Baobab Index

Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b continue to spread globally, causing major outbreaks in wild birds and poultry. In Africa, however, genomic data remain limited, restricting understanding of viral introduction routes and circulation patterns. Here, we report the whole-genome characterisation of an HPAI A(H5N1) virus detected in a common tern (Sterna hirundo) found dead on the Namibian coast during the most recent avian influenza outbreak recorded in the country. Viral RNA was subjected to whole-genome sequencing using the Illumina Viral Surveillance Panel v2 on a NextSeq 1000 platform. Complete or near-complete sequences were obtained for all eight genome segments and deposited in GenBank. Phylogenetic analyses, performed using African clade 2.3.4.4b H5Nx sequences and the closest related sequences identified through database searches, showed that the Namibian virus belonged to clade 2.3.4.4b and clustered within the EA-2024-DI.2 subgenotype. Across all segments, the virus grouped with contemporary European EA-2024-DI.2 viruses circulating during the 2024-2025 epidemic wave, supporting a likely Eurasian origin. For six of the eight segments, it also clustered closely with an EA-2024-DI.2 virus detected in a gull-billed tern in Uganda in December 2024. Molecular analysis identified a polybasic haemagglutinin cleavage site consistent with high pathogenicity and a mutational profile broadly similar to contemporary EA-2024-DI.2 viruses. The HA substitution, associated in previous studies with increased binding to mammalian-type α2-6 receptors, may warrant further investigation. These findings highlight the role of migratory seabirds in H5N1 dissemination and reinforce the need for strengthened genomic surveillance in African wild birds and poultry.

Global efforts to control and eliminate malaria are threatened by the emergence and spread of antimalarial drug resistance. The World Health Organization recommends surveillance of molecular markers of resistance as a complementary approach to therapeutic efficacy studies. Here, we report the first regional analysis of malaria drug resistance markers from genomic surveillance across six southern African countries spanning diverse transmission intensities and geographies. Dried blood spots, collected from rapid diagnostic test-positive individuals in Angola, Eswatini, Namibia, and Zambia in 2023, Mozambique in 2022, and South Africa between 2022 and 2024 using a standardized collection method, were analyzed using a

Bedaquiline, classified as a WHO 2019 group A drug, is a core component of BPaLM, revolutionizing the treatment of MDR/RR tuberculosis (TB). Since 2015, however, concerns about acquired and primary bedaquiline resistance have emerged. We report a diagnostically challenging case of a young asylum seeker from Afghanistan, previously treated for pulmonary TB with standard therapy for five months about four years earlier. After arriving in Switzerland, he presented with chronic dry cough, weight loss, and small upper-lobe nodular lesions. Rifampicin mono-resistant pulmonary TB was diagnosed, and BPaLM was initiated. Five weeks later, phenotypic antimicrobial susceptibility testing showed bedaquiline/clofazimine resistance. Next-generation sequencing revealed an IS6110 insertion in mmpR5. The patient had never received bedaquiline. An individualized regimen with pretomanid, linezolid, moxifloxacin, isoniazid, and pyrazinamide led to clinical and radiological improvement. Treatment was stopped after 9 months, with outcome classified as completed (not cured due to absent sputum production). The patient remains well 1.5 years after treatment completion. This case highlights the diagnostic and therapeutic challenges of primary bedaquiline resistance. Faster, reliable phenotypic and genotypic diagnostic methods, along with clear treatment recommendations, are urgently needed to identify bedaquiline-resistant patients promptly, treat them appropriately, and preserve the effectiveness of the BPaLM regimen.

Uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) is closely associated with the management of HIV and tuberculosis (TB) coinfection because it modulates the metabolism of antiretroviral (ARV) drugs. The frequency of UGT1A1 polymorphisms varies widely among sub-Saharan Africans. However, studies examining the frequency of UGT1A1 polymorphisms and their impact on drug response profiles, accounting for environmental factors, drug-drug and gene-drug interactions and non-compliance remain sparse. Given that HIV and TB treatments often involve complex drug regimens with a high risk of interactions, understanding the role of UGT1A1 polymorphisms in these contexts is crucial. Therefore, this scoping review aims to map existing evidence, synthesise findings on how genetic polymorphisms in the UGT1A1 gene affect the metabolism of ARVs and antituberculosis drugs, and identify gaps in literature regarding their impacts on drug efficacy, toxicity and treatment outcomes in sub-Saharan Africa (SSA). The methodology for this scoping review will follow the guidelines outlined in the Joanna Briggs Institute Methodology Manual. Using the keywords, UGT1A1 polymorphism, HIV and TB coinfection, treatment outcomes and SSA, we will search for articles on PubMed/Medline, Cochrane Library, Embase, Web of Science and Scopus to obtain relevant articles published from January 2010 to April 2026. Two independent reviewers will screen and assess quality of titles and abstracts against the predefined inclusion and exclusion criteria and manage the data using Microsoft Excel. Conflicts will be resolved through discussion and where necessary a third reviewer will be consulted. Findings will be narratively synthesised across polymorphisms and treatment outcomes. The reviewers will meet and discuss the themes that will arise as well as the interpretation of the themes to minimise bias in the findings. The scoping review relies on publicly available published resources, exempting it from ethical review board oversight. The review findings will be shared in a peer-reviewed journal.

Black-footed cats ( In the first genomic study of free-roaming individuals, we sequenced whole genomes of black-footed cats (N=44) from across their distribution. To do so, we incorporated whole genome sequences generated from both modern biological samples and century-old museum specimens. We assembled a highly contiguous reference genome using a combination of PacBio HiFi data and publicly available Hi-C data and investigated the demographic history, population structure, and genetic diversity of wild black-footed cats. We found evidence of historical effective population sizes of ~11,500 individuals, which is lower than estimates reported in other felid species. Consistent with modest historical population sizes, we found that present-day genome-wide diversity was low ( Overall, these results provide range-wide information about the demographic history and present-day genetic diversity of an understudied species. Together with analyses of population structure, we speculate that there may be greater connectivity between populations of black-footed cats than previously assumed. Our study underscores the utility of genomic data in providing insights into population dynamics for better conservation management.

Aridity alters soil carbon (C), nitrogen (N) and phosphorus (P) stoichiometry, yet the implications of these processes for soil microbial functional traits and potentials at the genomic level remain poorly synthesized. Here we combine measurements of soil C, N and P pools and ratios with shotgun metagenomes from 200 natural ecosystems spanning major biomes worldwide. Across sites, increased aridity is associated with lower soil C:N and N:P (and C:P) ratios and with a coordinated shift in microbial functional potential. Genes linked to catabolic resource acquisition-including carbohydrate-active enzymes and pathways for degradation of plant litter and organophosphorus compounds-are declined as C becomes relatively scarce. In contrast, genes supporting anabolic investment in growth and drought resistance, such as RNA transcription, protein synthesis and intracellular transport, are increased. These patterns indicate that aridity-related change in soil elemental ratios is coupled to a broad shift from catabolic to anabolic strategies in soil microbiomes. By linking soil elemental ratios to microbial functional traits across biomes, our study provides a framework for anticipating how climate-driven drying may reorganize microbial metabolism with consequences for carbon and nutrient cycling.

Widely accepted climate predictions indicate that drylands will expand to cover more than half of the Earth's terrestrial surface by the end of the 21st century. In these environments, harsh conditions, including nutrient and water limitations, restrict plant and animal life, thereby increasing the importance of soil microbial communities in nutrient cycling and ecosystem functioning. The Namib Desert is a distinctive dryland ecosystem characterized by a steep natural aridity gradient, transitioning from a coastal hyperarid zone influenced by frequent fog deposition to an inland arid region receiving seasonal rainfall. This study investigates the impact of water availability and moisture regime on microbial trace gas oxidation and community composition across this aridity gradient. Quantitative analyses revealed that total microbial abundance and activity indicators, including ATP concentrations and respiration rates, were significantly ( Drylands are expanding globally, yet the mechanisms that allow microbial life to persist under extreme and sustained water limitation remain poorly understood. This study demonstrates that atmospheric trace gas oxidation, particularly high-affinity hydrogen oxidation, supports active and resilient microbial communities in hyperarid soils of the Namib Desert, even in the absence of liquid water inputs. By revealing how microbes may couple trace gas metabolism to energy and water generation, our findings provide new insight into the lower limits of microbial activity in dry, hot desert soils and highlight the need to investigate how microbes persist and sustain soil ecosystem functioning.

The growing threat of artemisinin partial resistance prompted the WHO to recommend routine monitoring of drug efficacy and resistance. Advances in sequencing technologies and expanded laboratory capacity across Africa have made malaria molecular surveillance (MMS) a viable option for many countries. Despite improved access to next-generation sequencing platforms, the uptake of MMS for programmatic decision-making and the availability of antimalarial resistance marker data in southern Africa have lagged behind those in other regions. The Genomics of Malaria in the Elimination Eight (GenE8) initiative implemented a regional MMS model comprising 1) regional consensus-building and governance, 2) capacity strengthening, and 3) evidence generation. Through this initiative, standardized parasite genomic data across five southern African countries (Angola, Eswatini, Namibia, South Africa, and Zambia) were generated using a targeted amplicon deep-sequencing workflow. Regional laboratory and analytical skills were strengthened, and national malaria programs (NMPs) were capacitated to use genomic data for decision-making through a regional MMS fellowship and training workshops. Although the initiative achieved important successes, persistent challenges limited its overall impact despite the implementation of integrated mitigation strategies. Challenges included constraints in regional bioinformatics capacity, delays in sample shipment and cross-border data sharing, and a lack of sustained funding. In the present case study, the GenE8 model, operational experiences, and cross-cutting lessons learned are described. The GenE8 experience reveals that regional MMS is feasible in southern Africa and that near-real-time resistance data can inform policy and intervention decisions, but that it requires sustained investment in governance mechanisms, bioinformatics expertise, and institutionalized NMP capacity to be sustainable.

Herpes simplex virus (HSV) is an endemic pathogen, infecting over half of all adults world-wide. HSV infection can cause a wide spectrum of disease outcomes, ranging from asymptomatic infection or mild lesions to rare cases of infectious keratitis, encephalitis, and death. HSV genome sequences differ between individuals and within individuals. To date, the vast majority of publicly available HSV genomic data has come from Europe and North America. Populations in South America, Africa, and Asia are under-sampled, as are non-industrial (e.g., agricultural, pastoral) populations, for which the natural environment plays a large role in health and disease dynamics. We used Whatman FTA card stabilization of DNA to develop a procedure for capturing oral and genital swabs from a geographically isolated pastoralist population in a desert region of northern Namibia. This is the first study to document HSV genome sequences from this type of remote setting and these are the first HSV genomes from Namibia. The resulting HSV sequences, collected in 2015 and 2016 from remote settlements in Namibia, fit within the scope of viral genetic diversity previously defined by African strains. The methodological approaches developed in this study can be expanded to broaden viral detection, improve diagnostics, and raise public health awareness about the burden of pathogens in under-served populations.