Abstract
Rodents are important reservoirs of numerous viruses, some of which have significant impacts on public health. Ecosystem disturbances and decreased host species richness have been associated with the emergence of zoonotic diseases. In this study, we aimed at (a) characterizing the viral diversity in seven neotropical rodent species living in four types of habitats and (b) exploring how the extent of environmental disturbance influences this diversity. Through a metagenomic approach, we identified 77,767 viral sequences from spleen, kidney, and serum samples. These viral sequences were attributed to 27 viral families known to infect vertebrates, invertebrates, plants, and amoeba. Viral diversities were greater in pristine habitats compared with disturbed ones, and lowest in peri-urban areas. High viral richness was observed in savannah areas. Differences in these diversities were explained by rare viruses that were generally more frequent in pristine forest and savannah habitats. Moreover, changes in the ecology and behavior of rodent hosts, in a given habitat, such as modifications to the diet in disturbed vs. pristine forests, are major determinants of viral composition. Lastly, the phylogenetic relationships of four vertebrate-related viral families (Polyomaviridae, Flaviviridae, Togaviridae, and Phenuiviridae) highlighted the wide diversity of these viral families, and in some cases, a potential risk of transmission to humans. All these findings provide significant insights into the diversity of rodent viruses in Amazonia, and emphasize that habitats and the host’s dietary ecology may drive viral diversity. Linking viral richness and abundance to the ecology of their hosts and their responses to habitat disturbance could be the starting point for a better understanding of viral emergence and for future management of ecosystems.
Highlights
Viruses have conquered all living systems, infecting other microbes and more complex organisms, such as plants, invertebrates, and vertebrates.Most viruses have small genomes with high mutation rates [1], giving them the ability to evolve and adapt quickly to new environments and potentially the ability to infect new hosts.The development of metagenomic approaches applied to viruses [2,3] has improved our knowledge of the extent of viral diversity and of the host spectra of several viral families
While Amazonia is considered a hotspot of diversity for hosts and pathogens [133], most virome studies have been conducted in Asia and North America
In French Guiana, north of the Amazonian region, the description of the virome of seven neotropical rodent species allowed us to identify a large number of new viruses, most of which correspond to vertebrate viruses
Summary
The development of metagenomic approaches applied to viruses (viromics) [2,3] has improved our knowledge of the extent of viral diversity and of the host spectra of several viral families. This is, for instance, the case for hepaciviruses, with both the descriptions of novel viral species in mammals and the evidence of infection in non-mammal species [4,5]. Recent examples of virus spill-overs, such as the 2002 severe acute respiratory syndrome (SARS)
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