Baobab Index

Genetic introgression from Neanderthals and Denisovans shaped modern human genomes; however, introgressed structural variants (SVs ≥ 50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) haploid genomes with 94 published assemblies of diverse ancestry to infer an introgressed SV map. Introgressed SVs are enriched in genes (47%), including critical genomic disorder regions, and are most abundant in PNG genomes. We identified 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping of these 98 assemblies across 1363 samples revealed 16 adaptive SVs, many associated with immune-related genes and expression, in the PNG genomes. We hypothesize that archaic SVs contributed to reproductive success, underscoring introgression as a major force in human adaptive evolution.

Near Oceanic populations harbor substantial cultural, phenotypic, and genetic diversity yet are drastically underrepresented in human genomics. We generated 177 high-coverage Near Oceanian whole genomes and analyzed them alongside 1284 worldwide genomes, revealing major distinctions among and within islands, including long-term isolation and strong population bottlenecks. We reconstructed 1.897 billion base pairs of the archaic genome, including 831.9 million base pairs of Denisovan sequence, and found evidence for introgression from three Denisovan-like groups in Near Oceanians and adaptive Denisovan introgression at

Biallelic variants in the minor spliceosomal gene RNU4ATAC were successively identified in Taybi-Linder/Microcephalic osteodysplastic primordial dwarfism type I, Roifman, and Lowry-Wood syndromes, which are characterized by variable microcephaly, short stature, neurodevelopmental impairment, skeletal dysplasia, and immunodeficiency. Two-thirds of the reported individuals present with Taybi-Linder syndrome, the first-described and most severe form. We collected clinical and molecular data from individuals with biallelic RNU4ATAC variants through various French and European networks and clinics to refine the phenotypic spectrum of RNU4ATAC-opathies. We enrolled 69 participants and identified 18 new pathogenic variants. We report a significant proportion of attenuated or atypical presentations, novel rare symptoms, and, unexpectedly, a broad spectrum of autoimmune or inflammatory manifestations, affecting nearly half of the participants. Integrating our data with the 109 published cases, we propose a novel classification based on the main manifestations, immunodeficiency, and microcephalic primordial dwarfism. Using computer-assisted facial analysis, we also demonstrated the existence of a specific dysmorphic pattern in RNU4ATAC-opathies that is distinct among some sub-syndromes. We present a large cohort of individuals with RNU4ATAC-opathies and expand the phenotypic spectrum to paucisymptomatic forms, indicating that these diseases are likely to remain underdiagnosed.

Malaria parasite genomes have been generated predominantly using Illumina short-read sequencing that requires expensive equipment, is time-consuming with complex protocols, and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants. The portable Oxford Nanopore Technologies MinION platform generates long reads in real time and may overcome these limitations. We present compelling evidence that Nanopore sequencing delivers valuable additional information for malaria parasites with similar data fidelity for single nucleotide variant (SNV) calls compared to standard Illumina whole-genome sequencing. We demonstrate this through sequencing of pure

several studies have shown the evolution of SARS-CoV-2 between 2020 and 2023 in Guinea. This study provides updated information on the circulation dynamics of SARS-CoV-2 from 2024 to 2025 and the variants circulating in Guinea. as part of the integrated influenza/COVID-19 sentinel surveillance program, 2423 nasopharyngeal samples were analysed using RT-PCR, and those positive for SARS-CoV-2 were sequenced using the Illumina COVIDSeq Assay protocol. all age groups, ranging from <2 years to > 64 years, were affected by COVID-19, with an average SARS-CoV-2 positivity rate of 2.3%. The virus showed sporadic activity throughout the 2024-2025 period, with a higher level of activity during epidemiological week 42 (October) of 2024. Genomic analysis showed that only the Omicron variant circulated, along with its subvariants JN.1 and LF.7, in 2024. Subvariant LF.7 and recombinant XFJ also circulated in 2025. SARS-CoV-2 subvariants continue to circulate sporadically in Guinea, with the XFJ recombinant having been detected in humans. Therefore, it is imperative to strengthen sentinel, genomic, and environmental surveillance for the early detection of any new COVID-19 outbreak and the potential emergence of new variants.

Terpenes represent a diverse class of plant secondary metabolites that play important roles in development, ecological interactions, and aroma, and are synthesized by the terpene synthase (TPS) gene family. To investigate the evolutionary history and regulatory diversification of this family in coffee, we performed a genome-wide analysis of TPS genes in

Non-typeable A systematic search of PubMed, Scopus, Web of Science, Google Scholar, and ScienceDirect was conducted up to May 2025. Eligible studies reporting NT-Sp carriage, molecular typing, or AMR profiles were included. Data extraction and quality assessment followed PRISMA guidelines. A meta-analysis was performed to estimate pooled prevalence of NT-Sp carriage and resistance, with subgroup and meta-regression analyses exploring heterogeneity. Methodological quality was assessed using the Newcastle-Ottawa Scale adapted for cross-sectional studies. Only open-access and free full-text articles were included, which may have introduced selection bias. Forty studies from 23 countries were included. The pooled NT-Sp carriage prevalence was 4.64% (95% CI: 2.78%-6.92%), with substantial heterogeneity ( NT-Sp is a globally distributed and genetically diverse pneumococcal subset with considerable AMR potential. Its persistence post-PCV introduction and resistance gene carriage highlights the need for improved detection, molecular surveillance, and consideration in next-generation vaccine development. Specifically, clinical laboratories in high-prevalence settings should adopt molecular methods (e.g., PCR or WGS) to detect NT-Sp in carriage surveillance; empirical antibiotic guidelines for pediatric respiratory infections should consider NT-Sp resistance patterns, particularly the high prevalence of co-trimoxazole resistance (67%) and next-generation PCV trials should include NT-Sp carriage as an exploratory endpoint. Integrating NT-Sp into global pneumococcal control strategies is essential.

Avian influenza viruses continue to pose significant zoonotic and pandemic threat globally, with low-pathogenic avian influenza A(H9N2) being of particular concern due to sustained circulation in poultry, adaptability, and repeated human spillover. This study investigated the detection and genetic characterization of influenza viruses at the animal-human interface in Ghana in 2022, using a nationwide cross-sectional One Health approach. Samples were collected from poultry, pigs, the environment, and animal handlers across backyard farms, commercial farms, and live bird markets. Laboratory testing was conducted using real-time RT-PCR, while statistical associations were assessed using chi-square and logistic regression. Whole-genome sequencing and phylogenetic analysis were performed on selected positive samples. Out of 4056 samples, 1516 were poultry samples. A(H9N2) was detected exclusively in poultry, with a prevalence of 5.67%. The Northern belt recorded the highest prevalence. Live bird markets had significantly higher odds of A(H9N2) detection compared with commercial farms (odds ratio: 15.37,

The information age, fueled by globalization and technological advancements, has transformed the data landscape, impacting decision-making, management, governance, and policy intervention across various sectors. The health sectors are no exception, experiencing a data explosion driven by ongoing research initiatives and advancements. This transformation necessitates a shift towards evidence-based practices, emphasizing the importance of high-quality, timely, accessible data at all levels. Data science offers a compelling solution, particularly in Africa, where resource scarcity demands prudent allocation. By leveraging the abundance and diversity of data, data-driven decision-making and policymaking can be fostered. This approach holds immense potential to develop accurate, effective, measurable policies, addressing Africa's healthcare challenges. In this paper, we delve into the need for leveraging data on health decision-making and policy implementation in Africa. We further explore the intricate relationship between the burgeoning field of data science, Africa's persistent infrastructural deficiencies, and the continent's ongoing healthcare transformation challenges. We use available data, publications, and information resources across Africa to highlight the challenges, and opportunities and provide a roadmap and recommendation involving data-driven and policy-making decisions in the healthcare sector. We conclude by making proposals, and recommendations, and advocating for global and local approaches to data sharing and capacity-building initiatives by policymakers in collaboration with researchers to foster a system of data-driven decisions in health care. We emphasize the need for data-sharing partnership model, turning African biomedical data into treasures and valuable assets, and have highlighted different data elements that can contribute to data-driven decisions in healthcare.

Bloodstream infections (BSIs) pose a significant global health challenge, particularly in developing countries. Neonates are highly vulnerable due to underdeveloped immune systems and immature physical barriers, a risk amplified by poor hygiene and limited healthcare access in low- and middle-income countries (LMICs), leading to an estimated incidence of 5.5 cases per 1000 live births. This review aims to provide insight into the diagnostic and therapeutic challenges of neonatal BSIs in developing countries and to identify prospects for improving their diagnosis and treatment. This review employed a nonsystematic narrative approach. A comprehensive literature search was conducted using multiple electronic databases, including PubMed/MEDLINE, Scopus, Web of Science, Google Scholar, and ScienceDirect. The search prioritized peer-reviewed articles, clinical trials, and systematic reviews published within the past decade (2015-2025). Diagnosis is severely hampered by nonspecific symptoms and limitations of conventional methods like blood culture, especially in resource-constrained settings lacking advanced molecular diagnostics. This often necessitates empirical antibiotic treatment, which intensifies antimicrobial resistance (AMR), complicates therapy, and leads to adverse outcomes. Promising solutions include rapid diagnostic technologies, artificial intelligence (AI), clinical decision support systems (CDSS), novel antimicrobial agents, alternative therapies like maternal immunization, and robust public health strategies, such as antimicrobial stewardship and stringent infection prevention. Addressing this complex issue requires concerted global efforts, substantial investment in local laboratory infrastructure, enhanced healthcare provider training, and the development of context-appropriate, affordable solutions to improve neonatal outcomes in LMICs.