Detection and characterization of foot-and-mouth disease virus in sub-Saharan Africa

Genomic amplification of the VP1 gene of SAT-type foot-and-mouth disease virus (FMDV) was performed with published and novel oligonucleotide primers. The primer pair with the highest SAT-type recognition (67 %) was identified and selected for optimization. Modifications to primers significantly improved SAT-type detection (100 %), broadened the recognition range to European (A, O and C) and Asian (Asia-1) serotypes and improved test sensitivity. In addition to being able to confirm the presence of FMDV in a clinical specimen within 6 h of receipt, the PCR product, which is amenable to nucleotide sequencing, enables genetic characterization of viruses into serotype and topotype within 48 h. VP1 gene sequence analysis of isolates from seven African countries and representative of five of the six serotypes occurring on the continent, revealed that SAT-types have the highest levels of intratypic variation. lntratypic variation for the SAT-types ranged from 34-40,4% on nucleotide level, and from 24,1-27,5% on amino acid level. In addition, the methodology presented here was shown to be useful for determining the origin and tracing the course of epizootics in both wild and domestic cloven-hoofed animals.The articles have been scanned in colour with a HP Scanjet 5590; 600dpi. Adobe Acrobat X Pro was used to OCR the text and also for the merging and conversion to the final presentation PDF-format.mn201

Virus genome dynamics under different propagation pressures : reconstruction of whole genome haplotypes of West Nile viruses from NGS data

BACKGROUND : Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies population variants. These variants are not discernable in the consensus genome at the time of emergence, and the maintenance of mutationselection equilibria of population variants is greatly underestimated. The emergence of lineage 1 WNV strains has been studied extensively, but recent epidemics caused by lineage 2 WNV strains in Hungary, Austria, Greece and Italy emphasizes the increasing importance of this lineage to public health. In this study we explored the quasispecies dynamics of minority variants that contribute to cell-tropism and host determination, i.e. the ability to infect different cell types or cells from different species from Next Generation Sequencing (NGS) data of a historic lineage 2 WNV strain. RESULTS : Minority variants contributing to host cell membrane association persist in the viral population without contributing to the genetic change in the consensus genome. Minority variants are shown to maintain a stable mutation-selection equilibrium under positive selection, particularly in the capsid gene region. CONCLUSIONS : This study is the first to infer positive selection and the persistence of WNV haplotype variants that contribute to viral fitness without accompanying genetic change in the consensus genotype, documented solely from NGS sequence data. The approach used in this study streamlines the experimental design seeking viral minority variants accurately from NGS data whilst minimizing the influence of associated sequence error.The Agricultural Research Council (ARC) Onderstepoort Veterinary Institute (OVI) is thanked for providing the WNV strain and funding used in this study.CK was funded though an AgriSETA bursary.http://www.biomedcentral.com/bmcgenomicshb201

A mathematical epidemiological model of gram-negative Bartonella bacteria : does differential ectoparasite load fully explain the differences in infection prevalence of Rattus rattus and Rattus norvegicus?

We postulate that the large difference in infection prevalence, 24% versus 5%, in R. norvegicus and R. rattus, respectively, between these two co-occurring host species may be due to differences in ectoparasite and potential vector infestation rates.Acompartmental model, representative of an infectious system containing these two Rattus species and two ectoparasite vectors, was constructed and the coefficients of the forces of infection determined mathematically. The maximum difference obtained by the model in the prevalence of Bartonella in the two Rattus species amounts to 4.6%, compared to the observed mean difference of 19%. Results suggest the observed higher Bartonella infection prevalence in Rattus norvegicus compared to Rattus rattus, cannot be explained solely by higher ectoparasite load. The model also highlights the need for more detailed biological research on Bartonella infections in Rattus and the importance of the flea vector in the spread of this disease.The National Research Foundation (NRF)http://www.tandfonline.com/toc/tjbd20ab201

Assessment of risk of dengue and yellow fever virus transmission in three major Kenyan cities based on Stegomyia indices

Dengue (DEN) and yellow fever (YF) are re-emerging in East Africa, with contributing drivers to this trend being unplanned urbanization and increasingly adaptable anthropophilic Aedes (Stegomyia) vectors. Entomological risk assessment of these diseases remains scarce for much of East Africa and Kenya even in the dengue fever-prone urban coastal areas. Focusing on major cities of Kenya, we compared DEN and YF risk in Kilifi County (DEN-outbreak-prone), and Kisumu and Nairobi Counties (no documented DEN outbreaks). We surveyed water-holding containers for mosquito immature (larvae/pupae) indoors and outdoors from selected houses during the long rains, short rains and dry seasons (100 houses/season) in each County from October 2014-June 2016. House index (HI), Breteau index (BI) and Container index (CI) estimates based on Aedes (Stegomyia) immature infestations were compared by city and season. Aedes aegypti and Aedes bromeliae were the main Stegomyia species with significantly more positive houses outdoors (212) than indoors (88) (n = 900) (χ2 = 60.52, P < 0.0001). Overall, Ae. aegypti estimates of HI (17.3 vs 11.3) and BI (81.6 vs 87.7) were higher in Kilifi and Kisumu, respectively, than in Nairobi (HI, 0.3; BI,13). However, CI was highest in Kisumu (33.1), followed by Kilifi (15.1) then Nairobi (5.1). Aedes bromeliae indices were highest in Kilifi, followed by Kisumu, then Nairobi with HI (4.3, 0.3, 0); BI (21.3, 7, 0.7) and CI (3.3, 3.3, 0.3), at the respective sites. HI and BI for both species were highest in the long rains, compared to the short rains and dry seasons. We found strong positive correlations between the BI and CI, and BI and HI for Ae. aegypti, with the most productive container types being jerricans, drums, used/discarded containers and tyres. On the basis of established vector index thresholds, our findings suggest low-tomedium risk levels for urban YF and high DEN risk for Kilifi and Kisumu, whereas for Nairobi YF risk was low while DEN risk levels were low-to-medium. The study provides a baseline for future vector studies needed to further characterise the observed differential risk patterns by vector potential evaluation. Identified productive containers should be made the focus of community-based targeted vector control programs.A scholarship to SBA by the German Academic Exchange Service (DAAD), National Institutes of Health (NIH), Grant No. 1R01AI099736-01A1 to RS, UK's Department for International Development (DFID), Swedish International Development Cooperation Agency (Sida), the Swiss Agency for Development and Cooperation (SDC), and the Kenyan Government.http://www.plosntds.orgam2017Zoology and Entomolog

Mass die-off of African elephants in Botswana : pathogen-poison or a perfect storm?

Reports of a mass die-off of ~350 elephants (Loxodonta africana) in northern Botswana over a period of two months (May–June 2020), has fuelled speculation and concern regarding the cause. Although the area in which these mortalities occurred is not protected and is considered a hotspot for human– elephant conflict and poaching, both malicious poisoning and poaching are unlikely to have played a role as other species were not affected, and elephant carcasses were found with tusks intact. In the absence of a confirmed cause we sought to identify the lines of enquiry that are most likely to lead to a definitive answer. In particular, we consider viral and bacterial agents that could precipitate species-specific mortalities on this scale, potential environmental sources of poisoning and the samples and tests that would assist in excluding/ confirming these candidate causes. Whilst it may be argued that these mortalities are unlikely to negatively impact the broader elephant population of ~130 000 individuals in Botswana, the same cannot be said of the many vulnerable population pockets in other parts of Africa. For this reason, it is essential that the cause of the current die-off is identified as it is the only way to prevent similar losses of susceptible elephants elsewhere.https://journals.co.za/content/journal/wildpm2020Centre for Veterinary Wildlife StudiesZoology and Entomolog

Evidence of a contact zone between two Rhabdomys dilectus (Rodentia : Muridae) mitotypes in Gauteng province, South Africa

Recent studies have described the presence of several mitochondrial lineages within Rhabdomys, which was previously considered to be a monotypic genus. The exact distributional limits of the species and subspecies and their contact zones are unclear. In this study we demonstrate that two monophyletic Rhabdomys dilectus mitochondrial lineages are present at two northern Gauteng province sampling sites in South Africa. Cytochrome b gene sequences, 896 nucleotides in length, generated for 36 Rhabdomys samples identified 10 unique haplotypes corresponding to eight R. dilectus dilectus haplotypes (from 32 individuals) and two R. d. chakae haplotypes (from four individuals). The present study provides the first empirical evidence for a contact zone for two R. dilectus conspecific mitochondrial lineages and contributes to the refinement of Rhabdomys distributional maps in southern Africa.South African National Research Foundationhttp://www.tandfonline.com/loi/tafz202016-03-31hb201

Cryptic species, biogeographic complexity and the evolutionary history of the Ectemnorhinus group in the sub-Antarctic, including a description of Bothrometopus huntleyi, n. sp.

The biogeography of the South Indian Ocean Province (SIP) biotas has long been controversial. Much of the discussion has been based on interpretation of species distributions, based on morphological or anatomical delimitations. However, molecular phylogenetic approaches elsewhere have recently shown that interpretations based solely on morphological data may be misleading. Nonetheless, few studies have employed molecular phylogenetic approaches to understand the biogeography of the SIP biotas. We do so here for the Ectemnorhinus group of genera, a monophyletic unit of weevils endemic to the region. We use mitochondrial cytochrome oxidase I DNA sequence data to reconstruct relationships among 13 species and 22 populations in the genera Palirhoeus, Bothrometopus and Ectemnorhinus. On the basis of this analysis we find little support for separating the genus Palirhoeus from Bothrometopus, and little support for the morphologically-based species groups currently recognized within Bothrometopus. Using a molecular clock we show that dispersal among islands probably took place against the prevailing wind direction. These data also support a previous hypothesis of radiation of the epilithic genera Bothrometopus and Palirhoeus during the Pliocene/early Pleistocene, but reject the hypothesis that the genus Ectemnorhinus radiated following the last glacial maximum. We show that Bothrometopus parvulus (C.O. Waterhouse) on the Prince Edward Islands comprises two species that are not sister taxa.We name the second species Bothrometopus huntleyi n. sp. and provide a description thereof.http://journals.cambridge.org/action/displayJournal?jid=an

Bartonellae of the Namaqua rock mouse, Micaelamys namaquensis (Rodentia : Muridae) from South Africa

The aim of this study was to determine Bartonella prevalence and diversity in Namaqua rock mice, Micaelamys namaquensis, a species endemic to South Africa, which can attain pest status. A total of 100 heart samples collected monthly from March to December were screened for Bartonella genome presence using three primer sets targeting the citrate synthase (gltA) gene, the NADH dehydrogenase gamma subunit (nuoG) gene and the RNA polymerase b-subunit-encoding gene (rpoB). An overall prevalence of 44% was obtained, with no statistically significant differences or correlations between infection rates and rodent sex, month of capture or season of capture. Phylogenetic analysis of 34 unambiguous gltA sequences revealed the presence of three discrete Bartonella lineages in M. namaquensis, one of which corresponds to Bartonella elizabethae, a species with known zoonotic potential.The study was funded by grants awarded to ADSB and NCB by the South African National Research Foundation (NRF)http://www.elsevier.com/locate/vetmicab201

Inter-island dispersal of flightless Bothrometopus huntleyi (Coleoptera: Curculionidae) from the sub-Antarctic Prince Edward Island archipelago

Bothrometopus huntleyi is a flightless weevil endemic to the volcanically-formed sub-Antarctic Prince Edward Islands archipelago that arose approximately 0.5 million years ago (m.y.a.). Since emergence, a series of volcanic and glaciation events have occurred on Marion Island, whilst Prince Edward Island, the second island constituting the archipelago, has remained largely unaffected by glaciation. Cytochrome oxidase I gene analyses indicate that major historical dispersal events in this species are linked to the geologically discrete histories of these islands and underlie the high haplotype diversity (0.995) recovered for the Prince Edward Islands archipelago. The estimated time to haplotype coalescence of,0.723 m.y.a. is in keeping with estimated dates of island emergence, and the majority of individuals appear to have descended from a relict, high-altitude population that is still present on Marion Island. The first major inter-island dispersal event occurred,0.507 m.y.a., coinciding with the oldest dated rocks on Marion Island. Apart from this early inter-island colonization, only one other between-island dispersal event was detected. The genetically discrete B. huntleyi complexes on each of the islands of the Prince Edward Islands archipelago together with the low levels of inter-island gene flow reaffirm the need to control alien invasive mice, which are restricted to Marion Island, and which prey on this weevil species.http://journals.cambridge.org/action/displayJournal?jid=an

A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo : possible implications for disease management

Bovine tuberculosis (BTB) is endemic to the African buffalo (Syncerus caffer) of HluhluweiMfolozi Park (HiP) and Kruger National Park, South Africa. In HiP, the disease has been actively managed since 1999 through a test-and-cull procedure targeting BTB-positive buffalo. Prior studies in Kruger showed associations between microsatellite alleles, BTB and body condition. A sex chromosomal meiotic drive, a form of natural gene drive, was hypothesized to be ultimately responsible. These associations indicate high-frequency occurrence of two types of male-deleterious alleles (or multiple-allele haplotypes). One type negatively affects body condition and BTB resistance in both sexes. The other type has sexually antagonistic effects: negative in males but positive in females. Here, we investigate whether a similar gene drive system is present in HiP buffalo, using 17 autosomal microsatellites and microsatellite-derived Y-chromosomal haplotypes from 401 individuals, culled in 2002– 2004. We show that the association between autosomal microsatellite alleles and BTB susceptibility detected in Kruger, is also present in HiP. Further, Y-haplotype frequency dynamics indicated that a sex chromosomal meiotic drive also occurred in HiP. BTB was associated with negative selection of male-deleterious alleles in HiP, unlike positive selection in Kruger. Birth sex ratios were female-biased. We attribute negative selection and female-biased sex ratios in HiP to the absence of a Y-chromosomal sex-ratio distorter. This distorter has been hypothesized to contribute to positive selection of male-deleterious alleles and male-biased birth sex ratios in Kruger. As previously shown in Kruger, microsatellite alleles were only associated with male-deleterious effects in individuals born after wet pre-birth years; a phenomenon attributed to epigenetic modification. We identified two additional allele types: male-specific deleterious and beneficial alleles, with no discernible effect on females. Finally, we discuss how our findings may be used for breeding disease-free buffalo and implementing BTB test-and-cull programs.S1 Text. Sex chromosomal meiotic drive can explain genome-wide high-frequency occurrence of male-deleterious alleles.S2 Text. Frequency differences of DEmajority and SAEpooled alleles between HiP and Kruger.S1 Fig. Map with sampling localities.S2 Fig. Monthly rainfall in HiP.S3 Fig. Annual rainfall in HiP in the period 1979–2004.S4 Fig. Frequencies of DEmajority and SAEpooled alleles in HiP compared with Kruger.S5 Fig. Difference in Amale-spec between SAEindvN alleles from Kruger observed and not observed in HIP.S6 Fig. Allele frequency differences between northern Kruger and HiP per SAE allele type.S1 Table. List of SAEpooled and DEmajority alleles.S2 Table. List of individual alleles at the DE microsatellite loci.S3 Table. List of individual alleles at the SAE microsatellite loci.S4 Table. List of individual alleles at the SAE microsatellite loci with unknown linkage.S5 Table. Logistic regression of BTB-infection risk for each sex separately.S6 Table. Logistic regression of BTB-infection risk for dry and wet pre-birth years separately.S7 Table. Logistic regression between sex (dependent) and age and 3yr-pre-birth rainfall.The US NSF Division of Environmental Biology (Grant number 0090323 awarded to Dr Wayne M. Getz) and the M3B2 DST/NRF SARChI Chair, University of Pretoria.http://www.plosone.orgam2019Mammal Research InstituteZoology and Entomolog