Fecal, oral, blood and skin virome of laboratory rabbits

Abstract

Here, we investigated the fecal, oral, blood, and skin virome of 10 laboratory rabbits using a viral metagenomic method. In the oral samples, we detected a novel polyomavirus (RabPyV), and phylogenetic analysis based on the large T antigen, VP1 and VP2 regions indicated that the novel strain might have undergone a recombination event. Recombination analysis based on related genomes confirmed that RabPyV is a multiple recombinant between rodent-like and avian-like polyomaviruses. In fecal samples, three partial or complete genome sequences of viruses belonging to the families Picobirnaviridae, Parvoviridae, Microviridae and Coronaviridae were characterized, and phylogenetic trees were constructed based on the predicted amino acid sequences of viral proteins. This study increases the amount of genetic information on viruses present in laboratory rabbits.

Fig. 1

Genome organization of the rabbit polyomavirus and phylogenetic analysis of the novel polyomavirus identified in oral samples from laboratory rabbits. (A) Genomic organization of the rabbit polyomavirus. (B) Phylogenetic tree based on the amino acid sequence of the LTAg protein. (C) Phylogenetic tree based on the amino acid sequence of VP1. (D) Phylogenetic analysis was performed based on the amino acid sequence of VP2. The polyomavirus identified in this study is labeled in red

Fig. 2

Bootscan evidence for recombination in the RabPyV genome

Fig. 3

Phylogenetic analysis of the picobirnavirus identified in the fecal samples of laboratory rabbits based on partial amino acid sequences of the RdRp protein. The picobirnavirus identified in this study is labeled in red

Fig. 4

Genomic organization of the rabbit bocavirus (RBoV) and phylogenetic analysis of the bocavirus identified in laboratory rabbits. (A) Genomic organization of RBoV (distance in nt). (B) Phylogenetic tree based on the amino acid sequence of NS1. (C) Phylogenetic tree based on the amino acid sequence of VP1. The bocavirus identified in this study is labeled in red

Fig. 5

Phylogenetic analysis of the microvirus identified in fecal samples of laboratory rabbits based on partial amino acid sequences of the VP1 protein. The microvirus identified in this study is labeled in red

Fig. 6

Phylogenetic analysis of the coronavirus identified in laboratory rabbits. (A) Phylogenetic tree based on the amino acid sequence of the N protein. (B) Phylogenetic tree based on the amino acid sequence of the RdRp protein