Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits

Abstract

The advent of unbiased metagenomic virus discovery has revolutionized studies of virus biodiversity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing to identify RNA viruses in European field voles and rabbits. Accordingly, we identified a number of novel RNA viruses including astrovirus, rotavirus A, picorna-like virus and a narmovirus (paramyxovirus). In addition, we identified a sobemovirus and a novel luteovirus that likely originated from the rabbit diet. These newly discovered viruses were often divergent from those previously described. The novel astrovirus was most closely related to a virus sampled from the rodent-eating European roller bird (Coracias garrulous). PCR screening revealed that the novel narmovirus in the UK field vole had a prevalence of approximately 4%, and shared common ancestry with other rodent narmoviruses sampled globally. Two novel rotavirus A sequences were detected in a UK field vole and a French rabbit, the latter with a prevalence of 5%. Finally, a highly divergent picorna-like virus found in the gut of the French rabbit virus was only~35% similar to an arilivirus at the amino acid level, suggesting the presence of a novel viral genus within the Picornaviridae.

Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau

“…Nevertheless, the smaller number of invertebrate and plant virus sequences indicated high viral diversity, accounting for 22 families. Among them, several sequences of plant and insect viruses also occurred in intestine or fecal samples demonstrating the omnivorous diet of the rodents, consistent with prior reports 9,12 . Furthermore, unclassified viruses were observed in each pool, particularly in intestine and fecal samples, accounting for 0.01-7.06% of total viral-related www.nature.com/scientificreports/ sequencing reads.…”

“…The human infection risk is often positively correlated with the abundance of the rodent host population 9,10 . Continuously expanding human activities have promoted interactions between humans and infected rodents, and thus the opportunities for zoonotic transmission have been amplified 11 .Rodents are the largest group of mammals worldwide with approximately 2277 species recognized, accounting for over 40% of all mammals, including mice, rats, voles, and many others 7,12 . Rodents vector more than 60 human infectious diseases, such as members of the Bunyaviridae, Reoviridae, Picornaviridae, Coronaviridae, and Flaviviridae families [13][14][15] .…”

“…Rodents vector more than 60 human infectious diseases, such as members of the Bunyaviridae, Reoviridae, Picornaviridae, Coronaviridae, and Flaviviridae families [13][14][15] . The abundance of rodent species, together with their fast-paced lives, population dynamics, variety of habitats, and close contact with domestic animals and wildlife, makes them efficient amplifiers, spreaders, and transmitters of viruses between animals and humans 12,16 . Moreover, rodents play important roles in the natural circulation of vector-borne viruses 17 .…”

“…Rodents are the largest group of mammals worldwide with approximately 2277 species recognized, accounting for over 40% of all mammals, including mice, rats, voles, and many others 7,12 . Rodents vector more than 60 human infectious diseases, such as members of the Bunyaviridae, Reoviridae, Picornaviridae, Coronaviridae, and Flaviviridae families [13][14][15] .…”

Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species

“…Rodents were caught at two semirural sites in the UK: Leicestershire ( Rodents were captured as part of routine pest-management at both sites. Ethical approval for collection of rodent tissue had been previously been granted [23] by the University of Nottingham School of Veterinary Science Ethical Panel, reference numbers 1602 151102 and 1786 160518.…”