Baobab Index

Bats are the natural reservoirs for a variety of emerging and re-emerging viruses. Among them, rabies virus (genus Lyssavirus, family Rhabdoviridae) is one of the first and most emblematic described in these animals. Since its first description, several new bat lyssaviruses have been regularly identified. In addition to lyssaviruses, other bat rhabdoviruses have also been discovered, including members of the genera Vesiculovirus, Ledantevirus and, more recently, Alphanemrhavirus and Tupavirus. However, the family Rhabdoviridae is one of the most abundant and diverse viral families, with 434 officially recognized species, divided into 5 subfamilies and 56 different genera. The number of rhabdoviruses associated with bats is therefore probably higher than that currently available. In this study, we first developed and validated a combined nested RT-qPCR technique (pan-rhabdo RT-nqPCR) dedicated to the broad detection of animal rhabdoviruses. After validation, this technique was used for a large retrospective screening of archival bat samples (n = 1962), including blood (n = 816), brain (n = 723) and oral swab (n = 423). These samples were collected from various bat species over a 12-year period (2007-2019) in 9 different countries in Europe and Africa. A total of 23 samples (1.2%) from bat species Miniopterus schreibersii, Rhinolophus euryale and Rhinolophus ferrumequinum tested positive for rhabdovirus infection, including 17 (2.1%) blood and 6 (1.4%) oral swab samples, all collected from bats originating from the Mediterranean region. Complete virus genome sequences were obtained by next-generation sequencing for most of the positive samples. Molecular and phylogenetic analysis of these sequences demonstrated that the virus isolates, named Mediterranean bat virus (MBV), were closely related and represented a new species, Mediterranean vesiculovirus, within the genus Vesiculovirus. MBV was more specifically related to other bat vesiculoviruses previously described from China and North America, together clustering into a distinct group of bat viruses within this genus. Interestingly, our results suggest that MBV is widespread, at least in the western part of the Mediterranean region, where it circulates in the blood of several bat species. These results expand the host range and viral diversity of bat vesiculoviruses, and pave the way for further studies to determine the transmission route and dissemination dynamics of these viruses in bat colonies, as well as to assess their potential threat to public health.

A polygenic score (PGS) for Alzheimer's disease (AD) was derived recently from data on genome-wide significant loci in European ancestry populations. We applied this PGS to populations in 17 European countries and observed a consistent association with the AD risk, age at onset and cerebrospinal fluid levels of AD biomarkers, independently of apolipoprotein E locus (APOE). This PGS was also associated with the AD risk in many other populations of diverse ancestries. A cross-ancestry polygenic risk score improved the association with the AD risk in most of the multiancestry populations tested when the APOE region was included. Finally, we found that the PGS/polygenic risk score captured AD-specific information because the association weakened as the diagnosis was broadened. In conclusion, a simple PGS captures the AD-specific genetic information that is common to populations of different ancestries, although studies of more diverse populations are still needed to better characterize the genetics of AD.

Despite global efforts to eliminate HIV as a public health threat, sub-Saharan Africa (SSA) still harbours about the highest burden of the pandemic, home to around 70 % of people living with HIV with limited contribution in the field of HIV cure research, especially in West and Central Africa (WCA). This gap is mainly due to challenges that researchers of this region are facing in initiating and advancing HIV cure research locally, with lesser commitment from the French-speaking countries. Furthermore, capacity-building of early career scientists on HIV cure research remains constrained due to limited awareness and language barriers to existing opportunities. Even though HIV non-B subtypes represent 89 % of circulating subtypes worldwide, cure research has been extensively focused on subtype B (prevalent in America and Europe). Interestingly, WCA (known as HIV pandemic epicentre with a broad genetic diversity) offers a unique landscape for cure research with a likelihood of generalisability across various HIV subtypes. This viewpoint discusses the importance of establishing an HIV Cure Academy for WCA to support scientists, policymakers and community stakeholders from French-speaking countries in contributing to the global efforts towards HIV cure. Building on discussions, the establishment of an "HIV Cure Academy" emerges as a hallmark to: (i) raise awareness, (ii) build capacity, (iii) address scientific gaps, (iv) develop networks, and (v) foster advocacy and policy-briefing on integrating HIV cure research into national HIV agenda. The Academy is envisioned as a hub, facilitating relationships between community-based organizations, people living with HIV (PLHIV), research institutions and decision makers. This hub will also champion the "Advocacy for Cure" agenda in the sub-region, enhance multidisciplinary approach to identify local HIV cure research priorities that address the global problem. Of prime importance, research priorities in WCA include: (i) the measurement and characterization of viral reservoirs; (ii) investigation in immune responses including bNAbs, T-cell function, cytokines profiles and hosts genetic factors; (iii) identification of elite and post-treatment controllers; (iv) development of accessible technologies for point-of-care HIV DNA testing, biomarker detection, and latency-modifying agents to support functional cure strategies; (v) innovation in cost-effective and scalable therapeutic interventions suitable for low-resource settings; (vi) the strengthen of community involvement through citizen science, address ethical considerations, and engage PLHIV in the co-design of cure research initiatives; (vii) the establishment of regional training platforms, such as a Research-for-Cure Academy, to enhance scientific capacity and collaboration in West and Central Africa. Following the model of the International AIDS Society (IAS) Research-for-cure academy, the WCA HIV Cure Academy represents a key hub in achieving the goals of HIV cure, through local actions that contribute to addressing a global problem.

The spread of monkeypox virus (Orthopoxvirus monkeypox) clade Ib from the Democratic Republic of the Congo to neighbouring countries has raised global concerns, leading to WHO declaring mpox a public health emergency on Aug 14, 2024. We applied genomic epidemiology to investigate the causes of recurrent mpox outbreaks in the Central African Republic. We aimed to determine whether frequent zoonotic spillovers or increased human-to-human transmissions are driving mpox epidemiology. We performed a retrospective cross-sectional study of monkeypox virus genomic sequences among PCR-confirmed mpox cases detected in the Central African Republic between Feb 17, 2022, and Sept 17, 2024. We used hybridisation capture coupled to high throughput sequencing to analyse 46 samples from mpox outbreaks that occurred in eight of the 20 prefectures (14 of 35 health districts). Near-complete genomes were used for phylogenomic analyses. Between Jan 10, 2022, and Sept 15, 2024, 89 mpox cases were confirmed, including 53 cases in the first 9 months of 2024. We generated 41 near-complete genomes from this period, including 33 from 2024. All new and already published monkeypox virus genomes from the Central African Republic belonged to clade Ia. These genomes spanned the phylogenetic diversity of clade Ia viruses, and most likely represented several dozen independent transmission events to humans. The monkeypox virus phylogenetic diversity was geographically structured within the country. Plausibly linked cases often showed indistinguishable genomes. Conversely, we detected identical genomes in cases that epidemiological information would suggest were independent outbreaks. Finally, we found that three distinct viruses caused cases in the capital city of Bangui in July, 2024, with all three detected on the same day (July 24, 2024). We did not detect substantial enrichment of APOBEC3 editing, suggesting limited human-to-human transmission. The data indicate that mpox epidemiology in the Central African Republic is primarily driven by short-lived outbreaks resulting from many independent zoonotic spillover events, particularly in rural areas. Although evidence remains limited, in Bangui additional factors such as movement of people and importation of bushmeat from other regions might be introducing the virus into urban settings. Similar spillover patterns have been observed in the Democratic Republic of the Congo. The poorly understood nature of monkeypox virus reservoirs in both countries is a regional concern, as frequent spillovers increase the risk of outbreaks leading to sustained human transmission. Beyond strengthening surveillance and developing countermeasures, it is important to better understand the reservoirs and focus on reducing transmission opportunities to prevent further outbreaks. Pasteur Institute of Bangui, Africa CDC, AFROSCREEN, WHO, the Helmholtz Institute for One Health, and the Deutsche Forschungsgemeinschaft.

Understanding how host lifestyle and industrialization shape the human gut microbiome and intestinal physiology requires multimodal analyses across diverse global host contexts. Here, we generate multivariate data from the Global Microbiome Conservancy cohort, including gut microbiome, IgA-sequencing, host genotyping, diet, lifestyle and fecal biomarker profiles, to investigate host-microbiome interactions across gradients of industrialization and geography. We show that industrialization is associated with homogenized microbial compositions, reduced microbial diversity, and lower community stability, independent of host confounders. We further show that industrialization is linked to elevated markers of gut stress, increased IgA secretion, and altered patterns of IgA-bacteria interactions. Finally, we show that microbiome-based disease predictors trained on industrialized populations lose accuracy in less industrialized cohorts, highlighting limited cross-population transferability. Together, our results suggest profound restructuring of host-microbiome interactions due to industrialized lifestyles, and emphasize the need for inclusive, globally representative data to improve translational microbiome applications across diverse human populations.

To investigate the role of epidemic predictors in the mpox outbreak in Africa. This was a retrospective analysis of national-level mpox surveillance data from 20 mpox-affected African countries from January through December 2024. Predictors included viral clades, gross domestic product (GDP) per capita, and population density. A negative binomial regression model estimated the incidence rates ratio (IRR) [95% confidence interval] for mpox incidence and mortality. Random forest models assessed the influence of each predictor in the epidemic dynamic. Clade II was associated with lower mpox incidence (IRR = 0.15 [0.02-0.97]) and mortality (IRR = 0.09 [0.01-1.72]) compared to Clade I. GDP per capita was associated with a 95% reduction in cases count per US $1000 (IRR = 0.05 [0.38-0.74]). Population density was not significantly associated with mpox incidence or mortality. Random forest analysis confirmed GDP per capita as the strongest predictor of mpox burden. The 2024 mpox epidemic highlights how countries with low GDP per capita and Clade I face greater outbreak burdens. Strengthening health systems and addressing poverty as a key social determinant of health through a multisectoral approach are essential to ensure equitable outbreak prevention, control, and long-term resilience.

The emergence of high-threat pathogens-such as Ebola, Lassa fever, and most recently SARS-CoV-2-has highlighted critical weaknesses in global surveillance systems, particularly in resource-limited settings where many zoonotic spillovers originate. Despite the World Health Organization's (WHO) prioritization of these diseases for research and development (R&D), the current surveillance infrastructures in these regions remain under-resourced, fragmented, and often reactive rather than anticipatory. This narrative review explored the literature and structured relevant findings in three key dimensions: (i) the structural and operational limitations of existing surveillance systems for the WHO priority diseases in resource-limited settings including challenges in data integration, laboratory capacity, workforce, and community engagement; (ii) how these surveillance gaps could delay detection and hinder the response to future emerging threats, particularly a hypothetical but inevitable Disease X; and (iii) innovative and context-adapted strategies to strengthen epidemic intelligence including integrated One Health surveillance, digital and genomic tools, participatory approaches, and regional data-sharing mechanisms. We argue that building agile, equity-centered, and decentralized surveillance systems is not only essential for managing known threats, but also foundational to the early detection and rapid containment of the next public health emergency in resource-limited settings. This review uniquely frames surveillance limitations in resource-limited settings as a global security concern and outlines context-adapted, equity-centered innovations to strengthen epidemic intelligence in preparation for Disease X.

The inaugural

Transmission of human respiratory pathogens to wild, human-habituated great apes has been repeatedly documented within research and tourism projects. While the implementation of hygiene measures has significantly reduced the risk of pathogen introduction, vigilant surveillance remains essential to evaluate the effectiveness of the adopted measures and identify additional steps for risk reduction. Here, we combined behavioral observations and pathogen genomic surveillance in non-invasive samples to investigate three outbreaks of respiratory disease in human-habituated western lowland gorillas

Monkeypox virus (MPXV) is a zoonotic pathogen known to be endemic to the Congo basin and West Africa, and which causes characteristic lesions disseminated on all skin surfaces of infected cases. Multiple MPXV outbreaks have been reported in the Central African Republic (CAR), a country in the Congo basin, at an increased frequency since 2020. The genomic history of these outbreaks in CAR is poorly characterized due to undersampling, with only a recent expansion in the number of sequences from CAR. Here, we report twenty-six new near-complete genomes from six prefectures of CAR, selected to represent outbreaks that occurred in the country between 2019 and 2024. Our analysis shows the sustained homogeneity of genomes in CAR, as all of them belonged to Clade Ia, but with an expansion of sub-lineages and therefore increased MPXV diversity within CAR. We highlight the introduction into CAR of a lineage previously known to occur only in Gabon and Cameroon, as well as the apparent regional clustering of MPXV genomes in CAR. Our analysis reveals limited APOBEC3-mediated activity, which is consistent with recent zoonotic origins and short human-to-human transmission chains observed in CAR. These analyses provide an in-depth view of the genomic diversity of MPXV in the Central African region.