The Fecal Viral Flora of Wild Rodents

Abstract

The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.

Comparative Complete Genome Analysis of Chicken and Turkey Megriviruses (Family Picornaviridae): Long 3′ Untranslated Regions with a Potential Second Open Reading Frame and Evidence for Possible Recombination

“…Results of the secondary RNA structure analysis of the 5= UTR IRESs suggest that the chicken and turkey megriviruses have a hepacivirus/pestivirus-like type IVB IRES based on the sequence and secondary structural similarities to the IRESes of DHAVs and hepatitis C virus (23), although the considerable structural differences, e.g., the presence of an extended hairpin and the conservative apical "8" structure-which is probably functioning as a mobile genetic element similar to the stem-loop-2-like motif (s2m) found as a highly conserved fragment near the 3= end of many positive-stranded RNA viruses (29)-at the top of domain III, in analogy to other picornaviruses of avian origin (24), may suggest the possibility that this is a variant of the type IV IRES. The 3= genome regions (sequences after the STOP codon of the viral polyprotein-coding regions) of the chicken and turkey megriviruses were the longest after those of the newly described rosavirus (30) and, as identified in the megrivirus strains of CHK148 (GenBank accession no. JF424831) and TRK22 (GenBank accession no.…”

Human oral viruses are personal, persistent and gender-consistent

“…There also are detectable differences in the gut bacterial biota in response to diet changes and obesity (Ley et al, 2005Turnbaugh et al, 2006), which indicate that the microbiota have a role in the response to host metabolic challenges. Viromes from rodent feces harbor insect and plant viruses (Phan et al, 2011), suggesting that diet has substantial effects on viral encounters. Whereas viral communities are less well studied in humans, there also is evidence that the gut virome may respond to dietary changes (Minot et al, 2011).…”

A Distinct Class of Internal Ribosomal Entry Site in Members of the Kobuvirus and Proposed Salivirus and Paraturdivirus Genera of the Picornaviridae

“…The AV IRES also has distinct factor requirements: unlike all other IRESs that have been characterized to date, 48S complex formation on it is dependent on DHX29 (95), a ribosome-associated DExH-box helicase that has been implicated in the correct accommodation of structured mRNA in the mRNAbinding channel of the 40S subunit (1,71). The Kobuvirus genus currently comprises six accepted or proposed species: bovine kobuvirus (BKV), canine kobuvirus (CKoV), mouse kobuvirus (MKoV), sheep kobuvirus (SKV), AV, and PKV (33,41,67,74,90,93). It is distantly related to salivirus A (formerly known as klassevirus) of the proposed Salivirus genus (17,25,42,81) and to turdivirus 2 (TV2) and turdivirus 3 (TV3) of the proposed Paraturdivirus genus (89).…”