Baobab Index

Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87

The Central African Republic (CAR) is a high-risk country for poliomyelitis outbreaks because of difficulties in closing immunity gaps due to the lack of resources, logistics issues, and insecurity. The country experienced multiple poliomyelitis cases since 2019. A novel type 2 oral polio vaccine (nOPV2) engineered to lower the risk of reversion of the vaccine strain was deployed in the CAR in 2022-2023 to counter active serotype 2 poliovirus transmission. This study reports routine poliovirus surveillance conducted from November 2021 through October 2023 in the CAR. Polioviruses isolated from stools and wastewater were genetically characterized based on the VP1-encoding region that was sequenced by Sanger technique. Whole-genome sequencing was conducted on all nOPV2-derived isolates and on a subset of Sabin-2-derived isolates by using Illumina technology. Fifty-four vaccine-derived poliovirus type 2 isolates were identified, belonging to eight distinct emergences: four emergences were derived from the historical vaccine strain and four from the nOPV2. The nOPV2 derivatives that had kept the original 5' untranslated region (5'UTR) did not display any reversions in the modified domain V, which is the primary attenuation site. Nonetheless, some nOPV2 derivatives had lost this domain through recombination with members of species The novel oral polio vaccine of serotype 2 (nOPV2) was engineered to prevent the emergence of revertant polio vaccine strains, which caused numerous outbreaks in the 2000s and 2010. Since 2021, it has been used in many countries, especially in Sub-Saharan Africa, to contain poliomyelitis outbreaks. In 2023, double recombinant nOPV2-derived isolates that had lost all the attenuation determinants were detected in the Central African Republic (CAR). Several of these were the first nOPV2 revertant isolates ever reported to the Global Polio Eradication Initiative, thereby demonstrating that the engineered modifications in nOPV2 do not entirely prevent reversion via recombination with non-polio enteroviruses of species

Mpox remains a significant public health challenge in Africa, where endemic transmission persists alongside a high burden of other infectious diseases. Although the epidemiology and clinical impact of coinfections with human immunodeficiency virus (HIV) and varicella-zoster virus (VZV) remain poorly understood across the continent, these coinfections may influence clinical presentation, disease severity, and diagnostic accuracy. This aimed to describe the coinfections (VZV and HIV) patterns among confirmed mpox cases and characterize the trend of clinical presentation of mpox patients in Africa. Following PRISMA guidelines, we registered our protocol in PROSPERO (CRD420251133960) and conducted a systematic review and meta-analysis. We searched multiple electronic databases and grey literature through 27 February 2025, identifying observational studies from Africa that reported mpox coinfections (VZV and/or HIV) and associated clinical symptoms. Random-effects models were used to calculate pooled prevalence, while subgroup analyses and meta-regression explored sources of heterogeneity across WHO regions, countries, study designs, settings, and participant types. A total of 23 studies conducted across African countries were included. The pooled prevalence of VZV-mpox coinfection was 8.73% (95% CI: 2.05-30.43; 10 studies; n = 2,681; HIV and VZV coinfections with mpox pose a major yet possibly underestimated burden in Africa and are linked to more severe clinical presentations, particularly in hospital environments. The necessity of including clinical, epidemiological, and genomic in mpox monitoring systems is underscored by observed clinical differences across clades. Improving patient management and outbreak preparedness across the continent requires strengthening diagnostic capacity and routinely screening for coinfections. https://www.crd.york.ac.uk/PROSPERO/view/CRD420251133960, identifier CRD420251133960.

With the ongoing global resurgence of COVID-19, it is crucial to better understand past transmission dynamics to strengthen national preparedness for future surges. Since its emergence in Wuhan, China, in December 2019, SARS-CoV-2 has caused multiple waves of infection worldwide. The World Health Organization (WHO) has identified several variants of concern, including Alpha, Beta, Gamma, and Delta. At the end of 2021, the Omicron variant emerged in South Africa and rapidly spread across the globe. While many studies have explored the evolution and transmission of these variants, data from the Central African Republic remained limited. This study aimed to identify and characterize SARS-CoV-2 variants circulating in Bangui to support genomic surveillance and COVID-19 prevention strategies. Characterizing circulating variants provides essential information for the early detection of emerging lineages, the anticipation of potential epidemic waves, and the adaptation of public health strategies. We conducted a retrospective, descriptive study in Bangui, Central African Republic (CAR), from January to August 2022. A total of 102 nasopharyngeal samples positive for SARS-CoV-2 (Ct ≤ 30), selected from the biobank of the Pasteur Institute in Bangui, were reanalyzed using multiplex qPCR to confirm their Ct values. Eligible samples were then sequenced using the MinION MK1C (Oxford Nanopore Technologies) platform, following the ARTIC Network protocol at the Institut Pasteur, Paris (CIBU). Bioinformatics processing using reads mapping to a reference genome, followed by consensus sequence generation, included standard steps of basecalling, demultiplexing, quality filtering, genome alignment, primer trimming, consensus generation, and variant calling. The different variants were described using the Nexstrain web application. The results revealed that 66.7% of sequenced genomes (n = 68) had high coverage ≥ 80%, all belonging to the Omicron variant. Four sub-lineages were identified according to the Pangolin classification: BA.1 (14.7%), BA.2 (35.3%), BA.4.1 (4.4%), and BA.5.1 (45.6%). These sub-lineages were present in all eight districts, with a predominance in the eighth district, and were most frequently diagnosed in June (fourth wave of the epidemic). Omicron was the only variant detected among successfully sequenced samples, although limited sampling and sequencing success restrict broader generalisation. It is crucial to establish continuous surveillance of SARS-CoV-2 to detect any emerging variants in real time, while strengthening sequencing capabilities at the national level. Continuous genomic surveillance is crucial to anticipate potential future COVID-19 waves and to enable timely public health responses.

Enteroviruses (EVs) that infect humans cause a broad range of pathologies, notably neurological, respiratory, cutaneous and enteric diseases, leading to morbidity and mortality, especially in young children. These pathologies particularly affect countries in Asia and Sub-Saharan Africa. In the last decades, some EVs with a marked respiratory tropism have emerged as a source of acute respiratory illnesses: EV-D68 has been associated with outbreaks of severe respiratory distress and acute myelitis since 2014, while several respiratory genotypes belonging to the species

Land-use change can influence parasite transmission by reshaping ecological interactions among parasites, vectors, and hosts. In particular, deforestation and agricultural expansion modify habitat structure and resource availability, potentially altering the prevalence and distribution of vector-borne diseases. Fieldwork was conducted on São Tomé Island (Gulf of Guinea, Central Africa) across a land-use gradient from the core of an oil palm plantation to adjacent native forest. Culicoides biting midges and birds were sampled across four habitat types (village, oil palm plantation, at the border between the plantation and the forest, and forested areas) using Centers for Disease Control (CDC) traps and mist nets, respectively. DNA extracted from Culicoides and bird blood was used to screen for Plasmodium, Haemoproteus, and Leucocytozoon using nested polymerase chain reaction (PCR). Blood-fed Culicoides collected in the traps were analyzed by PCR to identify the host species. Linear models were used to assess differences in vector diversity, abundance, host-feeding preferences, and haemosporidian prevalence among habitats. Culicoides species richness did not differ significantly between habitats, but species abundances did vary. Overall abundance was lower in the oil palm plantation than in border and forest areas. Mammophilic Culicoides were more abundant in the village, whereas ornithophilic species were predominated in the forest. We screened 432 bird blood samples and 452 parous Culicoides for haemosporidian infections. Haemosporidian parasites were most frequently detected in Culicoides pools from the border area. Among birds, Plasmodium prevalence was significantly higher in the oil palm plantation than in border and forest habitats, while Leucocytozoon infections were completely absent in plantation birds. Anthropogenic habitat disturbance modifies vector communities and host-parasite associations, influencing the transmission dynamics of Haemoproteus parasites. These findings highlight the ecological consequences of agricultural expansion and the importance of preserving natural habitats to mitigate disease emergence under land-use change scenarios.

Methanogens are methane-producing archaea that are present in the human gut. Yet, their adaptation to diverse human lifestyles remains poorly understood. Here, we report the isolation of G0370_i3 growth relied on the presence of H These findings highlight the stress resilience and selective metabolic capabilities of

Central Africa is the largest region of human T-cell Leukaemia virus (HTLV-1) endemicity with several million people estimated to be infected. Based on the study of the LTR region, it is also the region with the highest HTLV-1 diversity, with the presence of genotypes a-b and d-g. However, complete genomic sequences are still lacking for Central African genotypes. Here, we report the first large collection of complete HTLV-1 sequences for genotypes b, d and f from Central Africa and neighbouring countries. We identified substantial diversity within the HTLV-1b genotype, including a newly defined clade that we designated HTLV-1b-del. It mainly comprises strains from the Democratic Republic of the Congo (COD) and neighbouring countries and is characterized by a distinctive 12-bp-long deletion. We also generated the complete sequence of the STLV-1 strain from

Type 2 diabetes (T2DM) is a metabolic disease characterized by chronic hyperglycemia. We investigated the relationship between the polymorphisms This case-control study was conducted at the Endocrinology Department of the University Hospital of Libreville. We enrolled 97 patients with T2DM and, from the general population, 87 control subjects who met the inclusion criteria. Genomic DNA was extracted with the Qiagen kit, and polymorphisms were analyzed using the RFLP method. For KCNJ11, the wild type (EE) genotype frequency was 62.2% in controls versus 42.6% in cases, whereas the mutant type (KK) genotype frequency was 28.7% in cases versus 21.1% in controls (P=0.0243). For TCF7L2, the wild type (CC) genotype was found in 51.7% of controls and 37.1% of cases, and the mutant type (TT) genotype was found in 22.7% of cases versus 9.2% of controls (P=0.0253). For SLC30A8, the wild type (CC) genotype occurred in 26.0% of cases and 24.6% of controls (P=0.9326). After adjustment for age and body mass index, the recessive transmission models of The

African elephants are keystone species facing severe declines due to the ivory trade and habitat loss. To investigate the genomic consequences, we analyze 232 high-coverage genomes from 17 African countries in the first continent-wide genomic analysis treating savanna (Loxodonta africana) and forest (L. cyclotis) elephants as distinct species. We find a deep divergence between species, with forest elephants showing higher heterozygosity and historically larger effective population sizes, while savanna elephants exhibit greater inbreeding and genetic load. Surprisingly, we detect widespread introgression of trace forest ancestry across savanna populations, suggesting a complex history of hybridization. Within species, historically high mobility promoted genetic connectivity, though we identify signs of human-induced isolation and drift in peripheral populations. Our findings highlight gene flow as a key force in African elephant evolution and underscore the urgency of understanding the impact of accelerating habitat fragmentation in these ecosystem engineers.