Additional file 1 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 1. PCR assays for detection of borna-, polyoma- and herpesviruses and mycoplasma

Additional file 10 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 10. Maximum clade credibility tree analysis of gammaherpesviruses based on conserved amino acid blocks of the DPOL sequences. Phylogenetic relationships of gammaherpesviruses, including classification of the novel viruses, based on conserved amino acid blocks of DPOL sequence. Branch support values displayed at the nodes correspond to their posterior probability. For further explanation see legend of Fig. 5

Additional file 7 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 7. Maximum clade credibility tree analysis of betaherpesviruses based on conserved amino acid blocks of the DPOL sequences. Phylogenetic relationships of betaherpesviruses, including classification of the novel viruses, based on conserved amino acid blocks of DPOL sequence. Branch support values displayed at the nodes correspond to their posterior probability. For further explanation see legend of Fig. 4

Additional file 2 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 2. Flow chart of multi-level PCR analysis for detection of squirrel polyomaviruses. Generic nested VP1 PCR (second-round product displayed as magenta-coloured bar) with degenerate primers was conducted. For full genome amplification, this was followed by specific nested long-distance PCR (LD-PCR; second-round product of approximately 5 kbp shown as red bar) and overlapping standard nested PCR (second-round product of approximately 800 bp shown as green bar) with specific primers. Grey bars represent coding sequences, black bar the non-coding control region

Additional file 12 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 12. Maximum clade credibility tree analysis of gammaherpesviruses based on conserved amino acid blocks of the gB sequences. Phylogenetic relationships of gammaherpesviruses, including classification of the novel viruses, based on conserved amino acid blocks of gB sequence. Branch support values displayed at the nodes correspond to their posterior probability. For further explanation see legend of Fig. 5

Additional file 4 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 4. Maximum clade credibility tree analysis of polyomaviruses based on conserved amino acid blocks of the LTAg sequences. Phylogenetic relationships of polyomaviruses, including classification of the novel viruses, based on conserved amino acid blocks of LTAg sequence. Branch support values displayed at the nodes correspond to their posterior probability. For further details see legend of Fig. 3

Additional file 5 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 5. Maximum likelihood tree analysis of polyomaviruses based on conserved amino acid blocks of the VP1 sequences. Phylogenetic relationships of polyomaviruses, including classification of the novel viruses, based on conserved amino acid blocks of VP1 sequence. Branch support values displayed at the nodes were assessed using Shimodaira-Hasagawa-like approximate likelihood ratio tests (SH-like aLRT). For further details see legend of Fig. 3

Additional file 11 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 11. Maximum likelihood tree analysis of gammaherpesviruses based on conserved amino acid blocks of the gB sequences. Phylogenetic relationships of gammaherpesviruses, including classification of the novel viruses, based on conserved amino acid blocks of gB sequence. Branch support values displayed at the nodes were assessed using Shimodaira-Hasagawa-like approximate likelihood ratio tests (SH-like aLRT). For further explanation see legend of Fig. 5

Additional file 8 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 8. Maximum likelihood tree analysis of betaherpesviruses based on conserved amino acid blocks of the gB sequences. Phylogenetic relationships of betaherpesviruses, including classification of the novel viruses, based on conserved amino acid blocks of gB sequence. Branch support values displayed at the nodes were assessed using Shimodaira-Hasagawa-like approximate likelihood ratio tests (SH-like aLRT). For further explanation see legend of Fig. 4

Additional file 3 of Search for polyoma-, herpes-, and bornaviruses in squirrels of the family Sciuridae

Additional file 3. Flow chart of multi-level PCR analysis for detection of squirrel herpesviruses. Generic nested DPOL PCR (product: bar in magenta) with degenerate primers was carried out. For extended sequence determination, this was followed by generic gB PCR (blue) with degenerate primers and subsequent long-distance PCR (LD-PCR) (red) with specific primers. Products of the second PCR rounds are shown. The sequences of the generic DPOL PCR product and the extended DPOL PCR product build a contiguous sequence of 0.4–0.5 kbp (black). The sequences of the generic gB and the generic DPOL PCR product build together with the LD-PCR-derived sequence a contiguous sequence of approximately 3.3 kbp (black). On top of the figure, coding sequences are displayed by grey bars. The arrow heads indicate the direction of transcription