Table 1.
Place of collection, bat species, numbers of bats, and samples collected in this study.
Fig 1.
Overview of the virome of Swiss bats.
A. Heatmap of viral reads from 16 virus families of vertebrates and 23 virus families of non-vertebrates and their distribution among all 18 bat species investigated shown as percentage of the total number of reads generated in each bat species. Number in parentheses indicate the numbers of different bat species in which sequences of a virus family have been detected. B. Read abundance of the different virus families.
Fig 2.
Electron microscopy of selected samples.
A. Negative stain electron micrograph of a ground stool pool homogenate from a Myotis myotis colony. B. Negative stain electron micrograph of a pooled liver and spleen homogenate from Pipistrellus nathusii.
Table 2.
Overview of reads assembled to different virus families categorized by sample type.
Fig 3.
Distribution of viral reads according to genome classes.
Because of the large differences in read numbers, the y-axis was divided into three parts to facilitate visualization of all virus genome classes in a single graph: part one from 0 to 1x 104 reads, part two from 1x 104 to 1.5x 106 reads, and part three from 2x 106 to >4.x 106 reads.
Fig 4.
Phylogenetic analysis of the RNA dependent RNA polymerase gene of the bat betacoronaviruses.
The sequence obtained in this study (GenBank acc. number MT818221) is shown in bold. Sequences from alphacoronaviruses are marked with a purple background and those of betacoronaviruses with a blue background. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.
Fig 5.
Phylogenetic analysis of the adenovirus DNA polymerase gene.
The sequences obtained in this study (GenBank acc. numbers MT8159528-29, MT815933-35) are shown in bold. Sequences of non-bat associated viruses are marked with a red background and those of bat associated viruses with a blue background. The pictograms on the right side represent the species in which the virus was detected. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.
Fig 6.
Phylogenetic analysis of specific regions of the rotavirus H genome.
The sequences obtained in this study (GenBank acc. numbers MT815961-69) are shown in bold. Sequences of non-bat associated viruses are marked with a red background and those of bat associated viruses with a blue background. The pictograms on the right side represent the species in which the virus was detected. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.
Fig 7.
Phylogenetic analysis of specific regions of the rotavirus H genome.
The sequences obtained in this study (GenBank acc. numbers MT815948-60) are shown in bold. Sequences of non-bat associated viruses are marked with a red background and those of bat associated viruses with a blue background. The pictograms on the right side represent the species in which the virus was detected. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.
Fig 8.
Phylogenetic analysis of specific regions of the rotavirus A genome.
The sequences obtained in this study (GenBank acc. numbers MT815937-47) are shown in bold. Sequences of non-bat associated viruses are marked with a red background and those of bat associated viruses with a blue background. The pictograms on the right side represent the species in which the virus was detected. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.
Fig 9.
Phylogenetic analysis of the NS1 region of parvoviruses.
The sequences obtained in this study (GenBank acc. numbers MT815971-73, MT815975, 77, 78) are shown in bold. Sequences of non-bat associated viruses are marked with a red background and those of bat associated viruses with a blue background. The pictograms on the right side represent the species in which the virus was detected. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.
Fig 10.
Phylogenetic analysis of the full genome of circoviruses.
The sequences obtained in this study (GenBank acc. numbers MT815980-82) are shown in bold. Sequences of non-bat associated viruses are marked with a red background and those of bat associated viruses with a blue background. The pictograms on the right side represent the species in which the virus was detected. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.
Fig 11.
Phylogenetic analysis of full and partial genome of hepeviruses.
The sequence obtained in this study (GenBank acc. numbers MT815970) is shown in bold. Sequences of non-bat associated viruses are marked with a red background and those of bat associated viruses with a blue background. The pictograms on the right side represent the species in which the virus was detected. Sequences were aligned using Muscle. For phylogenetic analysis, the Maximum likelihood tree with 1’000 bootstraps was used. Only values ≥ 70% are displayed.