Animal and human viral discovery has long been focused on pathogenic infections and viruses that could be readily grown in cell cultures and cause visible cytopathic effects. Viral metagenomics is a recent approach to analyzing mixtures of viral nucleic acids enriched directly from a variety of sources including animals, plants, protozoa, bacteria, archaea, and diverse environments without a prerequisite in vitro or in vivo amplification 
. Viral metagenomics has been successfully employed to identify both commensal viruses and viral pathogens and has the potential to detect all viruses recognizable through sequence similarity searches 
. We describe here the fecal viral flora in several species of wild rodents. Sequences closely and distantly related to known viral sequences were identified as well as many sequences of unknown taxonomic origin 
. A fraction of these currently unclassifiable sequences may be derived from still genetically uncharacterized viral families refractory to nucleotide or protein sequence similarity based searches. Multiple known DNA and RNA viral families infecting plants, insects, and mammals were also detected. Plant and insect viral sequences likely reflect the omnivorous diet of these rodents.
The number of Rep-containing circular DNA genomes recently found in various animal and environmental viral surveys has greatly expanded the genetic diversity in this group of viruses 
. Some of the Rep proteins of the small circular DNA genomes characterized here clustered with viruses in marine environment or in protozoan genomes. Type II RodSCVs contained two separate Rep ORFs in their genomes, separately encoding the viral Rep and RNA helicase with each gene individually smaller than those in single Rep containing genomes. The many novel circular DNA genomes seen here indicate the likely existence of several previously unknown viral families. The closest relatives of some Rep sequences found in rodent feces are those integrated in the Giardia intestinalis
genome, possibly reflecting their replication in protozoans in rodent guts.
We report on the first identification of a kobuvirus in mice (Peromyscus crinitus
and P. maniculatus
). Since its genetic characterization in 1998 in Japan 
, Aichi virus, the archetypical kobuvirus, has been associated with acute gastroenteritis worldwide 
. Other kobuvirus species have been reported in pigs and cows as well as in humans and associated with diarrhea 
. Our phylogenetic analysis revealed that the mouse kobuvirus clustered with human Aichi virus. A recent study describes a similar close relationship between a canine kobuvirus and Aichi virus 
. This close relationship between human, mouse, and canine kobuviruses suggests past zoonotic transmission of kobuviruses between these hosts or their recent ancestors followed by independent evolution leading to the close but distinct species seen today.
is another genus in the family Picornaviridae
and currently includes 3 species (www.picornaviridae.com
). While phylogenetically related to the enteroviruses, these viruses have a different type of internal ribosome entry site and a leader protein (www.picornaviridae.com
). A Sapelovirus-like genome fragment was identified in house mouse feces. Phylogenetically, this fragment clustered with the other Sapeloviruses. Mice therefore also appear to harbor Sapeloviruses, expanding the known host range of this group of viruses.
Two potential new picornaviridae genera we provisionally labeled Mosavirus and Rosavirus were genetically characterized. Only distantly related to the kobuvirus genus, the Rosavirus is also part of a larger clade containing several avian picornaviruses, including the recently described avian turdiviruses and turkey hepatitis virus 
. The recent characterization of numerous deep-branched members of the picornaviridae family (likely new genera) from mammals, birds, reptiles, and fish indicates this viral family is still greatly under sampled and likely to rapidly expand as more potential host species are analyzed (www.picornaviridae.com
). A second potential new genus distantly related to the cardioviruses was also characterized. Until recently cardioviruses consisted of the Theiloviruses and Encephalomyocarditis viruses infecting largely rodents and the Saffold virus group infecting humans 
. The Mosavirus also exhibited the large genetic distance relative to other picornaviruses required to tentatively qualify Mosavirus as a founding member of a new Picornaviridae genus.
Using consensus PCR primers PBV has been detected in the feces of mammals, birds, and snakes with or without diarrhea 
. Infection was common in wild rodents with 22/105 animals shedding PBV-like nucleic acids, the second highest group of mammalian virus-like sequences after the highly diverse small circular DNA genomes (). PBV therefore represent the largest quantity of viral nucleic acids released by these rodents into the environment. Two nearly complete PBV RdRp sequences clustered together with a larger clade of human PBV cluster I sequences possibly reflecting past rodent-human transmission. Complete PBV RdRp sequences from more animal species will be required to further test this hypothesis.
The number of mammalian astroviruses species has recently undergone a rapid expansion 
. The first astrovirus genome from a mouse clustered with a clade containing mink, sheep, and recently identified human astroviruses 
. The detection of multiple unrelated astrovirus species within some host species (human, pigs, and sea lions) may reflect frequent cross-species transmission rather than diversification from a common source.
AAV infects humans and other primate species 
. Although over 80% of humans are seropositive, AAV has not been associated with any diseases in humans 
. Members of the family Adenoviridae
infect various species of vertebrates, including humans 
. The majority of AdV infection cause upper respiratory diseases; however, AdV also causes other symptoms, such as acute gastroenteritis 
. The small AAV and AdV fragments identified here are too limited for definitive classification but provisionally appear to represent a fourth species of murine adenovirus 
Rodents are known reservoirs of numerous viruses capable of causing human diseases 
. The characterization of the viromes of animal species with frequent contacts with humans can provide baseline viral content to more quickly identify the possible sources of future zoonotic infections and therefore assist in their control. Changes in the baseline virome of various animal may also assist in identifying changes associated with future population crashes. The addition of annotated viral genomes to public databases will also facilitate their inclusion on microarrays as well as assist in their precise identification after high-throughput sequencing 
. Monitoring for rodent viruses in humans will require extensive geographical sampling in persons with high exposure such as hunters, hikers, and farmers, and in regions of high biodiversity. The large increase in rodent viral species and higher level taxa revealed here by a limited species, geographic, and individual sampling reflects the large extent of mammalian virus diversity awaiting characterization.