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The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski’s gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.

Background Bovine coronavirus (BoCV) causes significant economic losses to cattle farming due to mortality in calves, reduced growth performances and milk production in feedlots and dairy cattle. Worldwide distribution of BoCV has been demonstrated, although knowledge of its epidemiology in Africa, especially in the sub-Saharan region, is limited. Results In the present study, a total of 208 swab samples of wild ruminants and 435 bovines from different regions of Namibia were obtained and tested by a BoCV-specific qRT-PCR. Twenty-six bovine samples tested positive [26/435 (5.98%; 95CI: 3.94-8.64%)] while, among the wild ruminants, only Greater Kudu ( Tragelaphus strepsiceros ) were shown to be positive [13/52 (25.00%; 95CI: 14.03-38.95%)] of which 8 showed clinical signs. Analysis of partial nucleoprotein and spike protein gene sequences and comparison with international reference sequences demonstrated the existence of a unique Namibian clade, resulting from a single introduction event around 2010 followed by local evolution. Although the introduction source remains unknown, contact between bovine and wild animals appears likely. Conclusions The present study represents the first report of BoCV circulation in southern Africa, which showed a relatively high frequency and the ability of persisting and evolving locally in the absence of further foreign introductions. The implications for disease spread among domestic bovines and the potential impact on wildlife should encourage broader investigations on BoCV involving other African countries. Moreover, the Greater Kudu’s susceptibility to BoCV infection was also proven, further highlighting the host plasticity of this virus.

Background Malignant catarrhal fever (MCF) is a sporadic infectious disease of domesticated and non-domesticated ruminants including: cattle, sheep, bison, cervids, antelope and buffaloes, and is caused by gammaherpesviruses. Between March and May 2023, several cases of sudden death were observed in endangered species of dorcas gazelle ( Gazella dorcas osiris) in zoological garden in southeastern Poland. Given the rapid course of disease, MCF was suspected. During the epizootic investigation, other ruminants that could be a source of infection and routes of spread were examined, also taking into account the possibility of air-born and via rodents transmission. In total, tissue, blood, nasal swab and fecal samples were collected from 52 animals kept in the zoo between March 2023 and August 2025. Samples came from 10 ruminants species: dorcas gazelle ( Gazella dorcas ), blackbuck ( Antilope cervicapra ), lechwe ( Kobus leche ), Defassa waterbuck ( Kobus ellipsiprymnus defassa ), Reeves’s muntjac ( Muntiacus reevesi ), Kirk’s dik-dik ( Madoqua kirkii ), gemsbok ( Oryx gazella) , Barbary sheep ( Ammotragus lervia ), mhorr gazelle ( Nanger dama ) and domestic goat ( Capra hircus ). Additionally, environmental swabs and tissue samples from rats ( Rattus norvegicus ) trapped at the premises were collected. To identify possible causes of dorcas mortality, samples were tested using PCRs specific to gammaherpesviruses followed by characterisation of strains based on DNA polymerase fragment sequences. Clostridium spp. was also investigated in the differential diagnosis. Results In total 4 different strains of gammaherpesvirus were detected in 26.9% (14/52) of the tested ruminants, It was also established that the five gazelles with suspected MCF were infected with at least one of the two previously unknown gammaherpesviruses provisionally called: Gazelle dorcas gammaherpesvirus 1 and Gazelle dorcas gammaherpesvirus 2. Those viruses showed significant similarity to Rusa unicolor equina gammaherpesvirus later detected in asymptomatic dik-diks and Bovidae gammaherpesvirus 2 in healthy blackbucks, respectively. These viruses were not detected in newborn, nor in the two remaining dorcas survivors. Histopathological analysis showed changes that might be associated with MCF in kidneys, lungs and livers of two affected dorcas gazelles. C. perfringens type D co-infection was detected also in two adult dorcas which died suddenly. The same bacteria was also found in the feeder in one of the enclosures, suggestive of environmental contamination. Conclusion This is the first description of two novel gammaherpesvirus, associated with fatal disease in dorcas gazelles. Additionally, our results showed possibility of transmission of those viruses between different Antilopinae species. While ranges of those species do not overlap in their natural habitat, our results could have potential implication for conservation strategies and initiatives for endangered species.

Rabies in the Greater Kudu ( Tragelaphus strepsiceros) in Namibia is unique and found in such magnitude as has not been reported elsewhere in southern Africa. Reasons as to why Kudus appear to be exceptionally susceptible to rabies still remain speculative at best. Because the current severe rabies endemic in Kudus continues to have an enormous negative impact on the Namibian agricultural sector, we set out to question existing dogmas regarding the epidemiology of the disease in a unique experimental setting. In addition, we explored effective measures to protect these antelopes. Although we were able to confirm high susceptibly of kudus for rabies and sporadic horizontal rabies virus transmission to contact animals, we contend that these observations cannot plausibly explain the rapid spread of the disease in Kudus over large territories. Since parenteral vaccination of free-roaming Kudus is virtually impossible, oral rabies vaccination using modified life virus vaccines with a high safety profile would be the ultimate solution to the problem. In a proof-of-concept study using a 3rd generation oral rabies virus vaccine construct (SPBN GASGAS) we found evidence that Kudus can be vaccinated by the oral route and protected against a subsequent rabies infection. In a second phase, more targeted studies need to be initiated by focusing on optimizing oral vaccine uptake and delivery.

The 2016-2017 introduction of peste des petits ruminants virus (PPRV) into livestock in Mongolia was followed by mass mortality of the critically endangered Mongolian saiga antelope and other rare wild ungulates. To assess the nature and population effects of this outbreak among wild ungulates, we collected clinical, histopathologic, epidemiologic, and ecological evidence. Molecular characterization confirmed that the causative agent was PPRV lineage IV. The spatiotemporal patterns of cases among wildlife were similar to those among livestock affected by the PPRV outbreak, suggesting spillover of virus from livestock at multiple locations and time points and subsequent spread among wild ungulates. Estimates of saiga abundance suggested a population decline of 80%, raising substantial concerns for the species' survival. Consideration of the entire ungulate community (wild and domestic) is essential for elucidating the epidemiology of PPRV in Mongolia, addressing the threats to wild ungulate conservation, and achieving global PPRV eradication.

New technologies enable viral discovery in a diversity of hosts, providing insights into viral evolution. We used one such approach, the virome capture sequencing for vertebrate viruses (VirCapSeq-VERT) platform, on 21 samples originating from six dead Maxwell’s duikers (Philantomba maxwellii) from Taï National Park, Côte d’Ivoire. We detected the presence of an orthohepadnavirus in one animal and characterized its 3128 bp genome. The highest viral copy numbers were detected in the spleen, followed by the lung, blood, and liver, with the lowest copy numbers in the kidney and heart; the virus was not detected in the jejunum. Viral copy numbers in the blood were in the range known from humans with active chronic infections leading to liver histolytic damage, suggesting this virus could be pathogenic in duikers, though many orthohepadnaviruses appear to be apathogenic in other hosts, precluding a formal test of this hypothesis. The virus was not detected in 29 other dead duiker samples from the Côte d’Ivoire and Central African Republic, suggesting either a spillover event or a low prevalence in these populations. Phylogenetic analysis placed the virus as a divergent member of the mammalian clade of orthohepadnaviruses, though its relationship to other orthohepadnaviruses remains uncertain. This represents the first orthohepadnavirus described in an artiodactyl. We have tentatively named this new member of the genus Orthohepadnavirus (family Hepadnaviridae), Taï Forest hepadnavirus. Further studies are needed to determine whether it, or some close relatives, are present in a broader range of artiodactyls, including livestock.

Alcelaphine herpesvirus-1 (AlHV-1), a causative agent of malignant catarrhal fever in cattle, was detected in wildebeest (Connochaetes taurinus) placenta tissue for the first time. Although viral load was low, the finding of viral DNA in over 50% of 94 samples tested lends support to the possibility that placental tissue could play a role in disease transmission and that wildebeest calves are infected in utero. Two viral loci were sequenced to examine variation among virus samples obtained from wildebeest and cattle: the ORF50 gene, encoding the lytic cycle transactivator protein, and the A9.5 gene, encoding a novel polymorphic viral glycoprotein. ORF50 was well conserved with six newly discovered alleles differing at only one or two base positions. In contrast, while only three new A9.5 alleles were discovered, these differed by up to 13% at the nucleotide level and up to 20% at the amino acid level. Structural homology searching performed with the additional A9.5 sequences determined in this study adds power to recent analysis identifying the four-helix bundle cytokine interleukin-4 (IL4) as the major homologue. The majority of MCF virus samples obtained from Tanzanian cattle and wildebeest encoded A9.5 polypeptides identical to the previously characterized A9.5 allele present in the laboratory maintained AlHV-1 C500 strain. This supports the view that AlHV-1 C500 is suitable for the development of a vaccine for wildebeest-associated MCF.

Bovine viral diarrhoea virus 1 (BVDV-1) and Bovine viral diarrhoea virus 2 (BVDV-2) are two recognised bovine pestivirus species of the genus Pestivirus . Recently, a pestivirus, termed SVA/cont-08, was detected in a batch of contaminated foetal calf serum originating from South America. Comparative sequence analysis showed that the SVA/cont-08 virus shares 15–28% higher sequence identity to pestivirus D32/00_‘HoBi’ than to members of BVDV-1 and BVDV-2. In order to reveal the phylogenetic relationship of SVA/cont-08 with other pestiviruses, a molecular dataset of 30 pestiviruses and 1,896 characters, comprising the 5′UTR, N pro and E2 gene regions, was analysed by two methods: maximum likelihood and Bayesian approach. An identical, well-supported tree topology was observed, where four pestiviruses (SVA/cont-08, D32/00_‘HoBi’, CH-KaHo/cont, and Th/04_KhonKaen) formed a monophyletic clade that is closely related to the BVDV-1 and BVDV-2 clades. The strategy applied in this study is useful for classifying novel pestiviruses in the future.

Reports of equine herpesvirus (EHV) 1 and EHV-9 causing clinical disease in a wide range of species have been well documented in the literature. It is thought that zebras are the natural hosts of EHV-9 both in the wild and in captive collections. Concerns about potential interspecies transmission of EHV-1 and EHV-9 in a mixed species savannah exhibit prompted serologic and polymerase chain reaction surveys. Eighteen Burchell's zebras (Equus quagga), 11 Hartmann's mountain zebras (Equus zebra hartmannae), and 14 Thomson's gazelles (Eudorcas thomsonii) cohabitating the same exhibit were examined for EHV-1 virus neutralization titers, and evidence of virus via EHV 1-5 polymerase chain reactions. None of the animals had previous exposure to vaccination with EHV-1 or EHV-4. All tested zebras had positive EHV-1 titers, ranging from 4 to 384. All zebras and Thomson's gazelles had negative polymerase chain reaction results for all targeted equine herpesviruses. EHV-9–specific assays are not available but EHV-1, EHV-4, and EHV-9 cross-react serologically. Positive serology results indicate a potential latent equine herpesvirus in the zebra population, which prompted initiation of an equine herpesvirus vaccine protocol, changes in pregnant zebra mare management, and equine herpesvirus polymerase chain reaction screening prior to shipment to or from the study site.

In areas where foot-and-mouth disease (FMD) is endemic in wildlife hosts, such as the Kruger National Park (KNP) in South Africa, control measures are in place that ensure that potentially infected antelope and buffalo do not come into close contact with domestic animals. In South Africa several SAT-1 outbreaks occurred nearly simultaneously in cattle and impala between 1971–1981. Phylogenetic analysis based on partial 1D gene nucleotide sequencing indicated that several of these outbreaks were linked and it is probable that disease spread from the intermediary impala antelope host to cattle in close proximity. Evidence was found for the involvement of viruses from a single KNP genotype in precipitating outbreaks in impala over a 10-year period. In addition, several unrelated outbreaks affecting cattle and impala occurred within a single year. Characterisation of outbreak strains from Botswana similarly revealed that a single genotype affected different species over a 10-year period and that transboundary spread of SAT-1 virus occurred on at least one occasion. This retrospective analysis of outbreak strains has clearly demonstrated that FMD control policies that address the role of antelope as intermediaries in disease transmission are crucial as these wildlife species play an important role in disease dissemination.