Parsimony analysis of macroarray data for isolates from family D.

<p>Strain numbers and genotypes are indicated. Absence (−) or presence (+) of CDS considered as character changes in the parsimony analysis are given for each node and peripheral branch. IS605 and <i>cag</i>PAI are shown when present. Names in bold indicate CDSs of known function (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002259#pone-0002259-t001" target="_blank">Table 1</a>).</p

List and function of genes studied with macroarrays.

<p>List and function of genes studied with macroarrays.</p

Genealogy of family A, indicating the number and the genotypes of isolates for each member.

<p>Child-2, child-5 and child-7 were not infected. * name of the isolates studied on macro-arrays. S, name of the strains defined by macro-arrays.</p

Genealogy of family D, indicating the number and the genotypes of isolates for each member.

<p>The <i>hspA</i> and <i>glmM</i> alleles are designated H and G, respectively. The alleles are numbered according to the phylogenetic cluster to which they belong (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002259#pone-0002259-g004" target="_blank">Fig 4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002259#pone-0002259-g005" target="_blank">5</a>). Lower case letters were assigned when alleles differed by point mutations. * name of the isolates studied on macroarrays. S, name of the strains defined by macro-arrays. Age of children is in brackets.</p

Neighbor joining unrooted dendrogram for <i>glmM</i> sequences.

<p>The scale indicates the number of substitutions per site according to the Kimura model. Sequences are named as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002259#pone-0002259-g004" target="_blank">Figure 4</a>.</p

Parsimony analysis of macroarray data for isolates from family L.

<p>Strain numbers and genotypes are indicated. Absence (−) or presence (+) of CDS considered as character changes in the parsimony analysis are given for each node and peripheral branch. IS605 is shown when present. Names in bold correspond to CDSs of known function (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002259#pone-0002259-t001" target="_blank">Table 1</a>).</p

Parsimony analysis of macroarray data for isolates from family A.

<p>Bootstrap values above 70% are indicated at each node. Strain numbers and genotypes are indicated. Five strains (S6 to S10) were individualized. Strain S6 and S10 were clearly different from the other strains, according to their CDS content and their <i>hspA</i> and <i>glmM</i> alleles. Absence (−) or presence (+) of CDS considered as character changes in the parsimonious analysis are given for each node and peripheral branch. IS are shown when present. <i>cag</i>PAI is present in all the strains, except strain S6 from the father. Names in bold indicate CDSs of known function (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002259#pone-0002259-t001" target="_blank">Table 1</a>). Names in italics indicate remnant genes.</p

Genealogy of family L, indicating the number and the genotypes of isolates for each member.

<p>* name of the isolates studied on macro-arrays. S, name of the strains defined by macro-arrays.</p

Identification and distribution of sequences of vertebrate viruses of interest among the various bat specimens and tissue samples analyzed.

<p><b>Legend :</b></p>a<p>Br = brain, Li = liver, Lu = lungs.</p>b<p>Matching (HTS) or targeting (PCR/Sanger) viral genes (in brackets), with S = small, M = medium, L = large or polymerase, RdRp = RNA-dependent RNA polymerase.</p>c<p>+ = positive, - = negative.</p>d<p>PCR products larger than expected.</p>e<p>ND = not done.</p

Phylogenetic analysis of the bat gammaretrovirus-related sequence.

<p>(A) Schematic representation of the partial genome structure encompassing the pol (almost 3,580 nt encoding, the polymerase of almost 1,190 aa) gene of the porcine endogenous retrovirus (GenBank number Y17013), with black bars corresponding to the longest contig sequences (>900 nt) of bat gammaretrovirus (named Sers gammaretrovirus) identified in samples from b7 (<i>Eptesicus serotinus)</i>. The genomic region amplified by PCR is represented by a dashed bar, and the sequence used for phylogenetic analysis is indicated with an asterisk. (B) Phylogenetic tree produced from the amino-acid alignment based on a selected region (155 aa) of the translated sequence obtained from the PCR product (almost 288 aa, approximate positions 173 to 423 of the pol protein of the porcine endogenous retrovirus). The bat gammaretrovirus-related sequence is indicated in bold, with circles in black indicating bat gammaretroviruses. The scale bar indicates branch length, and bootstrap values ≥70% are shown next to the relevant nodes. The tree is midpoint-rooted for purposes of clarity only. REV, reticuloendotheliosis virus; FeLV, feline leukemia virus; GALV, gibbon ape leukemia virus; F-MuLV, Friend MuLV; R-MuLV, Rauscher murine leukemia virus; M-MuLV, Moloney MuLV; M-CRV, murine type C retrovirus; PreXMRV-1/2, pre-xenotropic MuLV-related virus 1 and 2; PERV-A, porcine endogenous type C retrovirus class A; PERV-B, porcine endogenous retrovirus B; PERV-C, porcine endogenous retrovirus C; RD114, feline RD114 retrovirus; MDEV, <i>Mus dunni</i> endogenous virus; KoRV, koala retrovirus; OOEV, <i>Orcinus orca</i> endogenous retrovirus; BaEV, baboon endogenous virus; RpuRV, <i>Rhinolophus pusillus</i>; RmRV, <i>Rhinolophus megaphyllus</i>; RaRV, <i>Rhinolophus affinis</i> retrovirus; MrRV, <i>Myotis ricketti</i> retrovirus; PaRV, <i>Pteropus alecto</i> retrovirus and MlRV, <i>Megaderma lyra</i> retrovirus.</p