In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
- MeSH
- fylogeneze MeSH
- lidé MeSH
- Mononegavirales * genetika MeSH
- viry * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
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.
- Publikační typ
- časopisecké články MeSH
Organisms living in high altitude must adapt to environmental conditions with hypoxia and low temperature, e.g. by changes in the structure and function of proteins associated with oxidative phosphorylation in mitochondria. Here we analysed the signs of adaptive evolution in 27 mitogenomes of endemic Ethiopian rats (Stenocephalemys), where individual species adapted to different elevation. Significant signals of positive selection were detected in 10 of the 13 mitochondrial protein-coding genes, with a majority of functional substitutions in the NADH dehydrogenase complex. Higher frequency of positively selected sites was found in phylogenetic lineages corresponding to Afroalpine specialists.
- MeSH
- fylogeneze MeSH
- genová introgrese MeSH
- mitochondriální proteiny chemie genetika MeSH
- mitochondrie genetika MeSH
- molekulární evoluce MeSH
- molekulární modely MeSH
- Murinae klasifikace genetika MeSH
- oxidativní fosforylace MeSH
- sekvenční analýza DNA metody MeSH
- selekce (genetika) MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Myxobolus pseudodispar Gorbunova, 1936 (Myxozoa) was originally described as a parasite of common roach, Rutilus rutilus (Linnaeus), with developing stages in muscles and spores disseminated in macrophage centres of different organs and tissues. Later, this parasite was described from several other cyprinids, but with relatively large intraspecific differences based on SSU rDNA gene sequences. Within our long-term study on myxozoan biodiversity, we performed a broad microscopic and molecular screening of various freshwater fish species (over 450 specimens, 36 species) from different localities. We investigated the cryptic species status of M. pseudodispar. Our analysis revealed four new unique SSU rDNA sequences of M. pseudodispar as well as an infection in new fish host species. Myxobolus pseudodispar sequence analysis showed clear phylogenetic grouping according to fish host criterion forming 13 well-recognised clades. Using 1% SSU rDNA-based genetic distance criterion, at least ten new species of Myxobolus Bütschli, 1882 may be recognised in the group of M. pseudodispar sequences. Our analysis showed the paraphyletic character of M. pseudodispar sequences and the statistical tests rejected hypothetical tree topology with the monophyletic status of the M. pseudodispar group. Myxobolus pseudodispar represents a species complex and it is a typical example of myxozoan hidden diversity phenomenon confirming myxozoans as an evolutionary very successful group of parasites with a great ability to adapt to a new hosts with subsequent speciation events.
- MeSH
- biodiverzita * MeSH
- biologická evoluce MeSH
- hostitelská specificita * MeSH
- interakce hostitele a parazita * MeSH
- Myxobolus klasifikace fyziologie MeSH
- parazitární nemoci u zvířat parazitologie MeSH
- ribozomální DNA analýza MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.
- Publikační typ
- časopisecké články MeSH
The presence of Neospora caninum Dubey, Carpenter, Speer, Topper et Uggla, 1988 in small mammals (i.e. murid rodents, Erinaceomorpha, Eulipotyphla and Scadentia) was explored for first time in South-East Asia. A total of 192 individuals from six localities across Thailand were analysed. A general prevalence of N. caninum of 22% was observed, with some variation among localities (5-36%). Four main types of habitat were included and rodents trapped in dry-land habitat (17 positive among 41 individuals) were more likely to be infected with N. caninum than those from other habitats (forest, rain-fed land and settlement). Rodent species identity and individual rodent weight had no influence on individual infection. Our results provided the first data on the presence of N. caninum in rodents in South-East Asia and first report of N. caninum in the order Scadentia.
- MeSH
- ekosystém MeSH
- hlodavci * MeSH
- ježkovití * MeSH
- kokcidióza epidemiologie parazitologie veterinární MeSH
- nemoci hlodavců epidemiologie parazitologie MeSH
- Neospora izolace a purifikace MeSH
- prevalence MeSH
- Tupaia * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Thajsko MeSH
The Ethiopian highlands are the most extensive complex of mountainous habitats in Africa. The presence of the Great Rift Valley (GRV) and the striking elevational ecological gradients inhabited by recently radiated Ethiopian endemics, provide a wide spectrum of model situations for evolutionary studies. The extant species of endemic rodents, often markedly phenotypically differentiated, are expected to possess complex genetic features which evolved asa consequence of the interplay between geomorphology and past climatic changes. In this study, we used the largest available multi-locus genetic dataset of the murid genus Stenocephalemys (347 specimens from ca 40 localities across the known distributional area of all taxa) to investigate the relative importance of disruptive selection, temporary geographic isolation and introgression in their adaptive radiations in the Pleistocene. We confirmed the four main highly supported mitochondrial (mtDNA) clades that were proposed as four species in a previous pilot study: S. albipes is a sister species of S. griseicauda (both lineages are present on both sides of the GRV), while the second clade is formed by two Afro-alpine species, S. albocaudata (east of GRV) and the undescribed Stenocephalemys sp. A (west of GRV). There is a clear elevational gradient in the distribution of the Stenocephalemys taxa with two to three species present at different elevations of the same mountain range. Surprisingly, the nuclear species tree corresponded only a little to the mtDNA tree. Multispecies coalescent models based on six nuclear markers revealed the presence of six separate gene pools (i.e. candidate species), with different topology. Phylogenetic analysis, together with the geographic distribution of the genetic groups, suggests a complex reticulate evolution. We propose a scenario that involves (besides classical allopatric speciation) two cases of disruptive selection along the elevational ecological gradient, multiple crosses of GRV in dry and cold periods of the Pleistocene, followed by hybridization and mtDNA introgression on imperfect reproductive barriers. Spatial expansion of the currently most widespread "albipes" mtDNA clade was followed by population fragmentation, lineage sorting and again by hybridization and mtDNA introgression. Comparison of this genetic structure to other Ethiopian endemic taxa highlight the geographical areas of special conservation concern, where more detailed biodiversity studies should be carried out to prevent many endemic taxa from going extinct even before they are recognized.
- MeSH
- cytochromy b chemie klasifikace genetika MeSH
- ekosystém MeSH
- fylogeneze MeSH
- haplotypy MeSH
- hybridizace genetická MeSH
- karyotyp MeSH
- mitochondriální DNA chemie izolace a purifikace metabolismus MeSH
- molekulární evoluce * MeSH
- Murinae anatomie a histologie klasifikace genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Etiopie MeSH
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.
- MeSH
- fylogeneze MeSH
- genetická variace * MeSH
- genom virový * MeSH
- hostitelská specificita * MeSH
- imunitní únik MeSH
- Muromegalovirus genetika MeSH
- myši virologie MeSH
- polymorfismus genetický MeSH
- zeměpis MeSH
- zvířata MeSH
- Check Tag
- myši virologie MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
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.
- MeSH
- genom virový genetika MeSH
- genomika MeSH
- hantavirové infekce veterinární virologie MeSH
- Hantavirus genetika MeSH
- Murinae virologie MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Etiopie MeSH
- MeSH
- feces parazitologie MeSH
- fylogeneze * MeSH
- lidé MeSH
- polymerázová řetězová reakce MeSH
- primáti parazitologie MeSH
- sekvenční analýza DNA MeSH
- Trichuris * genetika parazitologie MeSH
- vejce MeSH
- zoonózy etiologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
