The virome of the white-winged vampire bat Diaemus youngi is rich in circular DNA viruses

Abstract

In the Neotropical region, the white-winged vampire bat (Diaemus youngi) is the rarest of the three species of vampire bats. This bat species feeds preferentially on bird blood, and there is limited information on the viruses infecting D. youngi. Hence, this study aimed to expand the knowledge about the viral diversity associated with D. youngi by sampling and pooling the lungs, liver, kidneys, heart, and intestines of all animals using high-throughput sequencing (HTS) on the Illumina MiSeq platform. A total of three complete and 10 nearly complete circular virus genomes were closely related to gemykrogvirus (Genomoviridae family), smacovirus (Smacoviridae family), and torque teno viruses (TTVs) (Anelloviridae family). In addition, three sequences of bat paramyxovirus were detected and found to be closely related to viruses reported in Pomona roundleaf bats and rodents. The present study provides a snapshot of the viral diversity associated with white-winged vampire bats and provides a baseline for comparison to viruses detected in future outbreaks.

Keywords: Diaemus youngi; High-throughput sequencing; South America; Vampire bat; Virome.

Fig. 1

Metagenomic graphic results presenting the generated sequence distribution. a All reads obtained from this analysis; and b eukaryotic virus representativeness

Fig. 2

a Genomic organization of TTDyV-1 (Xitorquevirus) and b TTDyV-7 (proposed Yodtorquevirus genus); and c linearized genomic organization of TTDyV- 4 and 5 (Xitorquevirus) and d TTDyV-6 (proposed Yodtorquevirus genus). The arrows represent the directions and reading frame of each putative ORF (ORF1-ORF3). A closed green box indicates the GC-rich regions

Fig. 3

Phylogenetic analysis performed based on the ORF1 nucleotide sequences of the 11 TTDyVs, their most closely related sequences in GenBank and representative members of each genus

Fig. 4

a Genome map of giant panda-associated gemykrogvirus 1 isolate Diaemus youngi (GiGemyV). Genes encoding the replication-initiation protein (Rep) and capsid protein (Cap) are shown with arrows. A putative ORF3 is also represented by an arrow. The position of the nonanucleotide (TAATATATT) at the potential stem-loop structure is also indicated; and b Rep amino acid phylogenetic tree of Genomoviridae. The sequences were analyzed through the maximum likelihood method with the LG + G + I model. Analyses were conducted with 1000 bootstrap replicates. Bootstrap values higher than 50% are shown. The sequence detected in the present study is highlighted with a circle

Fig. 5

a Mapping of bat paramyxovirus contigs ViroVet1, 2, and 3 in the complete genome of a reference bat paramyxovirus (MZ328288.1); b partial L; c partial F; and d partial M amino acid phylogenetic trees of Paramyxoviridae reference sequences and unclassified “bat paramyxovirus”. For the partial L tree, sequences of the Pneumoviridae family were included as outgroups. There were 86, 75, and 74 amino acid sequences, respectively, and 148 positions in the final dataset. The sequences were analyzed through the Maximum likelihood method with LG + G + I model. Analyses were conducted with 1000 bootstrap replicates. Bootstrap values higher than 50% are shown. The sequences detected in the present study were highlighted with circles

Fig. 6

a Genome map of Diaemus youngi-associated smacovirus-related virus. Genes encoding the replication-initiation protein (Rep) and capsid protein (Cap) are shown with arrows. The position of the nonanucleotide at the potential stem-loop structure is also indicated; and b Phylogenetic analysis of 69 translated Rep sequences of smacoviruses. The smacovirus described in the present study is highlighted with a circle. Two arrows indicate the genomes with unisense orientation. The evolutionary history was inferred by using the maximum likelihood method based on the LG model. A discrete gamma distribution was used to model evolutionary rate differences among sites (5 categories (+ G, parameter = 3.4474)). Amino acid sequences of Banana bunchy top virus (NP604483) and Cardamom bushy dwarf virus (AHF47677) were used as outgroups representing the Nanoviridae family. All positions with less than 95% site coverage were eliminated. There were a total of 196 positions in the final dataset. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Evolutionary analyses were conducted in MEGA6