Additional file 1 of Promoter activity of Merkel cell Polyomavirus variants in human dermal fibroblasts and a Merkel cell carcinoma cell line

Additional file 1 Supplementary Fig. S1. Early and late promoter activity of seven MCPyV NCCR variants in MCC13 and human dermal fibroblasts. Supplementary Fig. S2. Relative promoter activity of the immediately early cytomegalovirus and the consensus early MCPyV promoter in MCC13 and human dermal fibroblasts. Supplementary Fig. S3. Putative transcription factor binding sites in the consensus MCPyV NCCR. Supplementary Table S1. Detection of MCPyV in benign and diseased human tissues other than Merkel cell carcinoma. Supplementary Table S2. MCPyV isolated in sewage water and environmental surfaces. Supplementary Table S3. MCPyV NCCR variants and mutations compared to the consensus sequence. Supplementary Table S4. Putative transcription factor binding sites in the consensus MCPyV NCCR

Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach-1

<p><b>Copyright information:</b></p><p>Taken from "Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach"</p><p>http://www.virologyj.com/content/4/1/84</p><p>Virology Journal 2007;4():84-84.</p><p>Published online 6 Sep 2007</p><p>PMCID:PMC2014757.</p><p></p>esence (+) of LNA-PtroLCV1 and/or LNA-PtroRHV1. The electropherogram is shown. Below, the amplified DPOL sequences are indicated. Marker: 100 bpladder (lanes 1 and 8)

Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach-0

<p><b>Copyright information:</b></p><p>Taken from "Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach"</p><p>http://www.virologyj.com/content/4/1/84</p><p>Virology Journal 2007;4():84-84.</p><p>Published online 6 Sep 2007</p><p>PMCID:PMC2014757.</p><p></p>0copy numbers). Real-time PCR was carried out in the presence or absence of LNA-PtroLCV1 or LNA-EBV

Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach-4

<p><b>Copyright information:</b></p><p>Taken from "Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach"</p><p>http://www.virologyj.com/content/4/1/84</p><p>Virology Journal 2007;4():84-84.</p><p>Published online 6 Sep 2007</p><p>PMCID:PMC2014757.</p><p></p>0copy numbers). Real-time PCR was carried out in the presence or absence of LNA-PtroLCV1 or LNA-EBV

Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach-3

<p><b>Copyright information:</b></p><p>Taken from "Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach"</p><p>http://www.virologyj.com/content/4/1/84</p><p>Virology Journal 2007;4():84-84.</p><p>Published online 6 Sep 2007</p><p>PMCID:PMC2014757.</p><p></p>el primate herpesviruses and of known human and non-human primate herpesviruses, available in GenBank. A multiple alignment of concatenated 1100 aa was analysed with the neighbor-joining method. A midpoint-rooted phylogram is shown. The branch length is proportional to evolutionary distance (scale bar). Results of bootstrap analysis (100-fold) are indicated at the nodes of the tree, to the left of the first vertical divider. In addition, the alignment was analysed with Tree-Puzzle 5.0. Support values, estimated by the quartet puzzling (QP) tree search and expressing the QP reliability in percent, are indicated at the nodes of the tree to the left of the vertical divider. Nodes with values below 70% in both analyses were depicted as pat of a multifurcation (black bar). Viruses, which are entirely novel or viruses for which additional sequence information was generated, are highlighted with black arrows. Herpesvirus genera and families are indicated. Full names of known viruses and their nucleotide sequence accession numbers are listed in the section

Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach-2

<p><b>Copyright information:</b></p><p>Taken from "Discovery of herpesviruses in multi-infected primates using locked nucleic acids (LNA) and a bigenic PCR approach"</p><p>http://www.virologyj.com/content/4/1/84</p><p>Virology Journal 2007;4():84-84.</p><p>Published online 6 Sep 2007</p><p>PMCID:PMC2014757.</p><p></p>tial sequences of the ORFs UL57, UL55 and UL54, obtained through PCR with deg/dI primers, are depicted by thin solid lines, and the type of gB sequence (gB1 or gB2) is indicated. LD amplimers are depicted by dashed lines. The solid line represents the final 8 kbp contiguous sequences of CgueCMV-1.1 and CgueCMV-1.2. Pairwise alignments of the UL56 and gB proteins and the partial DPOL proteins of CgueCMV-1.1 and CgueCMV-1.2 are shown. Dots represent identical amino acids, dashes indicate regions of non-colinearity

Chronogram of BKPyV and JCPyV-related polyomaviruses

<p>This tree was generated from the analysis of conserved blocks of a whole genome alignment using BEAST v1.8.2 under the model of nucleotide substitution best supported by jModelTest v2.1.4, assuming a lognormal relaxed clock and using a speciation prior (birth-death) on the tree shape. The same topology was obtained using PhyML v3. PtrotPyV1 is highlighted in blue. Branch support values are reported above branches (bootstrap values/posterior probability). Root posterior probabilities are reported under branches in black half circles; the tree is rooted on the best supported root. A grey half circle pinpoints the position of the root as determined in another PhyML analysis including the closest available outgroup (the sea otter polyomavirus 1, NC_025259). The accession numbers of the sequences appearing in this figure are as follows: AB269859, AB767295, AB767299, AY386378, AY614708, DQ435829, JX159985, KJ577598 and KT184855.</p

Putative proteins encoded by HPyV12 and amino acid identities between HPyV12 and other polyomaviruses.

a<p>Determined with blastX (pairwise).</p>b<p>Number of amino acids.</p>c<p>Accession numbers for TSPyV to GHPyV: GU989205; HM355825; NC_001538; NC_015150; JQ958892; FN356901; NC_004800.</p

Detection of polyomaviruses in gastrointestinal and lymphoid organs with generic PCR.

a<p>Detected with generic PCR.</p

Genome organization of HPyV12.

<p>Putative coding regions for VP1 to VP3, STAg antigen, and LTAg antigen are marked by arrows.</p