Frequency, kinetics and determinants of viable SARS-CoV-2 in bioaerosols from ambulatory COVID-19 patients infected with the Beta, Delta or Omicron variants

Airborne transmission of SARS-CoV-2 aerosol remains contentious. Importantly, whether cough or breath-generated bioaerosols can harbor viable and replicating virus remains largely unclarified. We performed size-fractionated aerosol sampling (Andersen cascade impactor) and evaluated viral culturability in human cell lines (infectiousness), viral genetics, and host immunity in ambulatory participants with COVID-19. Sixty-one percent (27/44) and 50% (22/44) of participants emitted variant-specific culture-positive aerosols <10μm and <5μm, respectively, for up to 9 days after symptom onset. Aerosol culturability is significantly associated with lower neutralizing antibody titers, and suppression of transcriptomic pathways related to innate immunity and the humoral response. A nasopharyngeal Ct <17 rules-in ~40% of aerosol culture-positives and identifies those who are probably highly infectious. A parsimonious three transcript blood-based biosignature is highly predictive of infectious aerosol generation (PPV > 95%). There is considerable heterogeneity in potential infectiousness i.e., only 29% of participants were probably highly infectious (produced culture-positive aerosols <5μm at ~6 days after symptom onset). These data, which comprehensively confirm variant-specific culturable SARS-CoV-2 in aerosol, inform the targeting of transmission-related interventions and public health containment strategies emphasizing improved ventilation.

Diversity of selected toll-like receptor genes in cheetahs (Acinonyx jubatus) and African leopards (Panthera pardus pardus)

The anthropogenic impact on wildlife is ever increasing. With shrinking habitats, wild populations are being pushed to co-exist in proximity to humans leading to an increased threat of infectious diseases. Therefore, understanding the immune system of a species is key to assess its resilience in a changing environment. The innate immune system (IIS) is the body's first line of defense against pathogens. High variability in IIS genes, like toll-like receptor (TLR) genes, appears to be associated with resistance to infectious diseases. However, few studies have investigated diversity in TLR genes in vulnerable species for conservation. Large predators are threatened globally including leopards and cheetahs, both listed as 'vulnerable' by IUCN. To examine IIS diversity in these sympatric species, we used next-generation-sequencing to compare selected TLR genes in African leopards and cheetahs. Despite differences, both species show some TLR haplotype similarity. Historic cheetahs from all subspecies exhibit greater genetic diversity than modern Southern African cheetahs. The diversity in investigated TLR genes is lower in modern Southern African cheetahs than in African leopards. Compared to historic cheetah data and other subspecies, a more recent population decline might explain the observed genetic impoverishment of TLR genes in modern Southern African cheetahs. However, this may not yet impact the health of this cheetah subspecies.

Harnessing the potential of data-driven strategies to optimise transfusion practice

No one doubts the significant variation in the practice of transfusion medicine. Common examples are the variability in transfusion thresholds and the use of tranexamic acid for surgery with likely high blood loss despite evidence-based standards. There is a long history of applying different strategies to address this variation, including education, clinical guidelines, audit and feedback, but the effectiveness and cost-effectiveness of these initiatives remains unclear. Advances in computerised decision support systems and the application of novel electronic capabilities offer alternative approaches to improving transfusion practice. In England, the National Institute for Health and Care Research funded a Blood and Transplant Research Unit (BTRU) programme focussing on 'A data-enabled programme of research to improve transfusion practices'. The overarching aim of the BTRU is to accelerate the development of data-driven methods to optimise the use of blood and transfusion alternatives, and to integrate them within routine practice to improve patient outcomes. One particular area of focus is implementation science to address variation in practice.

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)

We live in a world characterized by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict and illegal trafficking, there are only approximately 7100 individuals remaining in nature. We present the most comprehensive genome-wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (A. j. raineyi) are genetically distinct from Southern African individuals (A. j. jubatus), warranting their recognition as a distinct subspecies. We found strong genetic differentiation between all classically recognized subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was observed between the Asiatic and all the African subspecies. We detected high inbreeding in the Critically Endangered Iranian (A. j. venaticus) and North-western (A. j. hecki) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome-wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence-based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.

Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex

The Nubian ibex (Capra nubiana) is a wild goat species that inhabits the Sahara and Arabian deserts and is adapted to extreme ambient temperatures, intense solar radiation, and scarcity of food and water resources. To investigate desert adaptation, we explored the possible role of copy number variations (CNVs) in the evolution of Capra species with a specific focus on the environment of Capra nubiana. CNVs are structural genomic variations that have been implicated in phenotypic differences between species and could play a role in species adaptation. CNVs were inferred from Capra nubiana sequence data relative to the domestic goat reference genome using read-depth approach. We identified 191 CNVs overlapping with protein-coding genes mainly involved in biological processes such as innate immune response, xenobiotic metabolisms, and energy metabolisms. We found copy number variable genes involved in defense response to viral infections (Cluster of Differentiation 48, UL16 binding protein 3, Natural Killer Group 2D ligand 1-like, and Interferon-induced transmembrane protein 3), possibly suggesting their roles in Nubian ibex adaptations to viral infections. Additionally, we found copy number variable xenobiotic metabolism genes (carboxylesterase 1, Cytochrome P450 2D6, Glutathione S-transferase Mu 4, and UDP Glucuronosyltransferase-2B7), which are probably an adaptation of Nubian ibex to desert diets that are rich in plant secondary metabolites. Collectively, this study's results advance our understanding of CNVs and their possible roles in the adaptation of Nubian ibex to its environment. The copy number variable genes identified in Nubian ibex could be considered as subjects for further functional characterizations.

Sperm motility, kinematics, morphometry and morphology over two seasons in free-ranging African elephants (Loxodonta africana)

This study aimed to address the lack of information on quantitative semen and sperm characteristics of free-ranging African elephants. Nineteen ejaculates were collected from 12 elephant bulls by means of electroejaculation in spring (Season 1, end of dry season, n=7) and in autumn (Season 2, end of rainy season, n=12). While most elephant cows are in oestrus in the rainy season, it is not evident whether sperm quality also improves during this period. Semen samples were assessed using computer-aided sperm analysis (CASA), brightfield microscopy and transmission electron microscopy. Seasonal differences and individual variation in sperm quality of bulls were apparent, with ejaculates collected during Season 2 revealing higher percentages for total motility, progressive motility, rapid-swimming spermatozoa and kinematic parameters compared with Season 1 (P<0.05). Although normal sperm morphology percentage was similar over the two seasons, more sperm tail defects were found in Season 2 (P<0.05). The baseline reference data and multivariate sperm parameter associations reported in this study can be used to predict elephant bull sperm quality and potential to fertilise. It is clear that CASA can detect subtle differences in sperm quality of African elephant ejaculates and should be the approach for future investigations.

Quantitative sperm characteristics of Tankwa goats with special reference to hyperactivated motility

Computer-assisted semen analysis (CASA) is an automated and objective method of evaluating structural (e.g. morphology) and functional sperm parameters (e.g. motility and hyperactivation). Sperm hyperactivation is essential for successful fertilization and is thus an important aspect in determining the fertility potential of a male. In the current study, CASA was used for standard semen analysis and for comparison of the ability of phosphate buffered saline (PBS), BO sperm wash (10 mM caffeine), 4% lignocaine, and 5 mM procaine hydrochloride to induce hyperactivation in Tankwa goat spermatozoa. Twenty-nine ejaculates were collected from randomly selected male goats by electroejaculation. Although none of the four media affected percentage total sperm motility, lignocaine caused a significant decrease (P >0.05) in percentage progressive motility. Exposure to procaine resulted in an increase in swimming speed (P ≤0.05) and star-spin motility tracks, which are typical of sperm hyperactivation. Using PBS and procaine motility data from individually selected spermatozoa, receiver operator characteristic curves were constructed to distinguish the kinematic parameters employed as cut-off values for sperm hyperactivation. PBS and BO sperm wash did not induce hyperactivation (0.1 + 0.2% and 0.04  0.2% respectively), while lignocaine induced little hyperactivation (3.4 + 3.0%) and procaine hydrochloride had the highest percentage hyperactivation (25.3 + 13.6%). The large variation in hyperactivation (0–54.5%) may reflect inter-individual differences in sperm quality among these males. This study indicated procaine hydrochloride was the most promising hyperactivation-inducing medium for Tankwa goat spermatozoa and should be considered for similar assessments in other animal species Keywords: computer-aided sperm analysis, procaine hydrochloride, sperm kinematics, sperm morphometry, sperm motility

Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus)

Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30 ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade.

Seasonal changes in reproductive anatomy and gonadal hormone concentrations of African penguins (Spheniscus demersus)

Several standard descriptions of the avian male and female reproductive tract have been reported, including effects of age, stage of reproductive maturity and gonadal hormone concentrations. Limited information on penguin reproductive biology and a lack of information on the African penguin (Spheniscus demersus) necessitated a detailed description of salient structural features of this species and provided an opportunity to evaluate seasonal changes in gonadal steroid hormone concentrations. Tissues from 36 males (adults and juveniles) and 29 females (adults and juveniles) were used for macro-anatomical descriptions and histology of the testes and ovaries. In addition, concentrations of gonadal steroid hormones for eight captive African penguins (four females and four males) were quantified during two breeding and one non-breeding season. The testes were asymmetrical, with the right testis having smaller dimensions compared to the left testis. Marked spermatogenic cellular associations and spermatid developmental stages were present in adult testes only during the breeding season. There was variation in the dimensions of the single ovary during follicular development related to the age and breeding status of the females. Testosterone, dihydrotestosterone, and estradiol concentrations fluctuated during the breeding and non-breeding periods, with males and females having similar steroid concentrations. The results from this study confirm that the breeding status in African penguins can be deduced based on testicular and ovarian histological structures. The results from the present study focused on African penguin reproductive biology should be considered in management strategies for the conservation of the species.

Population genetic structure of the thick-tailed bushbaby (Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions

Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007-0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166-0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2-3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3-5 in coding region and 6-10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.

Canine parvovirus detected from a serval (Leptailurus serval) in South Africa

Canine parvovirus first emerged in domestic dogs (Canis familiaris), most likely as a variant of the feline panleucopaenia virus. Relatively recently, canine parvovirus-2a and canine parvovirus-2b infections have been identified in both symptomatic and asymptomatic domestic cats, while canine parvovirus infections have also been demonstrated in wild felids. This report documents the first known case of canine parvovirus-2b detected in unvaccinated serval (Leptailurus serval) from South Africa. The serval presented with clinical signs of vomiting, anorexia and diarrhoea that responded to symptomatic treatment. Two weeks later, severe leucopaenia, thrombocytopenia and death occurred. Typical enteric histological lesions of parvovirus infection were not observed on histopathological examination of the small intestine; however, histological lesions consistent with septicaemia were present. Canine parvovirus was detected in formalin-fixed paraffin-embedded small intestine using polymerase chain reaction. Phylogenetic analysis of the sequence of the canine parvovirus viral capsid protein gene showed similarities between the sample from the serval and canine parvovirus-2b isolates from domestic dogs in Argentina and South Africa. A case of canine parvovirus-2b in a domestic dog from South Africa in 2012 that fell within the same clade as the serval sample appears distantly related because of the long branch length. The significance of these findings is explored. More extensive surveys of canine parvovirus in domestic and wild felids and canids are needed to understand the epidemiology of canine parvovirus in non-domestic felids in South Africa.

Sperm structure and sperm motility of the African and Rockhopper penguins with special reference to multiple axonemes of the flagellum

This study evaluated the semen of two penguin species from separate genera with reference to unique features in sperm structure using light microscopy and transmission electron microscopy. Ejaculates from African penguin (n = 51) and Rockhopper penguin (n = 9) contained on average more than 60% motile spermatozoa and a sperm concentration of 3274 × 10⁶/ml and 1423 × 10⁶/ml, respectively. The percentage progressive motility was similar for the two species as well as all the kinematics parameters. The sperm morphology of these two penguin species is almost identical and largely resembles that of non-passerine birds in terms of the filiform head, small acrosome and mid-piece containing 13 spherical mitochondria, arranged around the proximal and distal centrioles in a single helix. Apart from a shorter mid-piece, penguin sperm morphometrics were similar to other non-passerine birds. The ultrastructure of the sperm principal piece revealed the typical 9 + 2 microtubular arrangement without any outer dense fibres. An unusual feature in both African and Rockhopper penguin spermatozoa was the occurrence of multiple axonemes contained in one plasmalemma in 4% of spermatozoa. These double, triple and quadruple axonemal arrangements have not been described previously albeit multiple tails were reported in other bird species. It is unclear whether such a unique structural feature will be of any advantage for sperm motility and might rather be a result of the absence of sperm competition. Multiple axonemes found in penguin flagella could be an apomorphism that distinguish them from other bird spermatozoa.

Next generation sequencing yields the mitochondrial genome of the critically endangered Sarothrura ayresi (white-winged flufftail)

The mitochondrial genome of Sarothrura ayresi was sequenced using next generation sequencing technology. The size of the genome is reported as 16,767 bp and comprises 13 protein-coding genes, 2 rRNAs and 22 tRNAs. The organization of the genome is comparable to that of other bird species. A phylogenetic comparison mapped the relative relationship of Sarothrura ayresi with respect to other species in the order Gruiformes.

Intrinsic factors, adrenal gland morphology, and disease burden in captive cheetahs (Acinonyx jubatus) in South Africa

Adrenal gland weight (AW) and corticomedullary ratio (ACMR) are used as indicators of stress in animals. Captive cheetahs (Acinonyx jubatus) have higher ACMRs than free-ranging ones and stress has been linked to gastritis, amyloidosis, glomerulosclerosis, and myocardial fibrosis. We reviewed age, sex, body weight (BW), kidney weight (KW), and left AW and ACMR with necropsy findings in 51 South African captive cheetahs. Eleven common histopathologic lesions were counted for each animal as measure of its disease burden. Adrenal corticomedullary hyperplasia was significantly correlated with left AW and ACMR. Males had significantly higher AWs than females; other parameters showed no difference between the sexes. Disease burden, gastritis, and myocardial fibrosis were moderately correlated with adrenal morphology supporting prior evidence that gastritis and myocardial fibrosis are linked to stress. Glomerulosclerosis was not correlated with adrenal morphology and neither kidney nor liver amyloidosis contributed significantly to variation in AW or ACMR on multivariate analyses. Interstitial nephritis showed much stronger correlations with kidney and liver amyloidosis than gastritis. All three adrenal parameters were correlated with age; age was the only significant variable affecting ACMR on the multivariate analyses; and disease burden as well as systemic amyloidosis and kidney disease (except for fibrosis) showed moderate correlations with age. Age may, therefore, be important in the pathogenesis of disease in captive cheetahs, particularly of amyloidosis and kidney disease. None of the intrinsic measurements or adrenal parameters were sufficiently closely linked to disease to be used as ante-mortem proxies for disease burden or specific diseases. Zoo Biol. 36:40-49, 2017. © 2016 Wiley Periodicals, Inc.

Lack of diversity at innate immunity Toll-like receptor genes in the Critically Endangered White-winged Flufftail (Sarothrura ayresi)

The White-winged Flufftail (Sarothrura ayresi) population is listed as globally Critically Endangered. White-winged Flufftails are only known to occur, with any regularity, in the high-altitude wetlands of South Africa and Ethiopia. Threats to the species include the limited number of suitable breeding sites in Ethiopia and severe habitat degradation and loss both in Ethiopia and South Africa. Toll-like receptors (TLRs) are increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune regions of the White-winged Flufftail similar to that observed in other bird species that have undergone population bottlenecks. Low TLR diversity in White-winged Flufftail indicates that this species is more likely to be threatened by changes to the environment that would potentially expose the species to new diseases. Thus, conservation efforts should be directed towards maintaining pristine habitat for White-winged Flufftail in its current distribution range. To date, no studies on immunogenetic variation in White-winged Flufftail have been conducted and to our knowledge, this is the first study of TLR genetic diversity in a critically endangered species.

Classical and Molecular Cytogenetics of the Panther Genet Genetta maculata (Mammalia, Carnivora, Viverridae)

Genets (Genetta) are a genus of African mammalian carnivorans with 14 currently recognized species, although taxonomic uncertainties remain, particularly regarding the number of species within the large-spotted genet complex. This study presents the first banded karyotype and molecular cytogenetic analysis of a genetically identified panther genet, Genetta maculata, the most common and widespread taxon of the large-spotted genet complex, with a wide distribution in sub-Saharan Africa. Sampled in Gauteng Province, South Africa, it could be assigned to the subspecies G. m. letabae on geographic grounds and had a similar karyotype (2n = 52, FNa = 96) to those published for a panther genet from Ethiopia and for the West African large-spotted genet G. pardina. Notably, the specimen had a different autosomal morphology (2 acrocentric chromosomes) from that previously attributed to letabae (a single acrocentric chromosome), but the latter assignment was uncertain because the studied individuals were captive born and assigned based solely on a presumed origin in the former Transvaal Province of South Africa. Fluorescence in situ hybridization with a telomere repeat probe revealed the presence of telomeric sequences in the centromeres of most chromosomes, the so-called interstitial telomeric sites (ITSs). Since genets seem to have a unique, highly rearranged karyotype among feliforms and relatively low interspecific karyotypic variation, and considering the known instability of ITSs, we suggest that the large amount of ITSs found here might be due to evolutionarily recent extensive genomic rearrangements. This study provides cytogenetic information that contributes to our understanding of chromosomal variation and genomic rearrangements in genets, and valuable baseline data for future studies of karyotype evolution in carnivores in general and viverrids in particular.

Diversity in the Toll-Like Receptor Genes of the African Penguin (Spheniscus demersus)

The African penguin, Spheniscus demersus, is listed as Endangered by the IUCN Red List of Threatened Species due to the drastic reduction in population numbers over the last 20 years. To date, the only studies on immunogenetic variation in penguins have been conducted on the major histocompatibility complex (MHC) genes. It was shown in humans that up to half of the genetic variability in immune responses to pathogens are located in non-MHC genes. Toll-like receptors (TLRs) are now increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune region of African penguins similar to that observed in New Zealand robin that has undergone several severe population bottlenecks. Single nucleotide polymorphism (SNP) diversity across TLRs varied between ex situ and in situ penguins with the number of non-synonymous alterations in ex situ populations (n = 14) being reduced in comparison to in situ populations (n = 16). Maintaining adaptive diversity is of vital importance in the assurance populations as these animals may potentially be used in the future for re-introductions. Therefore, this study provides essential data on immune gene diversity in penguins and will assist in providing an additional monitoring tool for African penguin in the wild, as well as to monitor diversity in ex situ populations and to ensure that diversity found in the in situ populations are captured in the assurance populations.

Diet of otters (Lutra lutra) in various habitat types in the Pannonian biogeographical region compared to other regions of Europe

Knowledge of the effect of habitat type and region on diet and feeding behaviours of a species facilitates a better understanding of factors impacting populations, which contributes to effective conservation management. Using spraint analysis and relative frequency of occurrence data from the literature, we described the dietary patterns of Eurasian otters (Lutra lutra) in 23 study sites within the Pannonian biogeographical region in Hungary. Our results indicated that diet composition varied by habitat type and is therefore context dependant. The differences among habitat types were however lower than expected. We noticed a decline in the fish consumption with a concomitant increase in trophic niche breadth and amphibian consumption in rivers, ponds (fish farms), backwaters, marshes and small watercourses. The main differences in diet were not attributed to the consumption of primary and secondary food types (fish and amphibians), but rather to differences in other, less important food types (mammals, birds). Using hierarchical cluster analysis, rivers and ponds could clearly be separated from other habitat types. We found the main fish diet of otters in most of these areas consisted of small (<100 g), eurytopic, littoral and non-native, mostly invasive species. Dietary studies from 91 sites in six European biogeographical regions showed that fish are consumed most frequently in the Atlantic and Boreal, less in the Continental and Pannonian, and least in the Alpine and Mediterranean regions. Comparative analysis indicated that the Mediterranean region (with frequent crayfish consumption) and Alpine region (frequent amphibian consumption) cluster separate from the other regions.

Pangolin genomes and the evolution of mammalian scales and immunity

Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress and reduced pangolin vulnerability to infection. Further evidence of specialized adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction system. This study provides insights into mammalian adaptation and functional diversification, new research tools and questions, and perhaps a new natural IFNE-deficient animal model for studying mammalian immunity.

Feline panleukopaenia virus in captive non-domestic felids in South Africa

An outbreak of feline panleukopaenia virus (FPLV) infection was diagnosed by pathology, electron microscopy and polymerase chain reaction (PCR) in vaccinated captive-bred subadult cheetahs in South Africa. Subsequent to this disease outbreak, 12 cases of FPLV diagnosed on histology were confirmed by PCR in captive African black-footed cat, caracal, cheetah, lion, ocelot and serval. Phylogenetic analyses of the viral capsid protein gene on PCR-positive samples, vaccine and National Center for Biotechnology Information (NCBI) reference strains identified a previously unknown strain of FPLV, present since at least 2006, that differs from both the inactivated and the modified live vaccine strains. A previously described South African strain from domestic cats and cheetahs was identified in a serval. Surveys of FPLV strains in South African felids are needed to determine the geographical and host species distribution of this virus. Since non-domestic species may be reservoirs of parvoviruses, and since these viruses readily change host specificity, the risks of FPLV transmission between captive-bred and free-ranging carnivores and domestic cats and dogs warrant further research.

The 'Toolbox' of strategies for managing Haemonchus contortus in goats: What's in and what's out

A dynamic and innovative approach to managing the blood-consuming nematode Haemonchus contortus in goats is critical to crack dependence on veterinary anthelmintics. H. contortus management strategies have been the subject of intense research for decades, and must be selected to create a tailored, individualized program for goat farms. Through the selection and combination of strategies from the Toolbox, an effective management program for H. contortus can be designed according to the unique conditions of each particular farm. This Toolbox investigates strategies including vaccines, bioactive forages, pasture/grazing management, behavioural management, natural immunity, FAMACHA, Refugia and strategic drenching, mineral/vitamin supplementation, copper Oxide Wire Particles (COWPs), breeding and selection/selecting resistant and resilient individuals, biological control and anthelmintic drugs. Barbervax(®), the ground-breaking Haemonchus vaccine developed and currently commercially available on a pilot scale for sheep, is prime for trialling in goats and would be an invaluable inclusion to this Toolbox. The specialised behaviours of goats, specifically their preferences to browse a variety of plants and accompanying physiological adaptations to the consumption of secondary compounds contained in browse, have long been unappreciated and thus overlooked as a valuable, sustainable strategy for Haemonchus management. These strategies are discussed in this review as to their value for inclusion into the 'Toolbox' currently, and the future implications of ongoing research for goat producers. Combining and manipulating strategies such as browsing behaviour, pasture management, bioactive forages and identifying and treating individual animals for haemonchosis, in addition to continuous evaluation of strategy effectiveness, is conducted using a model farm scenario. Selecting strategies from the Toolbox, with regard to their current availability, feasibility, economical cost and potential ease of implementation depending on the systems of production and their complementary nature, is the future of managing H. contortus in farmed goats internationally and maintaining the remaining efficacy of veterinary anthelmintics.

New insights into samango monkey speciation in South Africa

The samango monkey is South Africa's only exclusively forest dwelling primate and represents the southernmost extent of the range of arboreal guenons in Africa. The main threats to South Africa's forests and thus to the samango are linked to increasing land-use pressure and increasing demands for forest resources, resulting in deforestation, degradation and further fragmentation of irreplaceable habitats. The species belongs to the highly polytypic Cercopithecus nictitans group which is sometimes divided into two species C. mitis and C. albogularis. The number of subspecies of C. albogularis is also under debate and is based only on differences in pelage colouration and thus far no genetic research has been undertaken on South African samango monkey populations. In this study we aim to further clarify the number of samango monkey subspecies, as well as their respective distributions in South Africa by combining molecular, morphometric and pelage data. Overall, our study provides the most comprehensive view to date into the taxonomic description of samango monkeys in South Africa. Our data supports the identification of three distinct genetic entities namely; C. a. labiatus, C. a. erythrarchus and C. a. schwarzi and argues for separate conservation management of the distinct genetic entities defined by this study.

First records of reproductive behaviour and early development of the bearded goby Sufflogobius bibarbatus

Data on developmental characteristics from fertilization to 2 days post-hatching during captivity of the anoxia tolerant bearded goby Sufflogobius bibarbatus, one of the keystone prey species for many of the commercial fish populations, sea mammals and birds in south-west Africa, are presented.

Molecular detection of Yaba monkey tumour virus from a vervet monkey

Yaba monkey tumour virus (YMTV) was first diagnosed in a colony of captive rhesus monkeys (Macaca mulatta) in Yaba, Nigeria. It has been implicated as the cause of cutaneous nodules in wild baboons (Papio species), rhesus monkeys (Macaca mulatta) and cynomolgus monkeys (Macaca fascicularis). This article reports a case of cutaneous pox lesions caused by YMTV in a  free-ranging  adult  female  vervet  monkey  (Chlorocebus  pygerythrus)  from  the  Umkomaas coastal area in South Africa. The virus was identified by molecular sequencing from fragments of the insulin metalloprotease-like protein and intracellular mature virion membrane protein as well as the DNA polymerase genes. Phylogenetic analyses of these gene regions revealed a 99% similarity of the sample to YMTV. Although human disease caused by YMTV is normally mild,  it  is  recommended  that  persons  in  contact  with  non-human  primates  in  the  area  of Umkomaas who develop cutaneous lesions should inform their doctors of the possibility of this infection. The extent and significance of the virus to human and non-human primates in South Africa are not known. To the authors’ knowledge, this is the first diagnosis of YMTV in South Africa and in vervet monkeys.

The home range of a recently established group of Southern ground-hornbill (Bucorvus leadbeateri) in the Limpopo Valley, South Africa

Little is known about Southern ground-hornbill (SGH) population ecology outside of large, formally protected areas where the largest declines in numbers have been recorded. The SGH has started re-colonising, establishing group territories and breeding successfully in the Limpopo Valley on the northern border of South Africa, following localised extinction from the 1950s to the 1970s. A group of SGH was monitored over a period of 14 months by means of radio telemetry across privately owned land in order to investigate their seasonal habitat movements in this semi-arid, predominantly livestock-based environment. We also investigated seasonal fluctuations in invertebrate prevalence, as an indication of food availability and its influence on seasonal SGH group movements and foraging activity patterns. There was a clear increase in food availability during the summer rainfall period allowing the group to forage over a wider area, whilst winter foraging remained localised within their range. Kernel home range analysis indicated a marked difference in size between the summer (13 409 ha) and winter (5280 ha) home ranges, with an overall home range of 19 372 ha, which is approximately double that of home ranges recorded that fall within formally and informally protected reserves. In this article, we proposed that food availability is the driving force for home range size and seasonal activity patterns in a semi-arid livestock-ranching habitat.Conservation implications: The Limpopo Valley SGH population is one of the most significant outside protected areas in South Africa. This population is especially vulnerable to threats such as poisoning, persecution for window breaking and drought, as shown by their near extirpation from the area. Conservation efforts need to focus on awareness amongst local farmers, provision of artificial nests and continued monitoring of groups.

Effect of diet on the incidence of and mortality owing to gastritis and renal disease in captive cheetahs (Acinonyx jubatus) in South Africa

Seventy-two adult cheetahs were evaluated for the degree of gastritis by endoscopic biopsy and for renal disease by serum creatinine. Cheetahs free of Grade 3 gastritis and renal disease were placed on Trial A; remaining cheetahs were placed on Trial B, which ran concurrently. All cheetahs were monitored for 4 years. Cheetahs exited Trial A and entered Trial B if they developed Grade 3 gastritis or renal disease. Cheetahs exited Trial B if they developed clinical gastritis or renal disease that required a dietary change or aggressive medical therapy or died owing to either disease. Cheetahs on Trial A were fed either a supplemented meat diet (N = 26) or commercial cat food (N = 22). Cheetahs on Trial B were fed either the same meat diet (N = 28) or a commercial dry cat food formulated for renal disease (N = 16). Cheetahs fed meat on Trial A had a daily hazard of developing Grade 3 gastritis 2.21 times higher (95% CI 0.95-5.15) than cheetahs fed commercial cat food. This hazard was not statistically significant (P = 0.07). Mean gastritis scores were not significantly different between the two groups. Cheetahs fed commercial cat food in both Trials had lower serum urea levels and higher creatinine levels than those fed meat. Evidence for the effect of diet in cheetahs with gastritis and/or renal disease (Trial B) was inconclusive. The number of cheetahs dying of gastritis or renal disease at the facility has dropped markedly since the study began. These results indicate that diet may play an important role in the incidence of Grade 3 gastritis and that dietary and/or therapeutic management of gastritis may reduce mortality owing to gastritis and renal disease in captive cheetahs.

Vulture rescue and rehabilitation in South Africa: an urban perspective

South Africa is home to 9 vulture species, of which 7 are endangered. While the cause of the population declines remains largely speculative, a vast amount of effort has been dedicated towards the protection of populations by ensuring sustainable and safe food sources for the various colonies. Limited focus was placed in the past on efforts related to the rescue and/or rehabilitation (R&R) of injured birds and the release of these birds back into the wild. This paper provides an overview of the causes, the impact and success of 3 organisations involved in R&R efforts of vultures in the Magaliesberg mountain range and surrounding areas over a period of 10 years. Study material included 162 Cape griffon (CGV) and 38 African white-backed (AWBV) vultures. Datasets include the number, sex and age of birds received, the reason the vultures were brought in for R&R, surgical interventions performed and outcomes of rescue efforts. The CGV dominated the rehabilitation attempts. Results further show that a large number of apparently healthy birds were presented for veterinary treatment. The R&R data clearly indicate that the major cause of injuries was birds colliding with overhead pylons, as a high number of soft tissue and skeletal injuries were observed. The study also shows that successful releases of rescued birds are possible. It is concluded that urbanisation has had a major negative impact on vultures around the Magaliesberg mountain range.

DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa

Poaching of wildlife animals for subsistence and commercial purposes has lead to population declines in Africa. In forensic cases, a need exists to identify the species of origin of carcasses, meat or blood. In the study presented here, the mitochondrial COI gene was sequenced to determine the species of unknown samples in three suspect South African forensic wildlife cases. In two cases the unknown samples were identified as originating from domestic cattle (Bos taurus) and in the third case the sample was identified as common reedbuck (Redunca arundinum). This is the first report of the COI sequence of common reedbuck. The study highlights the need for accurate wildlife reference material from each country in order to convict wildlife cases.

Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates

The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.

Mixed infections of Corynebacterium pseudotuberculosis and non-tuberculous mycobacteria in South African antelopes presenting with tuberculosis-like lesions

Routine meat inspection of antelope carcasses from a South African game reserve revealed a high prevalence of tuberculosis-like lesions. This study aimed to identify the causative agent of this disease and to describe its pathological features. In total, 139 antelopes were randomly harvested from the game reserve and subjected to meat inspection. Of these animals, 46 (33%) showed gross visible, tuberculosis-like lesions. Histopathological examination revealed the presence of encapsulated necrogranulomas in organs and/or lymph nodes of 22 of 27 animals tested. Tissue samples from lesions were processed for both non-selective bacterial culture and mycobacterial culture following decontamination. In non-selective cultures of lesions from 25 of 31 animals tested, Corynebacterium pseudotuberculosis was detected. Isolation of C. pseudotuberculosis was closely associated with the presence of necrogranulomas. In mycobacterial cultures of lesions from 9 of 41 animals tested, different species of non-tuberculous mycobacteria (NTMs) were detected. In 5 instances, depending on the culture procedure that was applied, either C. pseudotuberculosis or NTMs were isolated from the same tissue sample. Our results suggest that the disease has been caused by infections with C. pseudotuberculosis. In sub-Saharan Africa, the role of pathogens other than Mycobacterium bovis may be underestimated in causing tuberculosis-like lesions. In cases where potentially pathogenic NTMs are isolated from mycobacterial cultures of tuberculosis-like lesions, the non-use of additional non-selective culture techniques could lead to misinterpretations of the diagnostic test results.

Post mortem identification of Kalicephalus colubri colubri (Nematoda: Diaphanocephalidae) in a captive mole snake (Pseudaspis cana) in South Africa

Necropsy examination of a captive emaciated, dehydrated adult female Mole snake (Pseudaspis cana) in October 2007 revealed multiple cutaneous abscesses. Other findings included renal and hepatic atrophy, hepatic haemosiderosis, multifocal granulomatous hepatitis associated with acid-fast bacteria as well as pulmonary congestion and oedema. Large numbers of the nematode Kalicephalus colubri colubri were recovered from the oesophagus and stomach, representing the 1st reported case of K. colubri from a Mole snake in South Africa. The lesions caused by K. c. colubri were insignificant, but the presence of worms may have contributed to weight loss.

Naturally acquired antibodies to Bacillus anthracis protective antigen in vultures of southern Africa

Sera from 19 wild caught vultures in northern Namibia and 15 (12 wild caught and three captive bred but with minimal histories) in North West Province, South Africa, were examined by an enzyme-linked immunosorbent assay (ELISA) for antibodies to the Bacillus anthracis toxin protective antigen (PA). As assessed from the baseline established with a control group of ten captive reared vultures with well-documented histories, elevated titres were found in 12 of the 19 (63%) wild caught Namibian birds as compared with none of the 15 South African ones. There was a highly significant difference between the Namibian group as a whole and the other groups (P < 0.001) and no significant difference between the South African and control groups (P > 0.05). Numbers in the Namibian group were too small to determine any significances in species-, sex- or age-related differences within the raw data showing elevated titres in four out of six Cape Vultures, Gyps coprotheres, six out of ten White-backed Vultures, Gyps africanus, and one out of three Lappet-faced Vultures, Aegypius tracheliotus, or in five of six males versus three of seven females, and ten of 15 adults versus one of four juveniles. The results are in line with the available data on the incidence of anthrax in northern Namibia and South Africa and the likely contact of the vultures tested with anthrax carcasses. It is not known whether elevated titre indicates infection per se in vultures or absorption of incompletely digested epitopes of the toxin or both. The results are discussed in relation to distances travelled by vultures as determined by new tracking techniques, how serology can reveal anthrax activity in an area and the issue of the role of vultures in transmission of anthrax.

Body temperature daily rhythm adaptations in African savanna elephants (Loxodonta africana)

The savanna elephant is the largest extant mammal and often inhabits hot and arid environments. Due to their large size, it might be expected that elephants have particular physiological adaptations, such as adjustments to the rhythms of their core body temperature (T(b)) to deal with environmental challenges. This study describes for the first time the T(b) daily rhythms in savanna elephants. Our results showed that elephants had lower mean T(b) values (36.2 +/- 0.49 degrees C) than smaller ungulates inhabiting similar environments but did not have larger or smaller amplitudes of T(b) variation (0.40 +/- 0.12 degrees C), as would be predicted by their exposure to large fluctuations in ambient temperature or their large size. No difference was found between the daily T(b) rhythms measured under different conditions of water stress. Peak T(b)'s occurred late in the evening (22:10) which is generally later than in other large mammals ranging in similar environmental conditions.

Wildlife biomaterial banking in Africa for now and the future

The Wildlife Biological Resource Centre (wBRC) together with its partners in BioBank SA, have created a Biological Resource Bank (BRB) that is dedicated to the acquisition, processing, banking, using and provision of biomaterials to the scientific and conservation industry that are viable, diverse and representative of southern Africa's wildlife populations. Banked biomaterials include tissue such as muscle, kidney, fat, liver, embryos, fibroblast cultures, blood, sperm, hair, egg shells and other tissue, fluids and cells. Biomaterials are made available for research, biodiversity conservation and biotechnology development. Biomaterials are used in many disciplines, including genetics, reproduction, nutrition, and disease studies. Biomaterials from selected species are also useful for the detection and monitoring of Persistent Organic Pollutants and other potentially harmful substances found in the environment. Biomaterials are made available to third parties with prior consent from the biomaterials "owner" and only after the signing of a customised Material Transfer Agreement (MTA) or Cooperative Research and Development Agreement (CRADA). The training of staff from National and Provincial Game Reserves, Zoological Gardens, Animal Breeders and laboratories is carried out on a regular basis with the aim of securing good quality biomaterials. Sampling kits are made available to persons tasked with the collection of wildlife biomaterials. The Biobank SA consortium acts as an integrated resource centre linking partner collections. The consortium's operational arm, namely wBRC, is active in the development of relevant policy, regulations and legislation pertaining to biomaterials, including Access and Benefit Sharing systems. The main sponsor of the project is the Department of Science and Technology, National Government of South Africa.