Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca)

Abstract

The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals in the world; anthropogenic habitat loss and poaching still threaten the survival of wild pandas. Viral infection has become one of the potential threats to the health of these animals, but the available information related to these infections is still limited. In order to detect possible vertebrate viruses, the virome in the fecal samples of seven wild giant pandas from Qinling Mountains was investigated by using the method of viral metagenomics. From the fecal virome of wild giant pandas, we determined six nearly complete genomes belonging to the order Picornavirales, two of which may be qualified as a novel virus family or genus. In addition, four complete genomes belonging to the Genomoviridae family were also fully characterized. This virological investigation has increased our understanding of the gut viral community in giant pandas. Whether these viruses detected in fecal samples can really infect giant panda needs further research.

Keywords: Genomoviridae; Picornavirales; viral metagenomics; virome; wild giant panda.

Figure 1

Fecal virome detected in giant pandas. The percentage of virus reads in different virus groups was shown.

Figure 2

Genomic organization and phylogenetic analysis of the Picornavirales identified in the giant pandas. (A) Genomic organization of six sequences related to order Picornavirales. (B) Phylogenies of viruses belonging to Picornavirales identified in giant pandas. Bayesian inference tree based on amino acid sequences of RdRp of viruses belonging to Picornavirales identified here. Within trees, the viruses found in this study are marked with red line. Each scale bar indicates 0.4 amino acid substitutions per site.

Figure 3

Phylogenetic analysis and genomic organization of the family Genomoviridae in the giant pandas. (A) Genomic organization of four sequences related to family Genomoviridae. (B) The stem-loop structures of the four genomes identified in giant pandas. (C) The non-amer in the stem-loop structure of the four genomes identified in giant pandas. (D) Phylogenies of viruses belonging to family Genomoviridae identified in giant pandas. Bayesian inference tree based on amino acid sequences of Rep of viruses belonging to family Genomoviridae identified here. Within trees, the viruses found in this study are marked with red line. Each scale bar indicates 0.4 amino acid substitutions per site.