Co-infection of mammarenaviruses in a wild mouse, Tanzania.

Mammarenaviruses are bi-segmented RNA viruses. They encompass viruses responsible for several severe diseases in humans. While performing a de novo assembly of a new virus found in a wild single-striped grass mouse in Tanzania, we found a single S but two divergent L segments. Natural co-infections, common within reptarenaviruses in captivity, were never reported for mammarenaviruses and never in a wild sample. This finding can have implications for virus evolution as co-infection could trigger viral recombination/reassortment in natural reservoirs.

New Perspective on the Geographic Distribution and Evolution of Lymphocytic Choriomeningitis Virus, Central Europe.

Lymphocytic choriomeningitis virus (LCMV) is an Old World mammarenavirus found worldwide because of its association with the house mouse. When LCMV spills over to immunocompetent humans, the virus can cause aseptic meningitis; in immunocompromised persons, systemic infection and death can occur. Central Europe is a strategic location for the study of LCMV evolutionary history and host specificity because of the presence of a hybrid zone (genetic barrier) between 2 house mouse subspecies, Mus musculus musculus and M. musculus domesticus. We report LCMV prevalence in natural mouse populations from a Czech Republic-Germany transect and genomic characterization of 2 new LCMV variants from the Czech Republic. We demonstrate that the main division in the LCMV phylogenetic tree corresponds to mouse host subspecies and, when the virus is found in human hosts, the mouse subspecies found at the spillover location. Therefore, LCMV strains infecting humans can be predicted by the genetic structure of house mice.

Mitogenomics and Evolutionary History of Rodent Whipworms (Trichuris spp.) Originating from Three Biogeographic Regions.

Trichuris spp. is a widespread nematode which parasitizes a wide range of mammalian hosts including rodents, the most diverse mammalian order. However, genetic data on rodent whipworms are still scarce, with only one published whole genome (Trichuris muris) despite an increasing demand for whole genome data. We sequenced the whipworm mitogenomes from seven rodent hosts belonging to three biogeographic regions (Palearctic, Afrotropical, and Indomalayan), including three previously described species: Trichuris cossoni, Trichurisarvicolae, and Trichurismastomysi. We assembled and annotated two complete and five almost complete mitogenomes (lacking only the long non-coding region) and performed comparative genomic and phylogenetic analyses. All the mitogenomes are circular, have the same organisation, and consist of 13 protein-coding, 2 rRNA, and 22 tRNA genes. The phylogenetic analysis supports geographical clustering of whipworm species and indicates that T. mastomysi found in Eastern Africa is able to infect multiple closely related rodent hosts. Our results are informative for species delimitation based on mitochondrial markers and could be further used in studies on phylogeny, phylogeography, and population genetics of rodent whipworms.

Evolutionary history of Pneumocystis fungi in their African rodent hosts.

Pneumocystis is a genus of parasitic fungi infecting lung tissues in a wide range of mammal species, displaying a strong host specificity and patterns of co-speciation with their hosts. However, a recent study on Asiatic murids challenged these patterns reporting several Pneumocystis lineages/species shared by different host species or even genera in the Rattini and Murini tribes. Here we screened lung samples of 27 species of African rodents from five families for the presence of Pneumocystis DNA. Using reconstructed multi-locus phylogenies of both hosts and parasites, we tested the hypothesis of their co-evolution. We found that Pneumocystis is widespread in African rodents, detected in all but seven screened host species, with species-level prevalence ranging from 5.9 to 100%. Several host species carry pairs of highly divergent Pneumocystis lineages/species. The retrieved co-phylogenetic signal was highly significant (p = .0017). We found multiple co-speciations, sorting events and two host-shift events, which occurred between Murinae and Deomyinae hosts. Comparison of genetic distances suggests higher substitution rates for Pneumocystis relative to the rodent hosts on neutral loci and slower rates on selected ones. We discuss life-history traits and population dynamics factors which could explain the observed results.

Arenavirus infection correlates with lower survival of its natural rodent host in a long-term capture-mark-recapture study.

BACKGROUND: Parasite evolution is hypothesized to select for levels of parasite virulence that maximise transmission success. When host population densities fluctuate, low levels of virulence with limited impact on the host are expected, as this should increase the likelihood of surviving periods of low host density. We examined the effects of Morogoro arenavirus on the survival and recapture probability of multimammate mice (Mastomys natalensis) using a seven-year capture-mark-recapture time series. Mastomys natalensis is the natural host of Morogoro virus and is known for its strong seasonal density fluctuations. RESULTS: Antibody presence was negatively correlated with survival probability (effect size: 5-8% per month depending on season) but positively with recapture probability (effect size: 8%). CONCLUSIONS: The small negative correlation between host survival probability and antibody presence suggests that either the virus has a negative effect on host condition, or that hosts with lower survival probability are more likely to obtain Morogoro virus infection, for example due to particular behavioural or immunological traits. The latter hypothesis is supported by the positive correlation between antibody status and recapture probability which suggests that risky behaviour might increase the probability of becoming infected.

No measurable adverse effects of Lassa, Morogoro and Gairo arenaviruses on their rodent reservoir host in natural conditions.

BACKGROUND: In order to optimize net transmission success, parasites are hypothesized to evolve towards causing minimal damage to their reservoir host while obtaining high shedding rates. For many parasite species however this paradigm has not been tested, and conflicting results have been found regarding the effect of arenaviruses on their rodent host species. The rodent Mastomys natalensis is the natural reservoir host of several arenaviruses, including Lassa virus that is known to cause Lassa haemorrhagic fever in humans. Here, we examined the effect of three arenaviruses (Gairo, Morogoro and Lassa virus) on four parameters of wild-caught Mastomys natalensis: body mass, head-body length, sexual maturity and fertility. After correcting for the effect of age, we compared these parameters between arenavirus-positive (arenavirus RNA or antibody) and negative animals using data from different field studies in Guinea (Lassa virus) and Tanzania (Morogoro and Gairo viruses). RESULTS: Although the sample sizes of our studies (1297, 749 and 259 animals respectively) were large enough to statistically detect small differences in body conditions, we did not observe any adverse effects of these viruses on Mastomys natalensis. We did find that sexual maturity was significantly positively related with Lassa virus antibody presence until a certain age, and with Gairo virus antibody presence in general. Gairo virus antibody-positive animals were also significantly heavier and larger than antibody-free animals. CONCLUSION: Together, these results suggest that the pathogenicity of arenaviruses is not severe in M. natalensis, which is likely to be an adaptation of these viruses to optimize transmission success. They also suggest that sexual behaviour might increase the probability of M. natalensis to become infected with arenaviruses.

Spotted fever group rickettsiae detected in immature stages of ticks parasitizing on Iberian endemic lizard Lacerta schreiberi Bedriaga, 1878.

Spotted fever rickettsioses are tick-borne diseases of growing public health concern. The prevalence of rickettsia-infected ticks and their ability to parasitize humans significantly influence the risk of human infection. Altogether 466 Ixodes ricinus ticks (428 nymphs and 38 larvae) collected from 73 Lacerta schreiberi lizards were examined by PCR targeting the citrate synthetase gene gltA for the presence of Rickettsia spp. Rickettsial DNA was detected in 47% of nymphs and 31.6% of larvae. They were subsequently subjected to a second PCR reaction using primers derived from the outer membrane protein rOmpA encoding gene (ompA) to detect spotted fever group rickettsiae (SFG). This analysis shows that 41.4% of nymphs and 7.9% of larvae collected from the lizards contain DNA of SFG rickettsiae. Sequencing of 43 randomly selected samples revealed two different haplotypes, both closely related to R. monacensis (39 and 4 samples, respectively). The remaining ompA negative Rickettsia spp. samples were determined to be R. helvetica based on sequencing of ompB and gltA fragments. Our results indicate that the role of Iberian endemic lizard L. schreiberi and its ectoparasites in the ecology and epidemiology of zoonotic SFG rickettsioses may be appreciable.

Age at weaning, immunocompetence and ectoparasite performance in a precocial desert rodent.

We studied the effects of early weaning on immunocompetence and parasite resistance in a precocial rodent Acomys cahirinus. We hypothesized that if parasite resistance is energetically expensive and nutritional and immunological support from mothers are necessary for the long-term health of offspring, then early weaned animals would be immunologically weaker and less able to defend themselves against parasites than later weaned animals. We weaned pups at 14, 21 or 28 days after birth and assessed their immunocompetence and resistance against fleas Parapulex chephrenis when they attained adulthood. Immunocompetence was assessed using leukocyte concentration (LC) and a phytohaemagglutinin injection assay (PHA test). To estimate resistance against fleas, we measured performance of fleas via the number of produced eggs and duration of development and resistance to starvation of the flea offspring. We found a significant positive effect of weaning age on the PHA response but not on LC. The effect of age at weaning on flea egg production was manifested in male but not female hosts, with egg production being higher if a host was weaned at 14 than at 28 days. Weaning age of the host did not affect either duration of development or resistance to starvation of fleas produced by mothers fed on these hosts. We conclude that even in relatively precocial mammals, weaning age is an important indicator of future immunological responses and the ability of an animal to resist parasite infestations. Hosts weaned at an earlier age make easier, less-resistant targets for parasite infestations than hosts weaned later in life.

High prevalence of Rickettsia typhi and Bartonella species in rats and fleas, Kisangani, Democratic Republic of the Congo.

The prevalence and identity of Rickettsia and Bartonella in urban rat and flea populations were evaluated in Kisangani, Democratic Republic of the Congo (DRC) by molecular tools. An overall prevalence of 17% Bartonella species and 13% Rickettsia typhi, the agent of murine typhus, was found in the cosmopolitan rat species, Rattus rattus and Rattus norvegicus that were infested by a majority of Xenopsylla cheopis fleas. Bartonella queenslandensis, Bartonella elizabethae, and three Bartonella genotypes were identified by sequencing in rat specimens, mostly in R. rattus. Rickettsia typhi was detected in 72% of X. cheopis pools, the main vector and reservoir of this zoonotic pathogen. Co-infections were observed in rodents, suggesting a common mammalian host shared by R. typhi and Bartonella spp. Thus, both infections are endemic in DRC and the medical staffs need to be aware knowing the high prevalence of impoverished populations or immunocompromised inhabitants in this area.

Morphometrical and genetic comparison of two nematode species: H. spumosa and H. dahomensis (Nematoda, Heterakidae).

Heterakis is a genus of parasitic nematodes, the majority of which are found in ground-feeding birds and only rarely in mammals. The best-known species is Heterakis spumosa, a parasite associated with the cosmopolitan invasive rodent Rattus rattus of Asiatic origin. Heterakis dahomensis was described in 1911 as a parasite of the Gambian giant rat (Cricetomys gambianus) from Benin (Africa), subsequently synonymized to H. spumosa by Hall (1916). The study of helminths in African rodents is scarce and patchy. Since the original description of H. dahomensis, there have been only a few reports from Africa of species belonging to the genus Heterakis and the validity of this species has never in fact been confirmed or rejected. In the present study individual Heterakis spp. were collected from C. gambianus from Senegal. The morphological data taken point to differences between Heterakis dahomensis and H. spumosa, specifically in the number of tail papillae in males and in the vulva cuticular processes of females. In addition, molecular data revealed differences between these taxa and so H. dahomensis should be considered as a valid species. Moreover, recent changes in the systematics of the genus Cricetomys mean that it is now necessary to study the morphology and genetics of the Heterakis specimens collected from Cricetomys spp. (previously assigned to C. gambianus) in order to determine their taxonomic status as either H. dahomensis o H. spumosa.

Trichuris spp. (Nematoda: Trichuridae) from two rodents, Mastomys natalensis and Gerbilliscus vicinus in Tanzania.

During a survey of the helminth community of several rodent species in the Morogoro region (Tanzania), Trichuris whipworms (Nematoda: Trichuridae) were found in the ceca of the Natal multimammate mouse, Mastomys natalensis and a gerbil, Gerbilliscus vicinus (both Rodentia: Muridae). The taxonomic literature regarding Trichuris from African native rodents describes 10 species, but includes few metric and morphologic characters that discriminate between some of the pairs. The whipworms we sampled in Tanzanian Natal multimammate mice and gerbils were morphologically identified, respectively, as Trichuris mastomysi Verster, 1960 and Trichuris carlieri Gedoelst, 1916 sensu lato, but with characters that overlap or partially overlap with the cosmopolitan Murinae whipworm, Trichuris muris , already reported from several rodents in Africa. To clarify our identification, we sequenced the ITS-1, 5.8S, and ITS-2 ribosomal DNA region of the worms' nuclear genome. The genetic analyses clearly distinguish the whipworms we found in M. natalensis from those found in the gerbil, and both of these from T. muris whipworm reference sequences. The overlap of morphological characters between rodent whipworms suggests that reports of T. muris from rodent species not closely related to Murinae in other parts of Africa should be treated with caution.

Bartonella prevalence and genetic diversity in small mammals from Ethiopia.

More than 500 small mammals were trapped at 3 localities in northern Ethiopia to investigate Bartonella infection prevalence and the genetic diversity of the Bartonella spp. We extracted total DNA from liver samples and performed PCR using the primers 1400F and 2300R targeting 852 bp of the Bartonella RNA polymerase beta subunit (rpoB) gene. We used a generalized linear mixed model to relate the probability of Bartonella infection to species, season, locality, habitat, sex, sexual condition, weight, and ectoparasite infestation. Overall, Bartonella infection prevalence among the small mammals was 34.0%. The probability of Bartonella infection varied significantly with species, sex, sexual condition, and some locality, but not with season, elevation, habitat type, animal weight, and ectoparasite infestation. In total, we found 18 unique Bartonella genotypes clustered into 5 clades, 1 clade exclusively Ethiopian, 2 clades clustered with genotypes from central and eastern Africa, and the remaining 2 clades clustered with genotypes and species from Africa and Asia. The close relatedness of several of our Bartonella genotypes obtained from the 3 dominant rodent species in Tigray with the pathogenic Bartonella elizabethae from Rattus spp. in Asia indicates a potential public health threat.

Development and characterization of multiplex panels of microsatellite markers for Syphacia obvelata, a parasite of the house mouse (Mus musculus), using a high throughput DNA sequencing approach.

Syphacia obvelata is a common gastro-intestinal parasitic nematode of the house mouse (Mus musculus), a prime model rodent species. Investigations of the genetic structure, variability of parasite populations and other biological aspects of this host-parasite system are limited due to the lack of genetic resources for S. obvelata. To fill this gap, we developed a set of microsatellite markers for S. obvelata, using a 454 pyrosequencing approach. We designed three multiplex panels allowing genotyping of 10 polymorphic loci and scrutinized them on 42 samples from two different regions inhabited by two different house mouse subspecies (Mus musculus musculus and M. m. domesticus). The numbers of alleles ranged from 2 to 6 with mean observed heterozygosities 0.1476 and 0.2095 for domesticus and musculus worms, respectively. The described markers will facilitate further studies on population biology and co-evolution of this host-parasite system.

Is there sex-biased resistance and tolerance in Mediterranean wood mouse (Apodemus sylvaticus) populations facing multiple helminth infections?

Sex-biased parasitism is rarely investigated in relation to host tolerance and resistance, which are two defense strategies hosts can adopt when challenged by parasites. Health or fitness deteriorations in less tolerant individuals with increasing parasite burden would be faster than those in more tolerant ones. Hence, the body condition and reproductive potential of an infected individual host can be considered proxies for tolerance to parasitism. We studied Mediterranean populations of the wood mouse (Apodemus sylvaticus) and its helminth parasites. We assessed their resistance using the phytohemagglutinin test and spleen size, and their tolerance using body condition in males and females and testes mass in males. In order to avoid spurious correlations, we took into account the phylogeographic structure of the Mediterranean wood mouse populations. We used a mixed model adapted from the animal model used in quantitative genetics. While helminth infection did not differ between the two sexes, females and males differed in their measured defenses. Females seem to invest more in immune defense with increasing risk of parasite diversity, but also appear to be potentially more tolerant of parasitic diversity. These results suggest the existence of sexual differences in resistance and tolerance, and that measurements of parasitic loads alone could be insufficient to detect any underlying sexual differences in the two strategies that have evolved in response to multiple parasitic attacks.

Evolutionary genetics of MHC class II beta genes in the brown hare, Lepus europaeus.

The genes of the major histocompatibility complex (MHC) are attractive candidates for investigating the link between adaptive variation and individual fitness. High levels of diversity at the MHC are thought to be the result of parasite-mediated selection and there is growing evidence to support this theory. Most studies, however, target just a single gene within the MHC and infer any evidence of selection to be representative of the entire gene region. Here we present data from three MHC class II beta genes (DPB, DQB, and DRB) for brown hares in two geographic regions and compare them against previous results from a class II alpha-chain gene (DQA). We report moderate levels of diversity and high levels of population differentiation in the DQB and DRB genes (Na = 11, D (est) = 0.071 and Na = 15, D (est) = 0.409, respectively), but not for the DPB gene (Na = 4, D (est) = 0.00). We also detected evidence of positive selection within the peptide binding region of the DQB and DRB genes (95% CI, ω > 1.0) but found no signature of selection for DPB. Mutation and recombination were both found to be important processes shaping the evolution of the class II genes. Our findings suggest that while diversifying selection is a significant contributor to the generally high levels of MHC diversity, it does not act in a uniform manner across the entire MHC class II region. The beta-chain genes that we have characterized provide a valuable set of MHC class II markers for future studies of the evolution of adaptive variation in Leporids.

Presence of Mopeia virus, an African arenavirus, related to biotope and individual rodent host characteristics: implications for virus transmission.

The East African Mopeia virus (MOPV) is an arenavirus closely related to the highly pathogenic West African Lassa virus, even sharing the same reservoir rodent host Mastomys natalensis. Because MOPV is not known to cause human disease, it offers a unique alternative for studying Lassa virus transmission. We investigated how habitat, population density, and host characteristics are related to MOPV occurrence in M. natalensis populations in Morogoro, Tanzania. In 3 contrasting habitats, 511 M. natalensis individuals were trapped, 12.1% (58/480 tested individuals) of which tested seropositive for antibodies and 8.4% (41/489 tested individuals) for MOPV-RNA. Although population densities differ among habitats, density and habitat were not significantly correlated to MOPV-RNA or antibody presence. Antibody presence was not significantly correlated with any host characteristics. In contrast, MOPV-RNA presence was inversely related to weight, age, sexual maturity, and body mass index. The model with body mass index as predictor was the best at predicting infection probability. Thirty-five individuals were exclusively MOPV-RNA positive, 52 were exclusively antibody positive, and 6 were both MOPV-RNA and antibody positive. Interpreting these data using experimental infection results from studies on other arenaviruses, this would mean that these infections were very recent, old, and roughly 1-3 weeks after infection, respectively. The higher RNA prevalence in juveniles implies vertical transmission, or that horizontal transmission occurs mainly in this age group due to lack of immunity, higher susceptibility, and/or higher juvenile contact rates. This study demonstrates the strength of combining information on antibody and RNA presence with host characteristics, and how this information can provide valuable insights into transmission dynamics.

Homozygosity at a class II MHC locus depresses female reproductive ability in European brown hares.

The link between adaptive genetic variation, individual fitness and wildlife population dynamics is fundamental to the study of ecology and evolutionary biology. In this study, a Bayesian modelling approach was employed to examine whether individual variability at two major histocompatibility complex (MHC) class II loci (DQA and DRB) and eight neutral microsatellite loci explained variation in female reproductive success for wild populations of European brown hare (Lepus europaeus). We examined two aspects of reproduction: the ability to reproduce (sterility) and the number of offspring produced (fecundity). Samples were collected from eastern Austria, experiencing a sub-continental climatic regime, and from Belgium with a more Atlantic-influenced climate. As expected, reproductive success (both sterility and fecundity) was significantly influenced by age regardless of sampling locality. For Belgium, there was also a significant effect of DQA heterozygosity in determining whether females were able to reproduce (95% highest posterior density interval of the regression parameter [-3.64, -0.52]), but no corresponding effect was found for Austria. In neither region was reproduction significantly associated with heterozygosity at the DRB locus. DQA heterozygotes from both regions also showed a clear tendency, but not significantly so, to produce a larger number of offspring. Predictive simulations showed that, in Belgium, sub-populations of homozygotes will have higher rates of sterile individuals and lower average offspring numbers than heterozygotes. No similar effect is predicted for Austria. The mechanism for the spatial MHC effect is likely to be connected to mate choice for increased heterozygosity or to the linkage of certain MHC alleles with lethal recessives at other loci.

Sympatric occurrence of 3 arenaviruses, Tanzania.

To determine the specificity of Morogoro virus for its reservoir host, we studied its host range and genetic diversity in Tanzania. We found that 2 rodent species other than Mastomys natalensis mice carry arenaviruses. Analysis of 340 nt of the viral RNA polymerase gene showed sympatric occurrence of 3 distinct arenaviruses.

Effects of food abundance, age, and flea infestation on the body condition and immunological variables of a rodent host, and their consequences for flea survival.

Temporal variation in body condition and immunological variables of animals that harbor parasites may explain patterns of variation in infestation, as well as parasite impact on the host. We emulated such variability in Sundevall's jirds by manipulating food availability and flea infestation in juveniles and adults and examining how these changes affect survival of fleas on their hosts. Body condition of food-restricted jirds deteriorated, but there was no change in their immunological variables. Adult jirds were in better body condition and had higher immunocompetence than juveniles, however there were no significant effects of flea infestation on any of the variables examined. The main effects of flea infestation were a decrease in the response to phytohaemagglutinin injection, and an increase in the negative effects of food restriction on body mass. Flea survival was higher on juveniles, but fleas did not respond to temporal variability in body condition and immunocompetence of the jirds. We concluded that changes in body condition and immune responses due to growth or variability in food abundance are more important than changes caused by the fleas themselves. Flea infestation is more detrimental to jirds when they are not able to compensate for mass loss through increased food consumption.

Evolution and trans-species polymorphism of MHC class IIbeta genes in cyprinid fish.

The polymorphism of DAB genes encoding MHC IIbeta was investigated in 11 cyprinid species from central Europe. The species belonged to four subfamilies: Cyprininae, Tincinae, Gobioninae and Leuciscinae. Two paralogous groups of sequences, DAB1 and DAB3, were recognised according to the similarity of their nucleotide and amino-acid sequences and from phylogenetic analyses using either partial exon 2 or partial exon 3 sequences. A high allelic variability among species was found for exon 2, indicating extensive MHC polymorphism. Time divergence estimation supports the separation of DAB1 and DAB3 groups predating the separation into fish subfamilies, and a cyprinid origin of the DAB genes. Phylogenetic trees using exon 2 support the hypothesis of trans-species polymorphism, which appears to be limited to the subfamily level, i.e. the presence of sequences from different species in the same allelic group was more often recognised within subfamilies Cyprininae and Leuciscinae than between them. Phylogenetic trees using exon 3 reflect the phylogenetic patterns previously found for Cyprinidae systematics. Specific nucleotides and amino-acids in exon 3 that separate both subfamilies, as well as the species within the Cyprininae subfamily were observed. A lack of segregation in leuciscin species was recognised and the alleles of different leuciscin species tend to share similar motifs in exon 3. This could be explained by the ancient and complicated dispersion history of Cyprininae and the radiation of Leuciscinae. The effects of selective pressures were investigated: (1) within species, (2) among lineages, and (3) among sites. From intraspecific analyses, exon 2 sequences were identified as the targets of diversifying selection, whilst the evolution of exon 3 seems to be under the influence of purifying selection. The analyses among lineages indicate positive selection in many branches when using exon 2, therefore confirming trans-species polymorphism, whilst the DAB lineages of exon 3 are potentially submitted to purifying selection to some extent. Moreover, our results suggest the secondary acquisition of function of DAB1 group after duplication. The analyses among sites reveal that exon 2 exhibits sites under positive selection mostly corresponding to the putative PBR sites involved in the alpha-helix structure of the protein.