS-CoV-2 acute infections, immune responses, transmission dynamics, and symptomatic versus asymptomatic contacts in a unique cohort of unvaccinated primary school learners, their parents, teachers, and close contacts in semirural primary school settings.

Methods: Learners (grades 1-7) from primary schools in KwaZulu-Natal, South Africa, their parents, and teachers will be invited to enroll into the COVID kids school study (CoKiDSS).

Neprilysin-Mediated Amyloid Beta Clearance and Its Therapeutic Implications in Neurodegenerative Disorders.

Neprilysin (NEP) is a neutral endopeptidase, important for the degradation of amyloid beta (Aβ) peptides and other neuropeptides, including enkephalins, substance P, and bradykinin, in the brain, that influences various physiological processes such as blood pressure homeostasis, pain perception, and neuroinflammation. NEP breaks down Aβ peptides into smaller fragments, preventing the development of detrimental aggregates such as Aβ plaques. NEP clears Aβ plaques predominantly by enzymatic breakdown in the extracellular space.

Recommendations for the optimal introduction of novel antibiotics to treat uncomplicated gonorrhoea in the face of increasing antimicrobial resistance: a case study with zoliflodacin.

New, first-in-class oral antibiotics like zoliflodacin, developed in a public-private partnership, require an optimal introduction strategy while ensuring antibiotic stewardship. Zoliflodacin, given as a single dose for uncomplicated urogenital gonorrhoea, recently demonstrated non-inferiority to ceftriaxone plus azithromycin and safety in a phase 3 randomised controlled trial. Following regulatory approval, zoliflodacin could improve sexually transmitted infection (STI) management and help address the threat of untreatable gonorrhoea, as levels of resistance to current first-line treatments increase.

Structure-based drug designing for potential antiviral activity of selected natural product against Monkeypox (Mpox) virus and its host targets.

Unlabelled: (MPV/MPXV/hMPXV) is a zoonotic infection that is a causative agent of monkeypox disease, which is mainly endemic in West and Central Africa regions, but recent trends suggested that the virus is transmitted around 116 countries worldwide and is still spreading in multiple non-endemic countries, causing global outbreaks. The current therapeutic options for Mpox are limited, with the WHO temporarily recommending smallpox drugs. This suggests an urgent need to discover new therapeutics that may target both viral and host markers involved in the virus life cycle.

Exploring polyamine metabolism of the yeast-like fungus, Emergomyces africanus.

Emergomyces africanus is a thermally dimorphic pathogen causing severe morbidity and mortality in immunocompromized patients. Its transition to a pathogenic yeast-like phase in the human host is a notable virulence mechanism. Recent studies suggest polyamines as key players in dimorphic switching, yet their precise functions remain enigmatic.