Novel orthohepeviruses in wild rodents from Sao Paulo State, Brazil.
ABSTRACT: The Hepeviridae comprise single-stranded positive-sense RNA viruses classified into two genera, Orthohepevirus and Piscihepevirus. Orthohepeviruses have a wide host range that includes rodents, but previous studies had been restricted to rodents of the Muridae family. In this study, we applied a high-throughput sequencing approach to examine the presence of orthohepeviruses in rodents from São Paulo State, Brazil. We also used RT-PCR to determine the frequency of orthohepeviruses in our sampled population. We identified novel orthohepeviruses in blood samples derived from Necromys lasiurus (1.19%) and Calomys tener (3.66%). Therefore, our results expand the host range and viral diversity of the Hepeviridae family.
Project description:The <i>Hepacivirus</i> genus comprises single-stranded positive-sense RNA viruses within the family <i>Flaviviridae</i>. Several hepaciviruses have been identified in different mammals, including multiple rodent species in Africa, Asia, Europe, and North America. To date, no rodent hepacivirus has been identified in the South American continent. Here, we describe an unknown hepacivirus discovered during a metagenomic screen in <i>Akodon montensis</i>, <i>Calomys tener</i>, <i>Oligoryzomys nigripes</i>, <i>Necromys lasiurus,</i> and <i>Mus musculus</i> from São Paulo State, Brazil. Molecular detection of this novel hepacivirus by RT-PCR showed a frequency of 11.11% (2/18) in <i>Oligoryzomys nigripes</i>. This is the first identification of hepavivirus in sigmondonine rodents and in rodents from South America. In sum, our results expand the host range, viral diversity, and geographical distribution of the <i>Hepacivirus</i> genus.
Project description:Hepatitis E virus (HEV) is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis. Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of them may have zoonotic potential. In this study, we tested 278 specimens collected from seven wild small mammal species in Yunnan province, China, for the presence and prevalence of orthohepevirus by broad-spectrum reverse transcription (RT)-PCR. HEV-related sequences were detected in two rodent species, including Chevrier's field mouse (Apodemus chevrieri, family Muridae) and Père David's vole (Eothenomys melanogaster, family Cricetidae), with the infection rates of 29.20% (59/202) and 7.27% (4/55), respectively. Further four representative full-length genomes were generated: two each from Chevrier's field mouse (named RdHEVAc14 and RdHEVAc86) and Père David's vole (RdHEVEm40 and RdHEVEm67). Phylogenetic analyses and pairwise distance comparisons of whole genome sequences and amino acid sequences of the gene coding regions showed that orthohepeviruses identified in Chinese Chevrier's field mouse and Père David's vole belonged to the species Orthohepevirus C but were highly divergent from the two assigned genotypes: HEV-C1 derived from rat and shrew, and HEV-C2 derived from ferret and possibly mink. Quantitative real-time RT-PCR demonstrated that these newly discovered orthohepeviruses had hepatic tropism. In summary, our work discovered two putative novel genotypes orthohepeviruses preliminarily named HEV-C3 and HEV-C4 within the species Orthohepevirus C, which expands our understanding of orthohepevirus infection in the order Rodentia and gives new insights into the origin, evolution, and host range of orthohepevirus.
Project description:Hepatitis E virus (HEV) (family Hepeviridae) is one of the most common human pathogens, causing acute hepatitis and an increasingly recognized etiological agent in chronic hepatitis and extrahepatic manifestations. Recent studies reported that not only are the classical members of the species Orthohepevirus A (HEV-A) pathogenic to humans but a genetically highly divergent rat origin hepevirus (HEV-C1) in species Orthohepevirus C (HEV-C) is also able to cause zoonotic infection and symptomatic disease (hepatitis) in humans. This review summarizes the current knowledge of hepeviruses in rodents with special focus of rat origin HEV-C1. Cross-species transmission and genetic diversity of HEV-C1 and confirmation of HEV-C1 infections and symptomatic disease in humans re-opened the long-lasting and full of surprises story of HEV in human. This novel knowledge has a consequence to the epidemiology, clinical aspects, laboratory diagnosis, and prevention of HEV infection in humans.
Project description:Hepatitis A virus (HAV) and hepatitis E virus (HEV) are significant human pathogens and are responsible for a substantial proportion of cases of severe acute hepatitis worldwide. Genetically, both viruses are heterogeneous and are classified into several genotypes that differ in their geographical distribution and risk group association. There is, however, little evidence that variants of HAV or HEV differ antigenically or in their propensity to cause severe disease. Genetically more divergent but primarily hepatotropic variants of both HAV and HEV have been found in several mammalian species, those of HAV being classified into eight species within the genus Hepatovirus in the virus family Picornaviridae. HEV is classified as a member of the species Orthohepevirus A in the virus family Hepeviridae, a species that additionally contains viruses infecting pigs, rabbits, and a variety of other mammalian species. Other species (Orthohepevirus B-D) infect a wide range of other mammalian species including rodents and bats.
Project description:The family Hepeviridae consists of positive-stranded RNA viruses that infect a wide range of mammalian species, as well as chickens and trout. A subset of these viruses infects humans and can cause a self-limiting acute hepatitis that may become chronic in immunosuppressed individuals. Current published descriptions of the taxonomical divisions within the family Hepeviridae are contradictory in relation to the assignment of species and genotypes. Through analysis of existing sequence information, we propose a taxonomic scheme in which the family is divided into the genera Orthohepevirus (all mammalian and avian hepatitis E virus (HEV) isolates) and Piscihepevirus (cutthroat trout virus). Species within the genus Orthohepevirus are designated Orthohepevirus A (isolates from human, pig, wild boar, deer, mongoose, rabbit and camel), Orthohepevirus B (isolates from chicken), Orthohepevirus C (isolates from rat, greater bandicoot, Asian musk shrew, ferret and mink) and Orthohepevirus D (isolates from bat). Proposals are also made for the designation of genotypes within the human and rat HEVs. This hierarchical system is congruent with hepevirus phylogeny, and the three classification levels (genus, species and genotype) are consistent with, and reflect discontinuities in the ranges of pairwise distances between amino acid sequences. Adoption of this system would include the avoidance of host names in taxonomic identifiers and provide a logical framework for the assignment of novel variants.
Project description:Since the recognition of hantavirus as the agent responsible for haemorrhagic fever in Eurasia in the 1970s and, 20 years later, the descovery of hantavirus pulmonary syndrome in the Americas, the genus Hantavirus has been continually described throughout the World in a variety of wild animals. The diversity of wild animals infected with hantaviruses has only recently come into focus as a result of expanded wildlife studies. The known reservoirs are more than 80, belonging to 51 species of rodents, 7 bats (order Chiroptera) and 20 shrews and moles (order Soricomorpha). More than 80 genetically related viruses have been classified within Hantavirus genus; 25 recognized as human pathogens responsible for a large spectrum of diseases in the Old and New World. In Brazil, where the diversity of mammals and especially rodents is considered one of the largest in the world, 9 hantavirus genotypes have been identified in 12 rodent species belonging to the genus Akodon, Calomys, Holochilus, Oligoryzomys, Oxymycterus, Necromys and Rattus. Considering the increasing number of animals that have been implicated as reservoirs of different hantaviruses, the understanding of this diversity is important for evaluating the risk of distinct hantavirus species as human pathogens.
Project description:The predominant landscape of the Atlantic Forest of the Brazilian state of Rio de Janeiro is made up of forest fragments surrounded by a matrix of modified habitat, which may influence the occurrence and distribution of host species and their parasites in comparison with the original continuous forest. The present study describes the structure, composition, and diversity of the helminth community found in rodents in two areas of an open matrix of different status of conservation. The abundance, intensity, and prevalence were calculated for each helminth species in rodent species. The influence of biotic and abiotic factors on the abundance and prevalence of the helminth species was also investigated. Community structure was analyzed based on the beta diversity and a bipartite network. Nine helminth species were recovered from <i>Akodon cursor</i>, <i>Necromys lasiurus</i> and <i>Mus musculus</i>, with the greatest helminth species richness being recorded in <i>A. cursor</i> (S = 8), followed by <i>N. lasiurus</i> (S = 6), and <i>M. musculus</i> (S = 3). Only three of the helminths recorded in <i>A. cursor</i> had been recorded previously in this rodent in the Atlantic Forest, where 12 different helminths have been recorded, so that the other five are new occurrences for this rodent. All the helminth species of <i>N. lasiurus</i> had been reported previously in this rodent in the Cerrado and Caatinga regions. <i>Mus musculus</i> was infected with the same helminths as the local fauna. Host species and locality were the most important factors influencing helminth abundance and prevalence. Beta-diversity was high for infracommunities indicating more substitutions of helminth species than losses among individuals. Three helminths species were shared by the three host species. The reduced beta-diversity observed in the component communities was consistent with the overlap observed in the helminth fauna of the host species.
Project description:The plague caused by the <i>Yersinia pestis</i> bacterium is primarily a flea-transmitted zoonosis of rodents that can also be conveyed to humans and other mammals. In this work, we analyzed the spatial and temporal distribution of rodent populations during epizootic and enzootic periods of the plague in the municipality of Exu, northeastern Brazil. The geospatial analyses showed that all the rodent species appeared through the whole territory of the municipality, with different occurrence hotspots for the different species. Important fluctuations in the rodent populations were observed, with a reduction in the wild rodent fauna following the end of a plague epizootic period, mostly represented by <i>Necromys lasiurus</i> and an increase in the commensal species <i>Rattus rattus</i>. A higher abundance of rats might lead to an increased exposure of human populations, favoring spillovers of plague and other rodent-borne diseases. Our analysis highlights the role of wild rodent species as amplifier hosts and of commensal rats (<i>R. rattus</i>) as preserver hosts in the enzootic period of a specific transmission infection area.
Project description:We evaluated infection by Rickettsia spp. and Ehrlichia spp in small mammals and their ticks from two Atlantic forest conservation areas in the state of Rio Grande do Norte, northeastern Brazil. A total of 39 small mammals were captured during 2012-2013, encompassing 33 marsupials (29 Didelphis albiventris, four Monodelphis domestica), three Cricetidae rodents (two Necromys lasiurus, one Rattus rattus), one Caviomorpha rodent (Thrichomys apereoides) and two armadillos (Euphractus sexcinctus). The ticks Amblyomma auricularium, Ixodes loricatus, and Ornithodoros mimon were collected from D. albiventris, whereas only A. auricularium was collected from armadillos. Through immunofluorescence assay with Rickettsia spp. antigens, 6/28 (21%) D. albiventris and the single R. rattus specimen reacted to at least one rickettsial antigen, with highest seroprevalence and endpoint titers to Rickettsia amblyommatis. A total of 150 ticks (126 A. auricularium, nine I. loricatus, 15 O. mimon) was tested for rickettsial infection by PCR, which detected only R. amblyommatis in most of the A. auricularium ticks. Lung and spleen samples were collected from small mammals (two N. lasiurus, six D. albiventris, three M. domestica, one T. apereoides, one R. rattus) and were tested by PCR for Anaplasmataceae agents. The spleen from one D. albiventris contained a new ehrlichial agent, here named as Ehrlichia sp. strain Natal. Phylogenetic analysis inferred from the dsb gene of Ehrlichia spp. indicates that this novel agent is potentially a new species. Future studies should monitor the possible role of rickettsial and/or ehrlichial microorganisms as agents of emerging diseases in these degraded areas of Atlantic forest, just as has occurred with other agents in degraded areas of this biome in southeastern Brazil.
Project description:Hepatitis E virus (HEV) is a major cause of viral hepatitis globally. Zoonotic HEV is an important cause of chronic hepatitis in immunocompromised patients. The rapid identification of novel HEV variants and accumulating sequence information has prompted significant changes in taxonomy of the family Hepeviridae. This family includes two genera: Orthohepevirus, which infects terrestrial vertebrates, and Piscihepevirus, which infects fish. Within Orthohepevirus, there are four species, A-D, with widely differing host range. Orthohepevirus A contains the HEV variants infecting humans and its significance continues to expand with new clinical information. We now recognize eight genotypes within Orthohepevirus A: HEV1 and HEV2, restricted to humans; HEV3, which circulates among humans, swine, rabbits, deer and mongooses; HEV4, which circulates between humans and swine; HEV5 and HEV6, which are found in wild boars; and HEV7 and HEV8, which were recently identified in dromedary and Bactrian camels, respectively. HEV7 is an example of a novel genotype that was found to have significance to human health shortly after discovery. In this review, we summarize recent developments in HEV molecular taxonomy, epidemiology and evolution and describe the discovery of novel camel HEV genotypes as an illustrative example of the changes in this field.