Phasing of the S gene mutations Thr116Asn and Thr118Ser in the HBV genome.

<p>Each bar represents one read and the dots indicate a deletion. Both single nucleotide variants were called by MinION (A) and direct Sanger sequencing (B). The number of MinION reads called for each of the single nucleotide variant patterns (C).</p

HBV genetic diversity in three infected individuals characterized by sequencing whole genome PCR products using three different methods.

<p>HBV genetic diversity in three infected individuals characterized by sequencing whole genome PCR products using three different methods.</p

Mortality (A) and Bacteremia (B) of S286 and S286ΔpS286colV in a neonatal rat sepsis model.

<p>The same inoculum (4×10⁵ CFU) was injected intraperitoneally. <i>P</i> values below 0.05 were considered statistically significant and were denoted by *.</p

Alignment of nanopore reads of B6260.

<p>Complete and partial Nanopore sequence reads were aligned with the corresponding Sanger consensus sequence used as reference. The viral core, surface, polymerase and X proteins are indicated and positions provided according to the reference sequence AM282986. Four different types of Minion reads are shown: nearly complete HBV genome (blue); reads showing a 123-nt deletion (positions 2,968–3,090) in the PreS1 region (purple); reads with the 123-nt and an additional 24-nt deletion (positions 501–524) in the “a determinant” of the S region (green); and unclassified partial reads (yellow).</p

Read mapping statistics for HBV sequencing runs after error correction using NanoCorrect.

<p>Read mapping statistics for HBV sequencing runs after error correction using NanoCorrect.</p

RepPCR (Diversilab®) and UPGMA dendrogram obtained with 41 A/B1 CVP+ strains and 9 ECOR strains.

<p>(1) Phylogenetic group, as determined by PCR; (2) Phylogenetic group of ECOR strains; (3) ST: sequence type according to Achtmann's scheme; (4) STc: sequence type complexes according to Achtmann's scheme (corresponding phylogenetic group in brackets); (5) PCR O78. Strains were responsible for Urinary Tract nfection (UTI), Neonatal Meningitis (NM) or Bacteremia (B). Clusters of clinical isolates are framed in black and ECOR strains are underlined.</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

Fold changes of RNA transcripts of pS286colV (A) and pS88 (B) in iron deficiency environment.

<p>Relative expression of transcripts were calculated between growth in LB with an iron chelator comparatively to growth in LB. Only genes characteristics of the Conserved Virulence Plasmidic (CVP) region (grey) and other genes upregulated (black) are named. Fold changes were calculated by 2^−ΔΔCt method.</p

Distribution of unassembled read sequences after BLASTn analysis.

<p>(A) Percentage of sequences related to the main categories of existing viruses: vertebrate (blue), plant/fungal (green), invertebrate (brown), protozoan (yellow) viruses and bacteriophages (gray), and unassigned viral sequences (no taxonomic data concerning the family available, indicated in red). The total number of viral read sequences is indicated below each pie chart. (B) The percentage of sequences related to the most abundant viral families, indicated in the same colors for each main viral category as in (A): blue = vertebrate, brown = invertebrate, gray = phage. Viral families accounting for less than 2% of total sequences were pooled and represented as the “other” category (in purple), and read sequences with no available data concerning the taxonomic family were considered to be unassigned (in red).</p

Characteristics of the S286 transconjugants and variants.

<p>Characteristics of the S286 transconjugants and variants.</p