Patient page - Intrapatient HIV evolution

Introduction

Data summary of patient p3:

The different tabs below allow to browse

Clinical and summary data of patient p3 can be downloaded here.

Summary

Time [days]	RNA templates	F1	F2	F3	F4	F5	F6
146	1 000	ok	ok	ok	ok	low	ok
501	4 000	ok	ok	ok	ok	ok	ok
797	820	ok	ok	ok	ok	low	ok
1126	870	ok	ok	ok	ok	miss	ok
1476	800	ok	ok	ok	ok	low	ok
1934	1 000	ok	ok	ok	ok	miss	ok
2006	2 000	ok	ok	low	ok	low	ok
2344	5 000	ok	ok	ok	ok	ok	ok
2727	8 000	ok	miss	ok	ok	miss	ok
3079	3 000	ok	ok	ok	ok	ok	ok

Phylogenetic tree of V3 in patient p3.

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.

Phylogenetic trees

Representation:

Link color:

Region:

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

Region:

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

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.

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_p3.gb

Consensus sequences

Local haplotypes

These alignments are premade for regions of general interest.

Generate alignments for a custom genomic region.

PBMC samples available for patient p3

Sample	years on treatment	good reads	hypermutated
DNA 1	4.6	reads	reads
DNA 2	6.6	reads	reads
DNA 3	7.2	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).