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.

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.

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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.

As a consequence of environmental change, it is expected that shifts in temperature and precipitation patterns will infl uence parasite communities and their hosts with unpredictable impact. Parasites play a vital role in ecosystems but there is only limited quantitative data which describe the eff ects of environmental parameters under natural conditions. We investigated the infl uence of rainfall, relative humidity and temperature on the prevalence, abundance and infection intensity of nematodes in southern Africa by studying the gastro-intestinal helminth community of the striped mouse Rhabdomys pumilio. Along a precipitation gradient from the Cape of South Africa to northern Namibia we trapped 470 mice over a geographical distance of about 1400 km. Faecal egg counts of 439 sampled individuals and dissections of 161 gastro-intestinal tracts revealed 15 diff erent helminth species. Th e most abundant nematode species harboured in 62.6% of all infected mice were the oxyurid Syphacia obvelata followed jointly by two species (Heligmonina spira and Neoheligmonella capensis) of the subfamily Nippostrongylinae (43.7%). We found a signifi cant positive correlation between mean annual precipitation (rainfall and relative humidity) and nematode infestation rates of animals and a negative correlation with temperature. In addition, we found associations between precipitation and diff erent qualitative measurements of parasite burden (mean nematode species richness, mean number of nematode worms and infection intensity per individual host). Th e similarity in nematode species composition decreased with distance between all study sites. Our study indicates for the fi rst time an association between climatic variables and parasite prevalence and abundance along a continuous natural climatic gradient in a small mammal. Th ese results might be incorporated in the development of models which can predict possible threats for the balance of ecosystems and shifts in infestation patterns due to global changes.