Baobab Index

Species distributed across heterogeneous environments often evolve locally adapted populations, but understanding how these persist in the presence of homogenizing gene flow remains puzzling. In Gabon, Anopheles coluzzii, a major African malaria mosquito, is found in various ecological settings, including urban areas, remote rural villages, and forested environments away from any human presence. This study investigates the genomic signatures of local adaptation in populations from distinct environments including the urban area of Libreville, and two proximate sites 10 km apart in the La Lopé National Park (LLP), a village and its sylvatic neighbourhood. Whole genome re-sequencing of 96 mosquitoes unveiled 5.9 million high-quality single nucleotide polymorphisms. Coalescent-based demographic analyses suggest an ∼12,000-year-old divergence between Libreville and La Lopé populations, followed by a secondary contact (∼4000 ybp) resulting in asymmetric effective gene flow. The urban population displayed reduced effective size, evidence of inbreeding, and strong selection pressures likely associated to insecticides or pollution present in urban settings, as suggested by the hard selective sweeps detected in genes involved in detoxification and insecticide resistance. In contrast, the two geographically proximate LLP populations showed larger effective sizes, and distinctive selective signals, notably soft-selective sweeps on the standing genetic variation. Although presumably neutral loci failed to discriminate between LLP populations, our findings support that microgeographic adaptation can swiftly emerge through selection on standing genetic variation despite gene flow. This study contributes to the growing understanding of evolution of populations in heterogeneous environments amid ongoing gene flow and how major malaria mosquitoes adapt to humans and its environment.

A novel

We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas are abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti are similar to those in the Americas and reveal the first wild example of dengue vsmRNAs. African Ae. aegypti display vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lack viruses, yet two commercial strains are deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs reveal viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generate stably infected cell lines which produce vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can resist viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.

Though being prevalent worldwide, Mansonella parasites are among the most neglected filarial nematodes. The true prevalence and genetic diversity of this genus have yet to be fully understood. Mansonella sp. "DEUX" is a recently described filarial nematode infecting humans and other primates in Gabon and Cameroon, although its status as distinct species has been controversial. We investigated four different polymorphic regions to further explore the genetic differences between Mansonella species and to support their status as distinct species. We screened whole blood samples collected in EDTA tubes from individuals from rural areas in Gabon for mono-infections with only one Mansonella species, either Mansonella sp. "DEUX" or Mansonella perstans, as determined by quantitative polymerase chain reaction (qPCR) targeting the ITS1 region. We also included nine blood samples from Togo that had been collected as dried blood spots on 903™ protein saver cards and identified as M. perstans mono-infection. We further amplified, sequenced, and analyzed three molecular marker regions cox1, 12S rDNA, and 28S rDNA for their potential to discriminate between the two Mansonella species. In total, 93 mono-infected blood samples were identified. Distinct single-nucleotide polymorphism (SNP) patterns for the two investigated Mansonella species were consistently detected in all four loci. The observed nucleotide divergences were comparable to other Onchocercidae family members. Species identification based on the ITS1 marker region was fully concordant with the SNP patterns in all samples. A complete genetic dimorphism could be observed in each of the four marker regions investigated. The four polymorphic markers, ITS1, cox1, 12S rDNA, and 28S rDNA, consistently demonstrated clear dimorphism between the two Mansonella species. Our results support the classification of Mansonella sp. "DEUX" as a distinct, nonrecombining Mansonella species within the Onchocercidae family.

The global decrease in species diversity from low to high latitudes is among the most robust biogeographic patterns

Effective diagnosis of Schistosoma haematobium is critical for disease management. However, current tools often lack sensitivity for low-intensity infections, a challenge noted in the recent WHO Roadmap for Neglected Tropical Diseases. This study aimed to evaluate a novel cell-free DNA (cfDNA) quantitative Polymerase Chain Reaction (qPCR) assay, utilizing 20 µl of plasma with crude DNA extraction. This approach intends to improve diagnostic accuracy and lower implementation barriers for molecular tests in field settings. We compared its performance against urine filtration microscopy and the Up-converting Reporter Particle Lateral Flow Circulating Anodic Antigen (UCP-LF CAA) test in pregnant women from Lambaréné, Gabon. A prospective cross-sectional study was conducted on 296 pregnant women in Gabon. EDTA blood, urine, and stool samples were collected from December 2018 to November 2020. Urine samples were analyzed by urine filtration microscopy and UCP-LF CAA. The cfDNA qPCR assay was performed retrospectively on 20 µl of frozen plasma using a simplified DNA extraction method. Diagnostic accuracy was assessed via sensitivity, specificity, and agreement measures. Bayesian latent class analysis (BLCA) was used to estimate test performance in the absence of a gold standard. Diagnostic positivity varied: 24.3% by cfDNA qPCR, 18.6% by urine filtration microscopy, and 20.9% by UCP-LF CAA. Agreement between tests was limited. BLCA indicated qPCR to be the most sensitive (74.0%, 95% CrI: 57.2-90.8), followed by UCP-LF CAA (65.7%, 95% CrI: 49.0-82.8). Microscopy was the most specific (94.9%, 95% CrI : 89.6-99.3). Estimated prevalence ranged between 22.5 and 27.1%. Receiver operating characteristic (ROC) analysis confirmed good individual performance (AUC 0.837-0.868), with performance improving when combining any two tests (AUC up to 0.931). This study validates the high sensitivity of a novel cfDNA qPCR approach using only 20 µl of plasma, demonstrating performance comparable to microscopy and UCP-LF CAA. While microscopy maintains high specificity, combining it with a high-sensitivity test such as qPCR or UCP-LF CAA provides significant diagnostic improvement. Further optimizing the specificity of this streamlined qPCR assay brings us closer to a highly accurate, feasible point-of-care diagnostic crucial for schistosomiasis control programs in resource-limited settings.

Persistent high-risk human papillomavirus (HR-HPV) causes cervical precancerous lesions and cancer. While molecular HPV DNA testing offers superior sensitivity over cytology as a primary screening method, its limited specificity leads to unnecessary follow-up procedures. Therefore, identifying surrogate biomarkers to distinguish transient infections from clinically relevant, persistent ones is essential for improving risk stratification. A comprehensive literature search across PubMed/MEDLINE, Embase, Scopus, and Web of Science databases up to December 2025 identified studies evaluating HR-HPV viral load in cervical lesion progression. Oncogenic HPV viral load, the quantity of HPV genomes in a sample, is a promising biomarker. Levels correlated positively with HR-HPV persistence, increasing the risk of high-grade lesions and invasive cervical cancer. Furthermore, quantification provides prognostic information regarding disease severity, therapeutic response, and post-treatment recurrence. Recent standardization and validation of multiplex real-time PCR techniques supports integrating HPV viral load into clinical pratice. Incorporating viral load assessment into screening and management algorithms could significantly enhance diagnostic precision, enable personalized follow-up, and guide therapeutic decisions for women with HR-HPV-associated cervical disease. Refining these protocols will ultimately minimize over-treatment while ensuring rigorous monitoring for high-risk patients.

Speciation of tuberculosis (TB) causative organisms and drug sensitivity testing are important for TB management in high-TB burden countries, such as the Republic of Congo. This study determined the species diversity of A cross-sectional study involving 92 naïve patients with presumed pulmonary TB hospitalized at the Makelekele Hospital between October 2018 and October 2019. Liquid culture by the MGIT 960 system (Becton Dickinson) was applied for mycobacteria identification. Differentiation of MTBC organisms from non-TB mycobacteria was done using the BD MGIT TBc Identification Test. Species-level identification within the MTBC was performed using the Bruker HAIN Line Probe Assay MTBC. Drug susceptibility testing was performed using the indirect proportion method on the BACTEC MGIT 960 system. Of the 92 pulmonary TB presumptive enrolled, 48 (52.17%) were culture-positive. Among those, seven of 48 (14.6%) were non-tuberculous mycobacteria and 41 of 48 (85.4%) were identified as MTBC isolates. The MTBC strains were 80% This finding highlights a predominance of

SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019 and rapidly developed into a global health crisis. In this study, we analysed 173,194 SARS-CoV-2 genomes from the GISAID database to explore the intra-continental dynamics and distribution of variants across Africa between 2020 and 2024. We have identified 1377 distinct lineages, which were classified by clade to assess associations with infection and mortality rate. So, we conducted a Shannon entropy analysis to confirm the diversity and we applied a Correspondence Analysis (CA). Our findings revealed that one of the deadliest in Africa during the Delta wave, lineage AY.45 predominated in the South Africa cluster, whereas AY.34.1 drove transmission in the Atlantic West Africa cluster, underscoring regional heterogeneity. Furthermore, early in the pandemic, men exhibited a 39% higher risk of infection compared to women (aOR: 1.39, 95% CI [1.34-1.45]), particularly in association with clade G. By contrast, later stages were dominated by clade GRA, which disproportionately affected the elderly (≥70 years; aOR: 1.39, 95% CI [1.33-1.45]) and children (0-9 years; aOR: 1.26, 95% CI [1.20-1.33]). Our analysis highlighted that the pandemic on the African continent unfolded as a mosaic of epidemics shaped by diverse variants and regional epidemiological contexts. These findings emphasize the importance of genomic surveillance to capture local epidemic signatures and inform region-specific public health strategies.

Filarial infections continue to represent a considerable public health challenge in resource-limited communities in sub-Saharan Africa. In Gabon, the implementation of effective control strategies, such as mass drug administration (MDA), is hindered by a lack of contemporary data on the local distribution, molecular diversity, and associated risk factors of these infections, particularly in rural areas where A cross-sectional survey was conducted in August 2021 among 90 volunteers from Dienga, southeastern Gabon. Blood samples were analyzed by microscopy and quantitative PCR (qPCR) targeting the 28S rRNA gene and sequencing. Sociodemographic, clinical, and knowledge data were collected via standardized questionnaires. Statistical analyses employed chi-square tests and logistic regression. The overall filarial qPCR (23.33%) prevalence was 1.75-fold higher than microscopy (13.33%), confirming the superior sensitivity of qPCR for detecting sub-microscopic infections. This study provides the first molecular evidence of a high prevalence of