Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?

Genome-wide support for incipient Tula hantavirus species within a single rodent host lineage

Evolutionary divergence of viruses is most commonly driven by co-divergence with their hosts or through isolation of transmission after host shifts. It remains mostly unknown, however, whether divergent phylogenetic clades within named virus species represent functionally equivalent byproducts of high evolutionary rates or rather incipient virus species. Here, we test these alternatives with genomic data from two widespread phylogenetic clades in Tula orthohantavirus (TULV) within a single evolutionary lineage of their natural rodent host, the common vole Microtus arvalis. We examined voles from forty-two locations in the contact region between clades for TULV infection by reverse transcription (RT)-PCR. Sequencing yielded twenty-three TULV Central North and twenty-one TULV Central South genomes, which differed by 14.9-18.5 per cent at the nucleotide and 2.2-3.7 per cent at the amino acid (AA) level without evidence of recombination or reassortment between clades. Geographic cline analyses demonstrated an abrupt (<1 km wide) transition between the parapatric TULV clades in continuous landscape. This transition was located within the Central mitochondrial lineage of M. arvalis, and genomic single nucleotide polymorphisms showed gradual mixing of host populations across it. Genomic differentiation of hosts was much weaker across the TULV Central North to South transition than across the nearby hybrid zone between two evolutionary lineages in the host. We suggest that these parapatric TULV clades represent functionally distinct, incipient species, which are likely differently affected by genetic polymorphisms in the host. This highlights the potential of natural viral contact zones as systems for investigating the genetic and evolutionary factors enabling or restricting the transmission of RNA viruses.

Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity

Mastomys natalensis-borne mammarenaviruses appear specific to subspecific M. natalensis taxa rather than to the whole species. Yet mammarenaviruses carried by M. natalensis are known to spill over and jump hosts in northern sub-Saharan Africa. Phylogeographic studies increasingly show that, like M. natalensis, small mammals in sub-Saharan Africa are often genetically structured into several subspecific taxa. Other mammarenaviruses may thus also form virus-subspecific host taxon associations. To investigate this, and if mammarenaviruses carried by M. natalensis in southern Africa are less prone to spill-over, we screened 1225 non-M. natalensis samples from Tanzania where many small mammal taxa meet. We found mammarenavirus RNA in 6 samples. Genetic/genomic characterisation confirmed they were not spill-over from M. natalensis. We detected host jumps among rodent tribe members and an association between mammarenaviruses and subspecific taxa of Mus minutoides and Grammomys surdaster, indicating host genetic structure may be crucial to understand virus distribution and host specificity.

Historical demography and climatic niches of the Natal multimammate mouse (Mastomys natalensis) in the Zambezian region

The Natal multimammate mouse (Mastomys natalensis) is the most widespread rodent species in sub-Saharan Africa, often studied as an agricultural pest and reservoir of viruses. Its mitochondrial (Mt) phylogeny revealed six major lineages parapatrically distributed across open habitats of sub-Saharan Africa. In this study we used 1949 sequences of the mitochondrial cytochrome b gene to elaborate on distribution and evolutionary history of three Mt lineages inhabiting the open habitats of the Zambezian region (corresponding roughly to the African savannas south of the Equator). We describe in more detail contact zones between the lineages—their location and extent of co-occurrence within localities—and infer past population trends. The estimates are interpreted in the light of climatic niche models. The lineages underwent reduction in effective population size during the last glacial, but they spread widely after that: two of them after the last glacial maximum and the last one in mid-Holocene. The centers of expansion, i.e., possible long-term savanna refugia, were estimated to lie close to the Eastern Arc Mountains and lakes of the Great African Rift, geomorphological structures likely to have had long-term influence on geographical distribution of the lineages. Environmental niche modeling shows climate could also affect the broad scale distribution of the lineages but is unlikely to explain the narrow width of the contact zones. The intraspecific Mt differentiation of M. natalensis echoes phylogeographic patterns observed in multiple co-distributed mammal species, which suggests the mammal communities in the region are shaped by the same long-term processes.

Mammarenavirus Genetic Diversity and Its Biological Implications

Members of the family Arenaviridae are classified into four genera: Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus. Reptarenaviruses and hartmaniviruses infect (captive) snakes and have been shown to cause boid inclusion body disease (BIBD). Antennaviruses have genomes consisting of 3, rather than 2, segments, and were discovered in actinopterygian fish by next-generation sequencing but no biological isolate has been reported yet. The hosts of mammarenaviruses are mainly rodents and infections are generally asymptomatic. Current knowledge about the biology of reptarenaviruses, hartmaniviruses, and antennaviruses is very limited and their zoonotic potential is unknown. In contrast, some mammarenaviruses are associated with zoonotic events that pose a threat to human health. This review will focus on mammarenavirus genetic diversity and its biological implications. Some mammarenaviruses including lymphocytic choriomeningitis virus (LCMV) are excellent experimental model systems for the investigation of acute and persistent viral infections, whereas others including Lassa (LASV) and Junin (JUNV) viruses, the causative agents of Lassa fever (LF) and Argentine hemorrhagic fever (AHF), respectively, are important human pathogens. Mammarenaviruses were thought to have high degree of intra-and inter-species amino acid sequence identities, but recent evidence has revealed a high degree of mammarenavirus genetic diversity in the field. Moreover, closely related mammarenavirus can display dramatic phenotypic differences in vivo. These findings support a role of genetic variability in mammarenavirus adaptability and pathogenesis. Here, we will review the molecular biology of mammarenaviruses, phylogeny, and evolution, as well as the quasispecies dynamics of mammarenavirus populations and their biological implications.

Host-Associated Distribution of Two Novel Mammarenaviruses in Rodents from Southern Africa

Mammarenaviruses are hosted by several rodent species, a small number of which have been known to be zoonotic. Host surveillance among small mammals has identified a large diversity of previously undescribed mammarenaviruses. Intensified biosurveillance is warranted to better understand the diversity of these agents. Longitudinal host surveillance involving non-volant small mammals at a site in the Limpopo province, South Africa, was conducted. The study reports on the screening results of 563 samples for the presence of mammarenavirus RNA. PCR-positive samples were subjected to sequencing using Miseq amplicon sequencing. Sequences with close similarity to Mariental and Lunk viruses were identified from two rodent species, Micaelamys namaquensis and Mus minutoides. This represents the first description of these viruses from South Africa. The genomic sequences reported here partially satisfied the requirements put forward by the International Committee on the Taxonomy of Viruses' criteria for species delineation, suggesting that these may be new strains of existing species. The known distribution of these mammarenaviruses is thus expanded further south in Africa.

Luna Virus and Helminths in Wild Mastomys natalensis in Two Contrasting Habitats in Zambia: Risk Factors and Evidence of Virus Dissemination in Semen

Transmission dynamics and the maintenance of mammarenaviruses in nature are poorly understood. Using metagenomic next-generation sequencing (mNGS) and RT-PCR, we investigated the presence of mammarenaviruses and co-infecting helminths in various tissues of 182 Mastomys natalensis rodents and 68 other small mammals in riverine and non-riverine habitats in Zambia. The Luna virus (LUAV) genome was the only mammarenavirus detected (7.7%; 14/182) from M. natalensis. Only one rodent from the non-riverine habitat was positive, while all six foetuses from one pregnant rodent carried LUAV. LUAV-specific mNGS reads were 24-fold higher in semen than in other tissues from males. Phylogenetically, the viruses were closely related to each other within the LUAV clade. Helminth infections were found in 11.5% (21/182) of M. natalensis. LUAV–helminth co-infections were observed in 50% (7/14) of virus-positive rodents. Juvenility (OR = 9.4; p = 0.018; 95% CI: 1.47–59.84), nematodes (OR = 15.5; p = 0.001; 95% CI: 3.11–76.70), cestodes (OR = 10.8; p = 0.025; 95% CI: 1.35–86.77), and being male (OR = 4.6; p = 0.036; 95% CI: 1.10–18.90) were associated with increased odds of LUAV RNA detection. The role of possible sexual and/or congenital transmission in the epidemiology of LUAV infections in rodents requires further study, along with the implications of possible helminth co-infection.

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades

Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.

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.

Detection and genetic diversity of Mopeia virus in Mastomys natalensis from different habitats in the Limpopo National Park, Mozambique

Mammarenaviruses have been a growing concern for public health in Africa since the 1970s when Lassa virus cases in humans were first described in west Africa. In southern Africa, a single outbreak of Lujo virus was reported to date in South Africa in 2008 with a case fatality rate of 80%. The natural reservoir of Lassa virus is Mastomys natalensis while for the Lujo virus the natural host has yet to be identified. Mopeia virus was described for the first time in M. natalensis in the central Mozambique in 1977 but few studies have been conducted in the region. In this study, rodents were trapped between March and November 2019in villages, croplands fields and mopane woodland forest. The aim was to assess the potential circulation and to evaluate the genetic diversity of mammarenaviruses in M. natalensis trapped in the Limpopo National Park and its buffer zone in Massingir district, Mozambique. A total of 534 M. natalensis were screened by RT-PCR and the overall proportion of positive individuals was 16.9%. No significant differences were detected between the sampled habitats (χ2 = 0.018; DF = 1; p = 0.893). The Mopeia virus (bootstrap value 91%) was the Mammarenavirus circulating in the study area sites, forming a specific sub-clade with eight different sub-clusters. We concluded that Mopeia virus circulates in all habitats investigated and it forms a different sub-clade to the one reported in central Mozambique in 1977.

Host genetic factors associated with the range limit of a European hantavirus

The natural host ranges of many viruses are restricted to very specific taxa. Little is known about the molecular barriers between species that lead to the establishment of this restriction or generally prevent virus emergence in new hosts. Here, we identify genomic polymorphisms in a natural rodent host associated with a strong genetic barrier to the transmission of European Tula orthohantavirus (TULV). We analysed the very abrupt spatial transition between two major phylogenetic clades in TULV across the comparatively much wider natural hybrid zone between evolutionary lineages of their reservoir host, the common vole (Microtus arvalis). Genomic scans of 79,225 single nucleotide polymorphisms (SNPs) in 323 TULV‐infected host individuals detected 30 SNPs that were consistently associated with the TULV clades CEN.S or EST.S in two replicate sampling transects. Focusing the analysis on 199 voles with evidence of genomic admixture at the individual level (0.1–0.9) supported statistical significance for all 30 loci. Host genomic variation at these SNPs explained up to 37.6% of clade‐specific TULV infections. Genes in the vicinity of associated SNPs include SAHH, ITCH and two members of the Syngr gene family, which are involved in functions related to immune response or membrane transport. This study demonstrates the relevance of natural hybrid zones as systems not only for studying processes of evolutionary divergence and speciation, but also for the detection of evolving genetic barriers for specialized parasites.

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.

Linking Behavior, Co-infection Patterns, and Viral Infection Risk With the Whole Gastrointestinal Helminth Community Structure in Mastomys natalensis

Infection probability, load, and community structure of helminths varies strongly between and within animal populations. This can be ascribed to environmental stochasticity or due to individual characteristics of the host such as their age or sex. Other, but understudied, factors are the hosts' behavior and co-infection patterns. In this study, we used the multimammate mouse (Mastomys natalensis) as a model system to investigate how the hosts' sex, age, exploration behavior, and viral infection history affects their infection risk, parasitic load, and community structure of gastrointestinal helminths. We hypothesized that the hosts' exploration behavior would play a key role in the risk for infection by different gastrointestinal helminths, whereby highly explorative individuals would have a higher infection risk leading to a wider diversity of helminths and a larger load compared to less explorative individuals. Fieldwork was performed in Morogoro, Tanzania, where we trapped a total of 214 individual mice. Their exploratory behavior was characterized using a hole-board test after which we collected the helminths inside their gastrointestinal tract. During our study, we found helminths belonging to eight different genera: Hymenolepis sp., Protospirura muricola, Syphacia sp., Trichuris mastomysi, Gongylonema sp., Pterygodermatites sp., Raillietina sp., and Inermicapsifer sp. and one family: Trichostrongylidae. Hierarchical modeling of species communities (HMSC) was used to investigate the effect of the different host-related factors on the infection probability, parasite load, and community structure of these helminths. Our results show that species richness was higher in adults and in females compared to juveniles and males, respectively. Contrary to our expectations, we found that less explorative individuals had higher infection probability with different helminths resulting in a higher diversity, which could be due to a higher exposure rate to these helminths and/or behavioral modification due to the infection.

Three Immunocompetent Small Animal Models That Do Not Support Zika Virus Infection

Zika virus (ZIKV) is a mosquito-borne flavivirus that is primarily transmitted to humans through the bite of an infected mosquito. ZIKV causes disease in infected humans with added complications of Guillain-Barré syndrome and birth defects in infants born to mothers infected during pregnancy. There are several large immunocompetent animal models for ZIKV including non-human primates (NHPs). NHP models closely reflect human infection; however, due to sample size restrictions, investigations into the effects of transmission route and the impacts on disease dynamics have been understudied. Mice have been widely used for modeling ZIKV infection, yet there are few ZIKV-susceptible immunocompetent mouse models and none of these have been used to investigate sexual transmission. In an effort to identify a small immunocompetent animal model to characterize sexual transmission of ZIKV, we attempt experimental infection of multimammate mice, New Zealand white rabbits, and Hartley guinea pigs. The multimammate mouse is the natural reservoir of Lassa fever virus and has been identified to harbor other human pathogens. Likewise, while NZW rabbits are susceptible to West Nile virus, they have not yet been examined for their susceptibility to infection with ZIKV. Guinea pigs have been successfully used as models for ZIKV infection, but only in immunocompromised life stages (young or pregnant). Here, it was found that the multimammate mouse and New Zealand White (NZW) rabbits are not susceptible ZIKV infection as determined by a lack viral RNA in tissues and fluids collected. Sexually mature male Hartley guinea pigs were inoculated subcutaneously and by mosquito bite, but found to be refractory to ZIKV infection, contrary to findings of other studies in young and pregnant guinea pigs. Interestingly, here it is shown that adult male guinea pigs are not susceptible to ZIKV infection, even when infected by natural route (e.g., mosquito bite). Although a new small animal model for the sexual transmission for ZIKV was not established through this study, these findings provide information on outbred animal species that are not permissive to infection (NZW rabbits and multimammate mice) and new information surrounding limitations of a previously established animal model (guinea pigs).

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

Multiple Mammarenaviruses Circulating in Angolan Rodents

Rodents are a speciose group of mammals with strong zoonotic potential. Some parts of Africa are still underexplored for the occurrence of rodent-borne pathogens, despite this high potential. Angola is at the convergence of three major biogeographical regions of sub-Saharan Africa, each harbouring a specific rodent community. This rodent-rich area is, therefore, strategic for studying the diversity and evolution of rodent-borne viruses. In this study we examined 290 small mammals, almost all rodents, for the presence of mammarenavirus and hantavirus RNA. While no hantavirus was detected, we found three rodent species positive for distinct mammarenaviruses with a particularly high prevalence in Namaqua rock rats (Micaelamys namaquensis). We characterised four complete virus genomes, which showed typical mammarenavirus organisation. Phylogenetic and genetic distance analyses revealed: (i) the presence of a significantly divergent strain of Luna virus in Angolan representatives of the ubiquitous Natal multimammate mouse (Mastomys natalensis), (ii) a novel Okahandja-related virus associated with the Angolan lineage of Micaelamys namaquensis for which we propose the name Bitu virus (BITV) and (iii) the occurrence of a novel Mobala-like mammarenavirus in the grey-bellied pygmy mouse (Mus triton) for which we propose the name Kwanza virus (KWAV). This high virus diversity in a limited host sample size and in a relatively small geographical area supports the idea that Angola is a hotspot for mammarenavirus diversity.