HIV transmission of multiple viral variants in patient OW (recent infection) followed by a super-infection.

<p>For explanation of phylogenetic trees, pairwise distances, and time points of sampling, please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166746#pone.0166746.g001" target="_blank">Fig 1</a> legend.</p

HIV transmission of single viral variants in acutely infected patients B and G.

<p>Maximum likelihood trees inferred by PhyML and distribution of raw pairwise distances are shown. Numbers below each phylogenetic tree indicate time of sampling in days post-seroconversion. Both phylogenetic trees and histograms of pairwise distances are drawn to the patient-specific scale shown at left for each patient.</p

HIV transmission of multiple viral variants in patients A (acute HIV infection) and OG (recent infection).

<p>For explanation of phylogenetic trees, pairwise distances, and time points of sampling, please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166746#pone.0166746.g001" target="_blank">Fig 1</a> legend.</p

Simulation studies for the ratio withinss to betweenss threshold values.

<p>Simulation studies for the ratio withinss to betweenss threshold values.</p

HIV transmission of single viral variant in patient NA (recent infection) followed by a super-infection.

<p>For explanation of phylogenetic trees, pairwise distances, and time points of sampling, please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166746#pone.0166746.g001" target="_blank">Fig 1</a> legend.</p

HIV transmission of multiple viral variants in patients D (acute HIV infection) and PK (recent infection).

<p>For explanation of phylogenetic trees, pairwise distances, and time points of sampling, please see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166746#pone.0166746.g001" target="_blank">Fig 1</a> legend.</p

Sensitivity analysis.

<p>Frequency and rate of different types of HIV transmission in a cohort of 42 individuals with primary HIV-1C infection: phylogeny and pairwise distance analysis is compared with ratio <i>withinss</i> to <i>betweenss</i> threshold values.</p

A simplistic model for HIV transmission of closely related multiple viral variants.

<p>The dynamics of phylogenetic trees and pairwise distances are presented over time of HIV infection.</p

HIV-1 subtype C phylogenetic relationship and diversity of HIV non-structural genes is consistent with the multiplicity of HIV-1 infection determined by analysis of the <i>env</i>/<i>gag</i> genes.

<p>A maximum likelihood phylogenetic tree was reconstructed using Fastree2 (Price <i>et al</i>., 2010) using the GTR+G model for nucleotide substitution and visualized in Figtree v.1.1.3 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#pone.0035491-Rambaut1" target="_blank">[54]</a>. Alternative likelihood ratio tests <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#pone.0035491-Anisimova1" target="_blank">[55]</a> >0.95 are shown by an asterisk. Subjects infected with multiple viral variants are colored red. Patient B and D subtrees (individual trees on grey background) show branching topology of earliest sampling (0–90 days p/s) and represent examples of single (subject B) and multiple (subject D) HIV-1 transmission.</p

HIV-1 subtyping by analysis of phylogenetic relationships of HIV-1 non-structural genes.

<p>The analyzed region of HIV-1 genome corresponded to nucleotide positions 5,041 to 6,310 in HXB2. Three sequences were randomly selected for each study subject (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#s2" target="_blank">Methods</a>). A phylogenetic tree was inferred by Mr. Bayes using GTR model. The convergence was reached after 10 M MCMC run. The consensus tree was visualized in Figtree v.1.3.1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035491#pone.0035491-Rambaut1" target="_blank">[54]</a>. Clade credibility values of >0.95 shown by asterisk, Subtype D cluster showed the support of 0.93 indicated by + symbol. HIV-1 subtype C reference sequences are shown as blue circles. All non-subtype C group M reference sequences are shown at the bottom of the phylogenetic tree. SIV sequence (CPZ.CM98.CAM3.AF115393) was used as an outgroup.</p