Patients
p1 p2 p3 p4 p5 p6 p7 p8 p9 p10 p11

Patient p7

  Introduction
  Summary
subtype
B
# samples
11
Time [days] RNA templates F1 F2 F3 F4 F5 F6
1905 - miss miss ok miss miss miss
2248 33 ok miss ok ok miss ok
2311 80 ok ok ok ok ok ok
2668 220 ok ok ok ok ok ok
2970 250 ok ok ok ok ok ok
3437 4 000 ok ok ok ok ok ok
3934 840 ok ok ok ok ok ok
4445 800 ok ok ok ok ok ok
5034 4 000 ok ok ok ok ok ok
5392 6 000 ok ok ok ok miss ok
5811 1 000 ok ok ok ok low ok
This patient was not part of the initial study since we failed to amplify early samples. It was hence not suitable for an analysis of diversification and reversion.

Phylogenetic tree of V3 in patient p7.

Notes:
  • RNA template counts are estimated two limiting dilutions series using fragment 4
  • An orange label for a fragment indicates problematic amplification and possible loss of variation.
  • A red label indicates a missing fragment.
Viral load and CD4+ counts
Raw data: Viral load, CD4+ counts
Phylogenetic trees
Representation:
Link color:
Notes:
  • To display a phylogenetic tree of a particular region of the genome, select it in the pull-down menu.
  • Choices ending on minor include minor haplotypes from each time point, others display only consensus sequences
  • The size of the Tip circles indicate the frequency of the corresponding haplotype.
  • HIV recombines. Hence there trees don't necessarily depict the actual evolutionary history of the chosen part of the genome.
  • These are approximate maximum-likelihood trees generated with Fasttree
Genetic divergence and diversity in specific regions

Note: low diversity might be due, in addition to biological reasons, to a low RT-PCR efficiency in a specific amplicon.

Genome wide divergence and diversity patterns
Notes:
  • The top panels show divergence and diversity averaged in sliding windows of ??? bases for every position of the genome at particular time point.
  • The time point can be varied by moving the slider at the bottom.
Coverage
Notes:
  • The graph shows coverage at every postition in the genome.
  • The red line indicates the number of amplified RNA templates estimated from two limiting dilution series.
  • The each fragment corresponds to one of the peaks in coverage. Coverage tends to be lower towards the end of the fragments.
  • Where fragments overlap, the sum of reads from both fragments is reported
  • Some fragments amplify less well than other (F5 in particular). These tend to have low coverage or are sometimes missing completely.
Frequency dynamics of single nucleotide polymorphisms
Notes:
  • The top panel shows single nucleotide polymorphism (SNP) frequencies through time. Color indicates position along the genome.
  • The panel below shows SNP frequencies at each position for a given time point. The color of each point equals that of the corresponding trajectory in the top panel.
  • The time point shown in the second panel can be chosen via the slider on top.
  • Clicking on an annotated element of the genome will zoom into that element.
Genome sequence
Annotated genome sequence in genbank format: genome_p7.gb
Consensus sequences
Local haplotypes

Precompiled alignments

These alignments are premade for regions of general interest.

New alignments

Generate alignments for a custom genomic region.

From/To require HXB2 coordinates (both ends included).

NOTE: A few minutes might elapse while we prepare your data.

Proviral DNA from PBMCs
PBMC samples available for patient p7
Sample years on treatment good reads hypermutated
DNA 1 8.8 reads reads
DNA 2 8.5 reads reads
Notes:
  • Times indicate sampling times relative to start of treatment.
  • "Good" reads are those that map to p17gag and did not have obvious signs of hypermutation.
  • Hypermutated reads are those that map to p17gag and showed an excess of G-to-A mutations.

Tree of p17 before (RNA) and on treatment (DNA).