The fecal virome of red-crowned cranes

Abstract

The red-crowned crane is one of the rarest crane species, and its population is decreasing due to loss of habitat, poisoning, and infections. Using a viral metagenomics approach, we analyzed the virome of feces from wild and captive red-crowned cranes, which were pooled separately. Vertebrate viruses belonging to the families Picornaviridae, Parvoviridae, Circoviridae, and Caliciviridae were detected. Among the members of the family Picornaviridae, we found three that appear to represent new genera. Six nearly complete genomes from members of the family Parvoviridae were also obtained, including four new members of the proposed genus "Chapparvovirus", and two members of the genus Aveparvovirus. Six small circular DNA genomes were also characterized. One nearly complete genome showing a low level of sequence identity to caliciviruses was also characterized. Numerous viruses believed to infect insects, plants, and crustaceans were also identified, which were probably derived from the diet of red-crowned cranes. This study increases our understanding of the enteric virome of red-crowned cranes and provides a baseline for comparison to those of other birds or following disease outbreaks.

Fig. 1

The composition of the intestinal virome in red-crowned cranes. The percentage of virus sequence reads including bacteriophage, plant viruses, insect viruses, mammalian viruses and other unidentified viruses is shown on the left as a pie chart). The percentage of virus sequence reads belonging to different eukaryotic virus families is shown on the right as a pie chart). Different colors in the pie charts indicate different virus types or virus families

Fig. 2

Sequence comparison, genomic organization, and phylogenetic analysis of the novel picornaviruses identified in red-crowned cranes. (a) Phylogenetic analysis based on the complete amino acid sequence of P3 proteins of gapovirus, grusavirus, and 35 representative strains of all 35 genera of the family Picornaviridae. The virus indicated by a solid black circle was from the wild group, and the one marked with an unfilled black circle was from the ornamental group. (b) Phylogenetic analysis based on the complete amino acid sequences of P1 proteins of gapovirus, grusavirus, and the representative members of the genera Hepatovirus and Tremovirus. (c) Pairwise comparison of the novel picornavirus with representative members of the genera Hepatovirus and Tremovirus. (d) Genome organization of gapovirus

Fig. 3

Sequence comparisons, genomic organization, and phylogenetic analysis of the four novel picornaviruses of the genus Avihepatovirus identified in red-crowned cranes in this study. (a) Alignment of the encoded protein of GrHAV1-4 with that of the representative strain (NC_008250). (b) Phylogenetic analysis based on the amino acid sequence of the P1 region of GrHAVs, three DHAVs, and representative members of each of the 35 genera in the family Picornaviridae. (c) Pairwise comparison of GrHAV1-4 with representative strains of DHAV1-3 and a representative strain of the genus Avisivirus based on the P1 region

Fig. 4

Sequence comparison, genomic organization, and phylogenetic analysis four novel parvoviruses (GAPV1-4) identified in red-crowned cranes. (a) Genome organization of GAPV1-4. (b) Pairwise comparison of GAPV1-4 with other members of the proposed genus “Chapparvovirus”. (c) Phylogenetic analysis based on the complete amino acid sequence of NS1 of GAPV1-4 and the other members of the proposed genus “Chapparvovirus”. The virus indicated by a solid black circle was from the wild group, the one marked with an unfilled black circle was from the ornamental group, and the ones marked with unfilled triangles were from the breeding group

Fig. 5

Genomic organization and phylogenetic analysis of two novel parvoviruses belonging to the genus Aveparvovirus identified in red-crowned cranes. (a) Genome organization of RCPV1-2. (b) Phylogenetic analysis based on the complete amino acid sequence of NS1 of RCPV1-2 and those of representative members of all 10 genera of the family Parvoviridae

Fig. 6

Phylogenetic analysis and genomic organization of novel circo-like viruses and gemycircularviruses identified in red-crowned cranes. (a) Phylogenetic analysis was performed based on the amino acid sequence of the Rep protein. The sequence alignments included two gemycircularviruses and four novel circo-like viruses identified here, their best BLASTp matches in GenBank based on the Rep proteins, and representative strains of gemycircularviruses and circoviruses. The host or source of the viruses included in the phylogenetic analysis are indicated on the branches. (b and c) The genomic organization of the gemycircularviruses identified in red-crowned cranes. (d, e, f, and g) The genomic organization of GaCV1-4 identified in red-crowned cranes. (h) The stem-loop structures of circo-like viruses identified in red-crowned cranes

Fig. 7

Genomic organization and phylogenetic analysis of the novel calicivirus identified in red-crowned cranes. (a) Genome organization of RaCV1. The potential cleavage site and encodes proteins are shown. (b) Phylogenetic analysis based on the complete amino acid sequence of the ORF1 protein of RaCV1 and representative members of the family Caliciviridae