Virome comparisons in wild-diseased and healthy captive giant pandas

Abstract

Background: The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available.

Methods: Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals.

Results: The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda.

Conclusion: This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.

Keywords: Anellovirus; Gemycircularvirus; Giant panda; Papillomavirus; Picornavirus; Putative circovirus; Viral metagenomics; Virome.

Fig. 1

The composition and sample distribution of eukaryotic viruses detected in giant pandas. The pie chart in the center showed the approximate percentages of the nine virus groups detected in all types of sample. The nine circumjacent smaller pie charts indicated the approximate percentage of virus sequence from different type samples. Sample types were showed in different colors

Fig. 2

Virome comparisons of different samples of giant pandas based on BLASTx to the GenBank non-redundant database (E value of <10–5). a Percentage of virus-like sequence reads with similarity to eukaryotic viruses in the five libraries constructing based on five individual fecal samples. Viruses belonging to different groups were marked with different colors. b Percentage of anellovirus-related sequences in blood samples of different individual animals, where the bar related to the wild giant panda was marked with green and those related to the captive ones were marked with purple. c Percentage of papillomavirus-related sequences in the positive nasopharyngeal secretion swabs, where the bar related to the diseased giant panda was marked with purple and those related to captive ones were marked with green

Fig. 3

Genomic organization and phylogenetic analysis of the Papillomaviruses identified in the giant pandas. a Genomic organization of the AmPVs identified in the nasopharyngeal secretions of giant pandas. b Phylogenetic analysis was performed based on the amino acid sequence of L1 protein. The sequence alignments included the four AmPVs identified here, the best BLASTp matches in GenBank based on the L1 proteins of the AmPV1–4, and 66 representative species from each of the currently recognized genera. Silhouettes of the hosts included in the phylogenetic analysis were showed on branches. Papillomaviruses identified in this study was labeled with red dots

Fig. 4

Sequence comparison, genomic organization, and phylogenetic analysis of the novel picornavirus identified in the giant pandas. a Sequence similarity among the six novel picornaviruses (Aimelvirus1–6) were compared. b Un-rooted phylogenetic tree showed the genetic relationship of Aimelvirus1–6. c Genomic organization was showed in different colors. d Phylogenetic analysis based on the complete amino acid sequence of P1 proteins of Aimeilvirus 1–6, and 35 representative strains of all the 35 genera in Picornaviridae

Fig. 5

Genomic organization and phylogenetic analysis of the novel picornavirales identified in the giant pandas. a Positions of conserved domains within the polyproteins of pansaviruses and their related viruses were shown in different colors. b Phylogenetic analysis was performed based on the amino acid sequence of RDRP protein. The sequence alignments included the two pansaviruses identified here and related strains in GenBank. Silhouettes of the hosts included in the phylogenetic analysis were showed on branches. Pansaviruses identified in this study were labeled with diamond

Fig. 6

Phylogenetic analysis and co-infection of the novel anelloviruses identified in the blood samples of giant pandas. a Phylogenetic analysis was performed based on the amino acid sequence of ORF1 protein. The sequence alignments included the 19 anelloviruses identified here, their best BLASTp matches in GenBank based on the ORF1 proteins, and the representative anellovirus strains from GenBank. Silhouettes of the hosts included in the phylogenetic analysis were showed on branches. Anelloviruses identified in this study were labeled with red dots. b The co-infection of anellovirus in blood giant pandas. The 12 columns and 19 rows were set corresponding to 12 blood samples and 19 anelloviruses, respectively, with complete genomes. The small box with red color stands for positive, and the white box stands for negative

Fig. 7

Phylogenetic analysis and genomic organization of the novel gemycircularviruses and putative circoviruses identified in the giant pandas. a Phylogenetic analysis was performed based on the amino acid sequence of Rep protein. The sequence alignments included 15 gemycircularviruses and 4 putative circoviruses identified here, their best BLASTp matches in GenBank based on the Rep proteins, and the representative strains of gemycircularvirus and circovirus. Hosts or sources of these viruses included in the phylogenetic analysis were showed on branches. Viruses identified in this study were labeled with colored dots. b The consensus genomic organization of the gemycircularviruses identified in giant pandas. c The nonamer in stem-loop structure of gemycircularviruses identified in this study. d–g The genomic organizations of the four GpCVs. h The stem-loop structures of the four GpCVs identified in giant pandas

Fig. 8

Phylogenetic analysis of the partitivirus-like sequence identified in the giant pandas. Phylogenetic analysis was performed based on the amino acid sequence of RDRP protein. The sequence alignments included the partitivirus-like sequences identified in the giant pandas, four representative partitiviruses, and four representative picobirnaviruses. The partitivirus-like sequence identified in this study was labeled with a red dot