Sonja Matthee

Bats host major mammalian paramyxoviruses

The large virus family Paramyxoviridae includes some of the most significant human and livestock viruses, such as measles-, distemper-, mumps-, parainfluenza-, Newcastle disease-, respiratory syncytial virus and metapneumoviruses. Here we identify an estimated 66 new paramyxoviruses in a worldwide sample of 119 bat and rodent species (9,278 individuals). Major discoveries include evidence of an origin of Hendra- and Nipah virus in Africa, identification of a bat virus conspecific with the human mumps virus, detection of close relatives of respiratory syncytial virus, mouse pneumonia- and canine distemper virus in bats, as well as direct evidence of Sendai virus in rodents. Phylogenetic reconstruction of host associations suggests a predominance of host switches from bats to other mammals and birds. Hypothesis tests in a maximum likelihood framework permit the phylogenetic placement of bats as tentative hosts at ancestral nodes to both the major Paramyxoviridae subfamilies (Paramyxovirinae and Pneumovirinae). Future attempts to predict the emergence of novel paramyxoviruses in humans and livestock will have to rely fundamentally on these data. Supplementary information The online version of this article (doi:10.1038/ncomms1796) contains supplementary material, which is available to authorized users.

Evidence for novel hepaciviruses in rodents.

Hepatitis C virus (HCV) is among the most relevant causes of liver cirrhosis and hepatocellular carcinoma. Research is complicated by a lack of accessible small animal models. The systematic investigation of viruses of small mammals could guide efforts to establish such models, while providing insight into viral evolutionary biology. We have assembled the so-far largest collection of small-mammal samples from around the world, qualified to be screened for bloodborne viruses, including sera and organs from 4,770 rodents (41 species); and sera from 2,939 bats (51 species). Three highly divergent rodent hepacivirus clades were detected in 27 (1.8%) of 1,465 European bank voles (Myodes glareolus) and 10 (1.9%) of 518 South African four-striped mice (Rhabdomys pumilio). Bats showed anti-HCV immunoblot reactivities but no virus detection, although the genetic relatedness suggested by the serologic results should have enabled RNA detection using the broadly reactive PCR assays developed for this study. 210 horses and 858 cats and dogs were tested, yielding further horse-associated hepaciviruses but none in dogs or cats. The rodent viruses were equidistant to HCV, exceeding by far the diversity of HCV and the canine/equine hepaciviruses taken together. Five full genomes were sequenced, representing all viral lineages. Salient genome features and distance criteria supported classification of all viruses as hepaciviruses. Quantitative RT-PCR, RNA in-situ hybridisation, and histopathology suggested hepatic tropism with liver inflammation resembling hepatitis C. Recombinant serology for two distinct hepacivirus lineages in 97 bank voles identified seroprevalence rates of 8.3 and 12.4%, respectively. Antibodies in bank vole sera neither cross-reacted with HCV, nor the heterologous bank vole hepacivirus. Co-occurrence of RNA and antibodies was found in 3 of 57 PCR-positive bank vole sera (5.3%). Our data enable new hypotheses regarding HCV evolution and encourage efforts to develop rodent surrogate models for HCV.

Epifaunistic arthropod parasites of the four-striped mouse, Rhabdomys pumilio, in the Western Cape Province, South Africa.

Flea, lice, mite, and tick species associated with 510 Rhabdomys pumilio were collected at 9 localities in the Western Cape Province, South Africa. The aims of the study were first to quantify the species richness, prevalence, and relative mean intensity of infestation of epifaunistic arthropod species associated with R. pumilio, and second to determine temporal variations in the mean abundance of the parasitic arthropods. Each mouse was examined under a stereoscopic microscope and its parasites were removed, identified, and quantified. The epifaunal population was made up of more than 25,000 individuals and included 8 flea, 1 sucking louse, 11 mite, and 13 ixodid tick species. Female-biased sex ratios were noted for 9 (30%) of the ectoparasite species. Three undescribed mite and 1 undescribed tick species were recovered, and new locality records for 2 flea, the louse, and 2 mite species were documented. A phoretic host association between a nonparasitic mite species, Psylloglyphus uilenbergi kivuensis, and 3 flea species, Chiastopsylla rossi, Hypsophthalmus temporis, and Listropsylla agrippinae, was recorded. The mean abundance of the parasitic mite and insect species were higher during the cold wet season, whereas ticks were more numerous during the warm dry months. The large number of ectoparasite species on R. pumilio, a locally abundant and regionally widespread species, is of medical and veterinary importance particularly in relation to the transmission of pathogens such as Anaplasma marginale, Babesia caballi, and Babesia canis to domestic animals; Rickettsia conori; Yersinia pestis; and the viral disease Crimean-Congo hemorrhagic fever to humans.

Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy

Within southern Africa, a link between past climatic changes and faunal diversification has been hypothesized for a diversity of taxa. To test the hypothesis that evolutionary divergences may be correlated to vegetation changes (induced by changes in climate), we selected the widely distributed four-striped mouse, Rhabdomys, as a model. Two species are currently recognized, the mesic-adapted R. dilectus and arid-adapted R. pumilio. However, the morphology-based taxonomy and the distribution boundaries of previously described subspecies remain poorly defined. The current study, which spans seven biomes, focuses on the spatial genetic structure of the arid-adapted R. pumilio (521 specimens from 31 localities), but also includes limited sampling of the mesic-adapted R. dilectus (33 specimens from 10 localities) to act as a reference for interspecific variation within the genus. The mitochondrial COI gene and four nuclear introns (Eef1a1, MGF, SPTBN1, Bfib7) were used for the construction of gene trees. Mitochondrial DNA analyses indicate that Rhabdomys consists of four reciprocally monophyletic, geographically structured clades, with three distinct lineages present within the arid-adapted R. pumilio. These monophyletic lineages differ by at least 7.9% (±0.3) and these results are partly confirmed by a multilocus network of the combined nuclear intron dataset. Ecological niche modeling in MaxEnt supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that the geographic clades diverged between 3.09 and 4.30Ma, supporting the hypothesis that the radiation within the genus coincides with paleoclimatic changes (and the establishment of the biomes) characterizing the Miocene-Pliocene boundary. Marked genetic divergence at the mitochondrial DNA level, coupled with strong nuclear and mtDNA signals of non-monophyly of R. pumilio, support the notion that a taxonomic revision of the genus is needed.

PREVALENCE AND BIODIVERSITY OF HELMINTH PARASITES IN DONKEYS FROM SOUTH AFRICA

Seven donkeys (Equus asinus) from North-West and Mpumalanga Provinces in South Africa were examined at necropsy. Quantitative samples were collected from the gastrointestinal tract for recovery of helminth parasites from the stomach, small intestine, cecum, ventral colon, dorsal colon, descending colon, and cranial mesenteric artery. Fifteen genera and 29 species of helminths were identified comprising 27 species of nematodes in the Ascarididae, Atractidae, Habronematidae, Onchocercidae, Oxyuridae, and Strongylidae; 1 species of cestode in the Anoplocephalidae; and 1 species of trematode in the Paramphistomatidae. In addition, 2 species of oestrid fly larvae in the Gastrophiliidae were identified. The most abundant group in number of species was the cyathostomes (small strongyles) and, of these, Cyathostomum montgomeryi, Cylicocyclus sp. (a), and Cylicostephanus minutus were the most numerous. The most prevalent cyathostomes were C. montgomeryi and Cylicocyclus sp. n. (a). Strongylus vulgaris was the most abundant and prevalent large strongyle species. The occurrence of small strongyle species and their prevalences in this study are compared with 3 other studies on donkeys in Africa.

Parasite-specific variation and the extent of male-biased parasitism; an example with a South African rodent and ectoparasitic arthropods

We asked whether the occurrence and the extent of host gender-biased parasitism vary among higher parasite taxa, among individual species within these taxa and within parasite species among localities. To answer this question, we studied prevalence, abundance, species richness and the level of aggregation of ectoparasites (ticks, mites, lice and fleas) collected from male and female striped mice (Rhabdomys pumilio) in 9 localities of the Western Cape Province of South Africa. We used meta-analyses to compare parasitological variables between male and female hosts across localities for individual parasite species and higher taxa as well as across parasite species within a higher taxon. Whenever gender-biased parasitism was found, it indicated higher infestation of male than female hosts (except 1 low abundant mite species). We found that the occurrence and extent of gender-biased infestation varied mainly within a parasite species among localities and among parasite species within a higher taxon but not among parasite taxa. Our results suggest that the extent of a gender-biased pattern of parasite infestation of the same host may not only involve host-related mechanisms but also depends on biological features of a particular parasite species.

Biogeography and host‐related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts

Parasites and hosts interact across both micro‐ and macroevolutionary scales where congruence among their phylogeographic and phylogenetic structures may be observed. Within southern Africa, the four‐striped mouse genus, Rhabdomys, is parasitized by the ectoparasitic sucking louse, Polyplax arvicanthis. Molecular data recently suggested the presence of two cryptic species within P. arvicanthis that are sympatrically distributed across the distributions of four putative Rhabdomys species. We tested the hypotheses of phylogeographic congruence and cophylogeny among the two parasite lineages and the four host taxa, utilizing mitochondrial and nuclear sequence data. Despite the documented host‐specificity of P. arvicanthis, limited phylogeographic correspondence and nonsignificant cophylogeny was observed. Instead, the parasite–host evolutionary history is characterized by limited codivergence and several duplication, sorting and host‐switching events. Despite the elevated mutational rates found for P. arvicanthis, the spatial genetic structure was not more pronounced in the parasite lineages compared with the hosts. These findings may be partly attributed to larger effective population sizes of the parasite lineages, the vagility and social behaviour of Rhabdomys, and the lack of host‐specificity observed in areas of host sympatry. Further, the patterns of genetic divergence within parasite and host lineages may also be largely attributed to historical biogeographic changes (expansion‐contraction cycles). It is thus evident that the association between P. arvicanthis and Rhabdomys has been shaped by the synergistic effects of parasite traits, host‐related factors and biogeography over evolutionary time.

A COMPARISON OF THE INTESTINAL HELMINTH COMMUNITIES OF EQUIDAE IN SOUTHERN AFRICA

The intestinal helminth communities of 8 horses, 12 donkeys, 21 Hartmanns mountain zebras, and 44 Burchells zebras were compared using the original data from 6 studies in South Africa and Namibia. Necropsy and worm recovery techniques were comparable between the studies. Sixty helminth species (58 nematode, 1 cestode, and 1 trematode species) were recorded. There were significant differences in the helminth community structures of the 4 Equus species. The helminth communities of the 2 closely related zebra subspecies were most similar, and they jointly shared 7 helminth species with donkeys and only 1 with horses. Geographic variation and host-mixing contributed to the helminth species composition. Multiple confamilial species infections were the norm in the donkeys and zebra subspecies, and no single-species infection was recorded for the Strongylidae. Congeneric species were commonly recorded in 3 genera (Cyathostomum, Cylicocyclus, and Cylicostephanus). The shape of the occupancy frequency distributions for the donkeys and zebra subspecies was multimodal, with no clear satellite or core modes. Despite the presence of environmental variability and comparatively low parasite-host specificity, the phylogenetic signal within Equus helminth communities remains strong.

Life history strategy influences parasite responses to habitat fragmentation.

Anthropogenic habitat use is a major threat to biodiversity and is known to increase the abundance of generalist host species such as rodents, which are regarded as potential disease carriers. Parasites have an intimate relationship with their host and the surrounding environment and it is expected that habitat fragmentation will affect parasite infestation levels. We investigated the effect of habitat fragmentation on the ecto- and endoparasitic burdens of a broad niche small mammal, Rhabdomys pumilio, in the Western Cape Province, South Africa. Our aim was to look at the effects of fragmentation on different parasite species with diverse life history characteristics and to determine whether general patterns can be found. Sampling took place within pristine lowland (Fynbos/Renosterveld) areas and at fragmented sites surrounded and isolated by agricultural activities. All arthropod ectoparasites and available gastrointestinal endoparasites were identified. We used conditional autoregressive models to investigate the effects of habitat fragmentation on parasite species richness and abundance of all recovered parasites. Host density and body size were larger in the fragments. Combined ecto- as well as combined endoparasite taxa showed higher parasite species richness in fragmented sites. Parasite abundance was generally higher in the case of R. pumilio individuals in fragmented habitats but it appears that parasites that are more permanently associated with the hosts body and those that are host-specific show the opposite trend. Parasite life history is an important factor that needs to be considered when predicting the effects of habitat fragmentation on parasite and pathogen transmission.

Searching for generality in the patterns of parasite abundance and distribution: Ectoparasites of a South African rodent, Rhabdomys pumilio

We studied abundance and distribution of seven ectoparasite species (fleas Chiastopsylla rossi and Dynopsyllus ellobius, a louse Polyplax arvicanthis, mites Androlaelaps fahrenholzi and Laelaps giganteus and two ticks Haemaphysalis elliptica and Hyalomma truncatum) exploiting the same populations of the rodent host Rhabdomys pumilio in South Africa. We considered three general patterns of abundance and distribution, namely (i) aggregated distribution of parasites amongst individual hosts; (ii) positive relationships between mean parasite abundance and their prevalence; and (iii) applicability of a simple epidemiological model based on mean parasite abundance and its variance to predict the observed patterns of prevalence. Our aims were to evaluate the relative role of host- versus parasite-associated factors by looking at similarity amongst different parasites in these patterns. In general, all parasites demonstrated strong similarity in each of the three patterns of abundance and distribution. However, the strength of these patterns differed amongst parasite species. We conclude that these patterns are driven mainly by hosts, but differences are caused by differences between various life-history traits of parasite species. Our results support the idea that general laws apply to parasite population ecology.