Primary prevention includes interventions that prevent the initial occurrence of disease; in the context of pandemic origins, one class of primary preventative interventions involves reducing the risk of zoonotic pathogen spillover. Pandemics are rare events, therefore data on spillover events of known pandemic pathogens are also rare. In contrast, many zoonotic viruses spill over frequently but fail to spread efficiently between humans. We consider whether insights from frequent spillovers of poorly-spreading viruses should be used to inform primary prevention strategies aimed at viruses that spill over rarely but spread well human-to-human. We propose a set of principles to steer future research and guide deployment of preventative strategies. We believe that a precautionary approach, grounded in evidence from viruses that spill over frequently, offers the most practical empirical foundation for guiding primary spillover prevention.

Diseases caused by henipaviruses, exemplified by Hendra virus and Nipah virus, pose a serious risk to public health because of their epidemic potential and high case-fatality rates and the paucity of medical countermeasures to mitigate them. In December 2024, a group of 150 scientists from 16 countries convened in Geelong, Victoria, Australia, to mark the 30th anniversary of the discovery of Hendra virus. The Hendra@30 conference built upon its predecessor conference held in 2019 in Singapore, Nipah@20, by expanding its program across broader disciplines and integrating sessions on human sociology and disease ecology into the main scientific discussions. We describe key highlights from Hendra@30 and reflect on 4 key elements that have advanced henipavirus research and medical countermeasures research and development. We propose that integrating bat ecology into henipavirus research blueprints will enable development of ecologic countermeasures that prevent spillover and will complement existing preparedness and response efforts with evidence-based prevention strategies.

Bats host several emerging viruses, including filoviruses, coronaviruses, and paramyxoviruses. Land-use change and urbanisation increasingly bring bat species into closer contact with humans, thereby potentially increasing opportunities for viral exposure at the human-bat interface. Understanding viral dynamics in natural bat hosts is essential for assessing emergence risks. This study spanned 12 months of longitudinal virus surveillance in two molossid bat species (genus Mops) that roosted in close association with humans within two contrasting land-use systems in northeastern Eswatini. Bats were tested for filovirus, coronavirus, and paramyxovirus viral RNA with additional serosurveillance for filoviruses. In addition to identifying novel paramyxovirus diversity, the ongoing circulation of molossid-associated alphacoronaviruses was also confirmed. Coronavirus peak shedding was observed during spring (July-September), with shedding adults consistently displaying lower forearm-mass indices as compared to non-shedding bats. Recapture analysis showed that alphacoronavirus RNA was no longer detectable in most bats within a month, although a small number of individuals remained PCR-positive after several months, consistent with intermittent shedding or reinfection. While no filovirus RNA was detected, 29.5% (95% CI: 26.1–33.1%) of bats were sero-reactive with Bombali virus glycoprotein. These findings demonstrate the value of longitudinal wildlife surveillance for understanding seasonal viral dynamics, identifying periods of increased opportunities for human exposure and informing evidence-based surveillance at the human-bat interface.

Claims that zoonotic spillover is rising globally have shaped research priorities for decades, but this apparent rise can be a statistical artifact of changing detection effort, not a genuine biological signal. Methodological correction alone cannot resolve the ambiguity: closing the gap requires investment in surveillance infrastructure, not modeling. Testing three approaches—generalized linear models, generalized additive models, and double machine learning—against simulated data spanning detection-bias and prevalence conditions, we find trend direction is recoverable under simple bias but not under oscillating or shared-driver detection, and all methods risk false increases when true rates are stable. Applied to 27 years of bovine rabies surveillance in South Africa, independent methods agreed on the declining trend direction but produced magnitude estimates differing more than threefold, showing model disagreement is informative. We translate these findings into reporting guidelines: prioritize direction over magnitude, disclose method reliability, treat cross-model disagreement as signal, and flag high-risk detection regimes.

The taxonomy of the small, sub-Saharan, insectivorous bat, Afronycteris helios (Heller, 1912), has been unresolved for decades. The name A. cf. helios was introduced in the literature to recognise bats found in east and southern Africa that were like A. helios but had glands on the uropatagium. Cranio-dental morphology, bacular morphology, and molecular genetics (albeit the latter two being without representation of A. helios), provided evidence to formally describe "A. cf. helios", which is currently known from Kenya, Mozambique, and South Africa. Bayesian analyses based on cytochrome oxidase b, cytochrome c oxidase subunit 1, and 12S rRNA confirm that it belongs to the genus Afronycteris withA. nanus (Peter, 1852) and A. helios. These analyses also revealed genetic, bacular, and cranio-dental morphological differences withinA. nanus, which are described here. Pending a more thorough geographic analysis, including all existing synonyms, A. cf. nanus has been introduced to refer to bats that were smaller than A. nanus. Although co-occurring in north-eastern parts of South Africa, A. cf. nanus has a more westerly distribution extending to west Africa, relative to the more easterly distribution of A. nanus. Afronycteris sp. nov. showed at least a 6.9%, 3.4% and 2.9% nucleotide difference to its nearest relative based on cytochrome oxidase b, cytochrome c oxidase subunit 1, and 12S rRNA respectively. It is cranio-dentally smaller than A. helios, slightly smaller than A. nanus, and larger thanA. cf. nanus, with a distinct baculum, and a unique pair of glands on the uropatagium.

Limited linguistic inclusivity in public health communication leaves many South African communities underserved, particularly regarding critical information on zoonotic diseases such as rabies. This pilot study addresses this gap by developing and evaluating AI-driven methods for delivering reliable rabies information to Sepedi speakers, a low-resource language group. The study presents a novel, curated Sepedi dataset of 60 question–answer pairs, created through a systematic pipeline: thematic analysis of authoritative English sources guided the synthetic generation of QA pairs, which were then translated and manually verified by a native-speaking expert. This dataset was used to compare two large language models, GPT-4o and Gemini-1.5 Flash, under both base and fine-tuned conditions. Evaluation used a human-centred rubric assessing fluency, accuracy, and cultural appropriateness. The findings reveal a key nuance in applying LLMs to low-resource domains. The base GPT-4o model, with strong foundational multilingual capabilities, outperformed all other configurations, including its own fine-tuned variant.In contrast, fine-tuning provided a marked improvement for the less capable base Gemini model. This result indicates that fine-tuning can enhance weaker models; its benefits are not universal and may be outweighed by the strong zero-shot performance of state-of-the-art architectures when training data is scarce. The curated Sepedi rabies QA dataset will be released under an open licence to support future work in low-resource public health communication.

Rhinolophus bats harbour various alpha- and betacoronaviruses and are believed to be the progenitor host of SARS-CoV and SARS-CoV-2. These bats are widely distributed, with 38 species recognized in Africa. Although coronaviruses have been detected in several species in Africa, there is a lack of surveillance among South African rhinolophids. This study conducted longitudinal nucleic acid surveillance for Rhinolophus spp. coronaviruses from September 2021 to January 2024 in a mixed species cave in Limpopo, South Africa, using a hemi-nested RT-PCR assay. Among the 492 gastrointestinal samples collected, alphacoronavirus RNA was detected in 29.47% of samples, with betacoronavirus RNA identified among 7.11% of samples, with excretion peaks present in spring and summer (September-February). Based on GAMMs, the alphacoronavirus prevalence was strongly affected by season, total rainfall, and bat mass, whereas the betacoronavirus prevalence was influenced by forearm length, although the small sample size limits this finding. Rhinolophus acrotis contributed greatly to the interspecies sharing of alphacoronaviruses, and R. blasii was the primary origin of betacoronavirus interspecies sharing. This study expanded the known coronavirus diversity in African rhinolophids and highlighted the phylogeographic clustering of these viruses. The research emphasizes the need for more longitudinal studies involving African rhinolophids to better understand the ecological and behavioural factors that drive viral shedding for risk assessment and mitigation strategies.

Mpox has been declared a global health emergency twice by the World Health Organization due to its impacts within and beyond Africa. Enzootic in Central and West African wildlife, mpox outbreaks have resulted from zoonotic spillover, with recent events revealing increased human-to-human transmission. Factors like population growth and environmental disruption, alongside reduced smallpox immunity, increase emergence risk. In addition, the emergence in South Kivu of a distinct subclade of mpox virus points at a currently understudied aspect of mpox virus lineages and their dynamics in reservoir hosts. A One Health approach—integrating human, animal, and environmental science—is essential for reducing the risk of mpox emergence. This approach should encompass ecological studies to understand putative reservoir population dynamics and the potential for interventions, reducing activities that increase human-animal contacts, respectful community engagement to reduce spillover risk from cultural practices (such as hunting multiple species of wildlife for consumption), and socially acceptable and equitable access to medical and non-medical countermeasures to prevent or control ongoing human-to-human transmission. Politically supported collaborative efforts across disciplines with involvement of stakeholders are critical to promote and strengthen socially and environmentally sustainable practices to mitigate future outbreaks.

Rabies virus (RABV; species Lyssavirus rabies) causes rabies, a disease of the central nervous system that invariably results in the death of the host. In South Africa, studies have indicated that RABV is maintained by animal species that include four wildlife carnivore species—the black-backed jackal (Canis mesomelas), bat-eared fox (Otocyon megalotis), yellow mongoose (Cynictis penicillata), and aardwolf (Proteles cristatus)—and domestic dogs (Canis lupus familiaris). The complex natural ecology holds significant implications for the control and elimination of rabies. In this study, confirmed animal rabies case data, including geospatial features, were analyzed for 12,879 laboratory-confirmed animal cases reported on a database managed by the Department of Agriculture, Land Reform and Rural Development (DALRRD). Sequence data generated from animal rabies cases in South Africa were also analyzed, which included 1374 cytoplasmic domain of the glycoprotein and the G-L intergenic sequences using maximum likelihood (ML) and Bayesian inference. The analysis provides insights into the transmission dynamics involving several wildlife species and domestic dogs in South Africa. This information is crucial for the strategic planning for rabies control and elimination programs, and particularly in understanding the interlinked nature of some lineages and the importance of the cross-border spread of rabies. This analysis provided an improved understanding of the distribution of the RABV lineages in South Africa and identified areas that can be targeted for rabies control strategies to limit future spread of RABV, which is important due to the limited available resources that must be carefully managed to allow optimal control.

Rodents and other non-volant small mammals (like shrews) maintain major ecological and epidemiological roles as reservoirs of zoonotic pathogens. Their presence within human-modified landscapes and interfaces with people, wildlife, and livestock create frequent opportunities for viral spillover. Despite this, the pathogen diversity and true risk of viral transmission are poorly understood by these hosts in Africa. Here, we explored the diversity and host association of paramyxoviruses and coronaviruses in non-volant small mammals from South Africa through longitudinal and opportunistic sample collection and molecular detection of viral RNA and host genetic barcoding. A high diversity of viruses was identified, with prevalences of 11.9% and 1.79% for paramyxoviruses and coronaviruses, respectively. Five instances of coinfections involving multiple paramyxoviruses and a coronavirus were detected, as well as nine Bayesian-supported paramyxovirus host genus, subfamily, and family switching, signifying frequent unrestrained viral sharing. Though the zoonotic potential of these identified viruses is unknown, the frequency of host switching suggests that these viruses may be more prone to adaptation to new host species or utilize highly conserved entry mechanisms. This highlights the risks for potential cross-species transmission events to livestock, domestic animals, and people, warranting continued surveillance.

Hosting 1460 plant and 126 vertebrate endemic species, the Great Escarpment (hereafter, Escarpment) forms a semi-circular "amphitheater" of mountains girdling southern Africa from arid west to temperate east. Since arid and temperate biota are usually studied separately, earlier studies overlooked the biogeographical importance of the Escarpment as a whole. Bats disperse more widely than other mammalian taxa, with related species and intraspecific lineages occupying both arid and temperate highlands of the Escarpment, providing an excellent model to address this knowledge gap. We investigated patterns of speciation and micro-endemism from modeled past, present, and future distributions in six clades of southern African bats from three families (Rhinolophidae, Cistugidae, and Vespertilionidae) having different crown ages (Pleistocene to Miocene) and biome affiliations (temperate to arid). We estimated mtDNA relaxed clock dates of key divergence events across the six clades in relation both to biogeographical features and patterns of phenotypic variation in crania, bacula and echolocation calls. In horseshoe bats (Rhinolophidae), both the western and eastern "arms" of the Escarpment have facilitated dispersals from the Afrotropics into southern Africa. Pleistocene and pre-Pleistocene "species pumps" and temperate refugia explained observed patterns of speciation, intraspecific divergence and, in two cases, mtDNA introgression. The Maloti-Drakensberg is a center of micro-endemism for bats, housing three newly described or undescribed species. Vicariance across biogeographic barriers gave rise to 29 micro-endemic species and intraspecific lineages whose distributions were congruent with those identified in other phytogeographic and zoogeographic studies. Although Köppen-Geiger climate models predict a widespread replacement of current temperate ecosystems in southern Africa by tropical or arid ecosystems by 2070-2100, future climate Maxent models for 13 bat species (all but one of those analyzed above) showed minimal range changes in temperate species from the eastern Escarpment by 2070, possibly due to the buffering effect of mountains to climate change.

Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.

Abstract The global demand from multi-sectoral partners for operational tools for One Health implementation and capacity building is increasing, yet a validated global inventory of One Health tools did not exist. Here, we map and analyze available One Health tools and assess their suitability to support One Health implementation, including the One Health Joint Plan of Action 2022–2026 (OH JPA). Our objectives were to identify (i) publicly available One Health tools to support capacity building and OH JPA implementation; (ii) optimal outcomes for countries/regions using available One Health tools; (iii) linkages to OH JPA Action Tracks and pathways in the One Health Theory of Change (TOC); and (iv) gaps and priorities for the development of additional One Health tools. One Health High Level Expert Panel (OHHLEP) members compiled information on One Health tools that were publicly available and released up to June 30, 2023, via online sources and partner networks including the Quadripartite organizations. Inclusion criteria addressed One Health relevance, use at the national, subnational, or regional level in ≥5 locations, and publicly available information. Tools were assessed for applicability by OH JPA action track, TOC pathway, scope, and intended outcomes, as well as the extent to which tools addressed gender equality, social inclusion, and environmental dimensions of One Health. Of 132 candidate tools, 50 (38%) met the inclusion criteria. These tools addressed all six OH JPA Action Tracks, but relatively fewer tools addressed Action Tracks 4 (Food Safety), 5 (Antimicrobial Resistance), and 6 (Environmental Integration). Tools were available to support all three TOC outcome pathways, and many addressed more than one Action Track and TOC outcome pathway. Most available One Health tools addressed assessment and to a lesser extent implementation, with fewer tools available for action planning, prioritization, and monitoring. Gaps and opportunities for improving One Health tools were identified, including the integration of the environment dimension, gender equality, and social inclusion. Ultimately, our findings will contribute to further the advancement of One Health globally, including via OH JPA implementation, while spurring adjustments to existing One Health tools and the development of new ones to address key gaps. One Health impact statement The One Health approach is gaining momentum globally, and this study represents the first integrated mapping and analysis of globally available One Health tools. Our findings aim to improve the quality, applicability, and availability of tools to support One Health implementation at the subnational, national, regional, and global levels, including through the Quadripartite’s One Health Joint Plan of Action. By using the OHHLEP definition of One Health to assess available One Health tools and map them onto the One Health Joint Plan of Action, we identify the need for a systematic approach and enhanced integration across dimensions of One Health to lead to sustainable One Health systems.

Bats are recognized as reservoirs for diverse paramyxoviruses, some of which are closely related to known human pathogens or directly implicated in zoonotic transmission. The emergence of the zoonotic Sosuga virus (SOSV) from Egyptian rousette bats (ERBs), which caused an acute febrile illness in a reported human case in Africa, has increased the focus on the zoonotic potential of the Rubulavirinae subfamily. Previous studies identified human parainfluenza virus 2 (HPIV2)- and mumps (MuV)-related viruses in ERBs from South Africa, with HPIV2-related viruses restricted to gastrointestinal samples, an underexplored target for rubulavirus biosurveillance, suggesting that sample-type bias may have led to their oversight. To address this, we performed a longitudinal analysis of population-level fecal samples from an ERB maternity roost for rubulavirus RNA, employing a broadly reactive hemi-nested RT-PCR assay targeting the polymerase gene. We detected HPIV2- and MuV-related viruses in addition to numerous pararubulaviruses, highlighting significant viral diversity. Temporal analysis of three major clades revealed peaks in rubulavirus shedding that correlated with seasonal environmental changes and host reproductive cycles, although shedding patterns varied between clades. These findings identify specific periods of increased risk for the spillover of bat-associated rubulaviruses to humans, providing critical information for developing targeted mitigation strategies to minimize zoonotic transmission risk within the local community.

Globally, bats provide critical ecosystem services. Rabies, caused by rabies virus and related lyssaviruses, is one of the most significant zoonoses associated with bats. Bat biologists study bats in the laboratory and the field. To minimize the risk of disease, all bat handlers should be vaccinated against rabies and undergo routine serological testing to measure their rabies virus neutralizing antibody levels. They should use best practices to avoid exposures, such as personal protective equipment, especially gloves appropriate to the size of the bat(s) being handled. Attention to such details will prevent unnecessary exposures and avoid some of the accompanying negative perceptions that endanger bats on a global level. The small body sizes of many bats (<50 g, many <20 g) and small teeth makes their defensive bites easy to overlook. Breaks in the skin, however small, may result in exposure to lyssaviruses in the animals’ saliva. Exposure to blood-feeding bats is less common because these species are geographically restricted to the Neotropics and are the only species whose natural feeding behavior could involve transmission of rabies virus. Understanding viral transmission, preventing exposures, and responding appropriately to bites will minimize the consequences of this deadly zoonosis.

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species’ population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate ‘intactness scores’: the remaining proportion of an ‘intact’ reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region’s major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.