Baobab Index

Africa bears a disproportionate burden of infectious disease outbreaks and antimicrobial resistance, compounded by weaknesses in public health laboratory systems. In line with its mandate to safeguard public health, the Africa Centres for Disease Control and Prevention (Africa CDC) supports its Member States in strengthening public health laboratory capacity. However, gaps in laboratory leadership continue to threaten the resilience and sustainability of these systems. To address this need, Africa CDC convened a Laboratory Leadership Workshop under the Africa Pathogen Genomics Initiative (Africa PGI) - DETECT Project from 27-29 August 2025 in Mombasa, Kenya. The meeting brought together 24 heads of public health and reference laboratories and senior technical experts from 15 Member States. Combining expert presentations, country case studies, and roundtable discussions, participants examined system-level challenges affecting laboratory performance. Workshop proceedings were synthesized according to the predefined thematic areas that guided the workshop discussions, drawing on rapporteurs' reports and validated through participant review. Key issues included overreliance on external funding, fragile procurement and supply chains, limited equipment servicing, weak sample referral networks, fragmented data systems, and inadequate contingency planning. Comparative country experiences showed that stronger domestic financing and institutionalized leadership structures were linked to greater operational continuity. Emerging innovations such as hybrid decentralization of diagnostic services and integrated sample referral networks were discussed, with success contingent on strengthened leadership in strategic planning, resource mobilization, and cross-sector coordination. The workshop identified cross-cutting priorities, including financial independence, sustainable equipment servicing, quality management, One Health-aligned digital interoperability, and leadership networks for building resilient systems. The meeting concluded that beyond infrastructure, Africa's epidemic preparedness depends on empowered and committed leaders capable of overcoming challenges to steer resilient and sustainable laboratory systems.

Despite the global scale of SARS-CoV-2 genomic surveillance, data from West Africa are limited. In Mali 33,197 confirmed cases and 743 deaths (case fatality ratio: 2.23%) were recorded between March 2020 and August 2025. This study aimed to provide the first comprehensive genomic reconstruction of SARS-CoV-2 variant introductions, transmission pathways, and evolutionary trends in Mali from 2020 to 2023. A total of 548 Malian sequences were used for lineages assignment and variant tracking. For the reconstruction of transmission dynamic a high quality subset of 305 Malian sequences (passing 90% coverage) was analysed alongside 142 closely related global genomes (from 20 countries) identified using the UShER. Time-resolved phylogenetic reconstruction, ancestral trait inference, and molecular clock analyses were performed with TreeTime v0.11.4 to infer variant introductions, local transmission, and substitution rates. Genomic and epidemiological data revealed five distinct epidemic waves driven by the temporal succession of global variants, from 19A/20A lineages in early 2020 to dominant XBB sublineages in 2023. Multiple independent viral introductions were traced primarily to Europe and North America, followed by sustained local and intercontinental transmission, including reciprocal exchanges with neighbouring African countries. The substitution rate was estimated to be 1.56 x 10-3 substitutions per site per year, consistent with global evolutionary trends. Entropy analysis revealed high genetic variability within the spike gene, particularly in the receptor-binding domain. These findings underscore the persistent global connectivity and local evolutionary pressure shaping the trajectory of the pandemic in Mali. These call for the need for sustained genomic surveillance capacity to inform epidemic preparedness and response.

The emergence of drug-resistant Plasmodium falciparum highlights the need for tools to detect minor parasite subpopulations before resistant lineages expand. We developed and validated a targeted ultra-deep sequencing framework for the full-length sequences of 48 antimalarial resistance genes. Performance was evaluated using 3D7:Dd2 mock mixtures and clinical samples after selective whole-genome amplification. The panel achieved high depth and breadth, including for dried blood spot samples. Using Dd2-fixed markers, Mutect2 and HaplotypeCaller reproduced expected variant-allele frequencies, with Mutect2 exhibiting lower global bias and error. A conservative truth set derived from Dd2-pure controls yielded perfect recall and no false-positives in 3D7 controls, with high recovery of true Dd2 variants in mock mixtures for both callers. In clinical samples, the panel captured within-host diversity and minority resistance alleles. Overall, these results demonstrate that targeted deep sequencing offers a cost-efficient, high-resolution approach for routine molecular surveillance of emerging drug resistance.

A major limitation on the development of a malaria vaccine is the lack of validated T cell epitope targets. Plasmodium falciparum is the most prevalent malaria parasite affecting humans in Africa, whereas Plasmodium vivax is more widespread and is the main species that causes malaria in the Americas and Asia

The circulation of arboviruses in sub-Saharan African countries remains poorly documented. The associated health burden may be underestimated and masked by the significance of malaria. Here, we have investigated acute undifferentiated fevers for arboviral infections in Mali (2016-2024). To estimate the proportion of patients with arboviral infection, and in particular dengue. A retrospective (2016-2022) and a prospective (2023-2024) studies were conducted in patients from health centers and hospitals of Mali (mainly in the Bamako region) selected by health professionals. Studies included patients with acute fever lasting less than 7 days; the prospective sub-study excluding pyogenic, urinary, tuberculosis, viral hepatitis, typhoid fever and post-traumatic infections. Blood samples were tested for arboviruses using molecular detection (including serotyping) and genomic sequencing. We collected demographic data and results of malaria testing for all patients and, in the prospective study, a set of clinical data. A total of 2,022 patients were included. Dengue virus (DENV) was the most frequently detected pathogen (retrospective study: 7.6%, 16/210 patients; prospective study: 29.5%, 535/1812 patients). We also detected chikungunya virus (n = 7), West Nile virus (n = 2) and Rift Valley fever virus (n = 1). Three serotypes of dengue were identified: DENV-2 (n = 185), DENV-1 (n = 113) and DENV-3 (n = 105); 148 DENV cases could not be typed. For each serotype, phylogenetic analyses identified a major lineage recently originating from the subregion (DENV-1-III; DENV-2-II; DENV-3-III). In contrast to malaria, the dengue detection rate was higher among patients over 18 years of age. The most frequently observed symptoms were headache, asthenia, arthralgia, myalgia and back pain. The mean number of those symptoms per patient was significantly higher in dengue patients. We recorded 6 cases of hemorrhagic dengue, but no deaths and no case requiring transfer to intensive care. Our findings confirm the threat posed by arbovirus infections in Mali, and more specifically the growing burden of dengue fever on public health. Monitoring dengue fever has become a major challenge in sub-Saharan countries in order to determine the conditions necessary for the future implementation of a dengue vaccination policy tailored to the public health objectives of these countries.

Cancer mortality in sub-Saharan Africa is projected to double by 2030. African populations exhibit the highest genetic diversity worldwide, impacting cancer susceptibility, tumor biology, and therapeutic response, yet remain critically underrepresented in biomedical research. This narrative review examines biobanking and genomic research infrastructure in sub-Saharan Africa and its implications for precision oncology, highlighting that locally governed, sustainable biobanks and equitable international partnerships are fundamental prerequisites for Precision Oncology Without Borders.

The study aims to identify and characterize the SARS-Cov-2 variants circulating in West and Central Africa during the pandemic, between 2020 and 2022. From early 2020 to late 2022, naso-pharyngeal or oro-pharyngeal samples were collected in five countries: Burkina Faso, Côte d'Ivoire, Mali, Republic of Congo and Chad. SARS-CoV-2 positive samples (Ct-value < 30) were sequenced to identify the circulating variants in these countries during the different waves of the pandemic. Overall, 793 whole genomes of SARS-Cov-2 were generated: 308 in Côte d'Ivoire, 244 in the Republic of Congo, 91 in Chad, 87 in Burkina Faso and 63 in Mali. In 2020, early variants detected included B.1 and B.1.1. Lineage A.21 was identified in both Burkina Faso and Mali, while lineages A and A.18 were detected in Côte d'Ivoire and Mali. Some variants appeared to be country-specific, such as lineage B.1.1.404 in Burkina Faso. Chad exhibited a distinct pattern compared with the other countries, with Delta variants detected earlier than in the other locations. In 2021, the diversity of circulating variants increased and differed more markedly between countries. In 2022, the variant landscape was dominated by Omicron lineages in all countries. This study provides new resources concerning the SARS-CoV-2 variants circulating in West and Central Africa between 2020 and 2022, which are less represented in global datasets. The variants identified in this study were similar to the variants observed in other regions of the world.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Determining the drivers of non-native plant invasions is critical for managing native ecosystems and limiting the spread of invasive species