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.

Figure 1. Taxonomic classification of sequences with similarity to eukaryotic viruses.

Circles located next to taxa are logarithmically proportional to the total number of sequence reads with BLASTx E<10⁻⁵. The numbers of sequence read are also included.

Figure 2. Mouse papillomavirus.

A. Genome organization of a novel mouse papillomavirus. B. Phylogenetic tree generated with concatenated L1 and L2 capsid proteins of PmPV1_M-14 and representatives of all genera in the family Papillomaviridae. The novel mouse papillomavirus in this study is labeled with a black circle. The other murine papillomavirus MmiPV1 is highlighted in grey. The scale in this and every tree indicates amino acid substitutions per position.

Figure 3. Genomic organization of RodSCVs.

The novel rodent stool-associated circular viruses (RodSCVs) are classified into four different genomic organization categories. The location of putative Rep genes and other ORFs (greater than 100 amino acids long) are indicated by arrows.

Figure 4. Phylogenetic analysis of Rep proteins of RodSCV and single stranded circular viral genomes.

Phylogenetic tree obtained from amino acid sequences of complete Rep genes of members of the families Geminiviridae, Nanoviridae, Circoviridae, Gyrovirus, Canarypox virus, Circovirus-like genomes, Bifidobacterium pseudocatenulatum plasmid p4M, Giardia intestinalis, and Entamoeba histolytica. The novel RodSCVs in this study are highlighted in red.

Figure 5. Phylogenetic analysis of mouse kobuvirus.

Phylogenetic tree generated with complete 3D^pol protein of members of the genera Kobuvirus, Hepatovirus and Parechovirus in the family Picornaviridae. The human Aichi viruses are encircled. The novel mouse kobuvirus in this study is labeled by a black circle.

Figure 6. Phylogenetic analysis of Mosavirus and Rosavirus.

Phylogenetic tree obtained from amino acid sequences of complete 3D proteins of all taxonomic genera in the family Picornaviridae. Mosavirus and Rosavirus are labeled with black circles.

Figure 7. Phylogenetic analysis of rodent picobirnaviruses.

Phylogenetic tree obtained from nearly full-length RdRp protein of genogroup I and II picobirnaviruses in the family Picobirnaviridae. The novel picobirnaviruses are labeled by black circles.

Figure 8. Phylogenetic analysis of mouse astrovirus.

Phylogenetic tree obtained from complete ORF2 protein of astroviruses in the family Astroviridae. The novel astrovirus is labeled with a black circle.