Molecular detection and genomic characterization of diverse hepaciviruses in African rodents.

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about three per cent of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausible African origin of HCV genotypes, we have screened a large collection of small mammals samples from seven sub-Saharan African countries. Out of 4,303 samples screened, eighty were found positive for the presence of hepaciviruses in twenty-nine different host species. We, here, report fifty-six novel genomes that considerably increase the diversity of three divergent rodent hepacivirus lineages. Furthermore, we provide strong evidence for hepacivirus co-infections in rodents, which were exclusively found in four sampled species of brush-furred mice. We also detect evidence of recombination within specific host lineages. Our study expands the available hepacivirus genomic data and contributes insights into the relatively deep evolutionary history of these pathogens in rodents. Overall, our results emphasize the importance of rodents as a potential hepacivirus reservoir and as models for investigating HCV infection dynamics.

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.

Host subspecific viral strains in European house mice: Murine cytomegalovirus in the Eastern (Mus musculus musculus) and Western house mouse (Mus musculus domesticus).

Murine cytomegalovirus (MCMV) has been reported from house mice (Mus musculus) worldwide, but only recently from Eastern house mice (M. m. musculus), of particular interest because they form a semi-permeable species barrier in Europe with Western house mice, M. m. domesticus. Here we report genome sequences of EastMCMV (from Eastern mice), and set these in the context of MCMV genomes from genus Mus hosts. We show EastMCMV and WestMCMV are genetically distinct. Phylogeny splitting analyses show a genome wide (94%) pattern consistent with no West-East introgression, the major exception (3.8%) being a genome-terminal region of duplicated genes involved in host immune system evasion. As expected from its function, this is a region of maintenance of ancestral polymorphism: The lack of clear splitting signal cannot be interpreted as evidence of introgression. The EastMCMV genome sequences reported here can therefore serve as a well-described resource for exploration of murid MCMV diversity.

Hantavirus Strains in East Africa Related to Western African Hantaviruses.

Hantaviruses are RNA viruses primarily carried by rodents, soricomorphs, and bats. The data about the distribution and genetic diversity of these viruses are often limited, especially in most regions of sub-Saharan Africa. Moreover, the majority of representatives were identified in western African localities, while only three hantaviruses have been reported in East Africa to date. In this study, a total of 1866 small mammals captured between 2009 and 2014 in various countries of Eastern Africa (Ethiopia, Zambia, Mozambique, Kenya, and Tanzania) were molecularly screened for the presence of hantaviruses. Hantavirus RNA was detected in dried blood samples of the Cape pipistrelle bat (Neoromicia capensis) captured in Ethiopia and the African wood mouse (Hylomyscus endorobae) from Kenya. Phylogenetic analysis of partial genomic segments revealed that the Ethiopian sample represents a sister lineage of the Mouyassué virus (reported previously from the congeneric bat in Côte d'Ivoire), and the Kenyan sample is a sister lineage of the Sangassou virus (described from the same mouse genus in Guinea).

Complete genome characterisation and phylogenetic position of Tigray hantavirus from the Ethiopian white-footed mouse, Stenocephalemys albipes.

Hantaviruses, well-known human pathogens, have only recently been identified on the African continent. Tigray virus (TIGV) was found in Ethiopia in 2012 in a Murinae species, Stenocephalemys albipes, but the genetic data obtained at that time were too limited to correctly assess its phylogenetic position within the hantavirus tree. We used high throughput sequencing to determine the complete genome of TIGV, which showed a typical hantavirus organisation. The large (L), medium (M), and small (S) genome segments were found to be 6532, 3594 and 1908 nucleotides long, respectively, and the 5' and 3' termini for all three segments were predicted to form the panhandle-like structure typical for bunyaviruses. Nucleotide-based phylogenetic analyses revealed that all three coding segments cluster in the phylogroup III sensu Guo et al. (2013). However, while TIGV S segment is basal to the Murinae-associated hantaviruses, the M and L segments are basal to the Soricomorpha-associated hantaviruses. TIGV is the first Murinae-borne hantavirus showing this inconsistent segmental clustering in the hantavirus phylogenetic tree. We finally propose non-exclusive scenarios that could explain the original phylogenetic position of TIGV.

High diversity of RNA viruses in rodents, Ethiopia.

We investigated synanthropic small mammals in the Ethiopian Highlands as potential reservoirs for human pathogens and found that 2 rodent species, the Ethiopian white-footed mouse and Awash multimammate mouse, are carriers of novel Mobala virus strains. The white-footed mouse also carries a novel hantavirus, the second Murinae-associated hantavirus found in Africa.