ML phylogenetic tree of the global HIV-1 subtype B <i>pol</i> sequences.

<p>The phylogenetic tree was constructed by the general time-reversible with gamma-distributed rate heterogeneity across sites model of substitution implemented into RAxML. Branches are drawn on scale with the bar at the bottom, which represents 0.03 nucleotide substitution per site and a progressive bootstrap gradient value using FigTree, v. 1.4. The statistically highly supported nodes (bootstrap >70%) and the clusters with five or more related sequences are indicated by an asterisk (*).</p

Bayesian maximum clade credibility phylogeographic tree of the HIV-1 Subtype B by the Bayesian discrete approach in BEAST v1.7.5.

<p>The upper left bar represents the gradient of location probability. Nodes were drawn using a progressive ancestral probability location value of 0–1. Colours of terminal and internal branches indicate the sampling location for each sequence and the most probable ancestral location for each clade, respectively. The clusters of greatest epidemiological interest (≥5 patients grouped) are indicated by an asterisk (*).</p

Geographical distribution of the patients infected with HIV-1 non-B variants over the 2005–2012 period.

<p>The percentage of each subtype/CRF in relation to all the HIV-1 non-B genetic forms is shown in each region.</p

Bayesian maximum clade credibility phylogeographic tree of the HIV-1 Subtype B by the Bayesian discrete approach in BEAST v1.7.5.

<p>The upper left bar represents the gradient of location probability. Nodes were drawn using a progressive ancestral probability location value of 0–1. Colours of terminal and internal branches indicate the sampling location for each sequence and the most probable ancestral location for each clade, respectively. The clusters of greatest epidemiological interest (≥5 patients grouped) are indicated by an asterisk (*).</p

Global ML phylogenetic tree inferred for the main HIV-1 non-B genetic forms sampled in Eastern Andalusia.

<p>The phylogenetic tree was constructed by the general time-reversible with gamma-distributed rate heterogeneity across sites model of substitution implemented into RAxML. Branches are drawn on scale with the bar at the bottom, which represents 0.04 nucleotide substitution per site. Statistically highly supported nodes (bootstrap values >70%) are indicated by an asterisk (*). Andalusian clusters and international lineages are highlighted in yellow and blue, respectively. The Andalusian sequence names contain a three-part code: Sequence number, sampling site (AL: Almería, EJ: El Ejido GR: Granada, JA: Jaén, MO: Motril) and the code of the most likely country of infection.</p

Bayesian phylogenetic tree inferred for the subtype A1, C, F1 and G/CRF14_BG <i>pol</i> sequences sampled in Eastern Andalusia and genetically similar sequences from GenBank.

<p>Red branches correspond to the sequences sampled in eastern Andalusia from 2005 to 2012. Statistically highly supported nodes (posterior probability values above 0.9) are indicated with an asterisk (*). Andalusian clusters are highlighted in yellow. Andalusian sequences names contain a three-part code: Sequence number, sampling site (AL: Almería, EJ: El Ejido GR: Granada, JA: Jaén, MO: Motril) and the code of the most likely country of infection.</p

Distribution of the HIV-1 non-subtype B genetic forms detected in Eastern Andalusia over the 2005–2012 period.

<p>Distribution of the HIV-1 non-subtype B genetic forms detected in Eastern Andalusia over the 2005–2012 period.</p

Demographic, clinical and virological characteristics of the patients infected with HIV-1 non B variants sampled over the 2005–2012 period.

<p>Demographic, clinical and virological characteristics of the patients infected with HIV-1 non B variants sampled over the 2005–2012 period.</p

Demographic history of HIV-1 Subtype B in Andalusia.

<p>A demographic analysis was performed using the Bayesian Skyline Plot. The vertical axes represent the estimated effective population size on a logarithmic scale. The black line represents the median estimated for the effective population size with time. The blue area depicts the 95% HPD (high posterior density) confidence interval for this estimate.</p

Bayesian phylogenetic tree inferred for the CRF02_AG <i>pol</i> sequences sampled in Eastern Andalusia and genetically similar sequences from GenBank.

<p>Red branches correspond to the sequences sampled in eastern Andalusia from 2005 to 2012. Statistically highly supported nodes (posterior probability values above 0.9) are indicated with an asterisk (*). Andalusian clusters are highlighted in yellow. Andalusian sequences names contain a three-part code: Sequence number, sampling site (AL: Almería, EJ: El Ejido GR: Granada, JA: Jaén, MO: Motril) and the code of the most likely country of infection.</p