Relationships between the subtype D sequences inferred using maximum likelihood phylogeny (GenBank deposited <i>pol</i> sequences).

<p>Country-specific sequences are marked with the same color: red – Poland, blue – Uganda, green – Tanzania, yellow – Europe (except Poland), brown – Cameroon, magenta - Senegal, cyan- Sudan, dark green – other African countries, violet – South America, grey – Asia, orange – North America.</p

Drug resistance and treatment efficacy in the group infected with subtype D.

<p>*Percentage expressed adherence based on the number of months of medications dispensed by the number of months of follow-up; clinician assigned adherence based on the patient's statement regarding missed doses and treatment interruptions.</p

Frequency of baseline drug resistance mutations among treatment-naive patients.

<p>Frequency of baseline drug resistance mutations among treatment-naive patients.</p

Phylogenetic trees of the subtype D sequences from Northwestern Poland.

<p>Figure a - maximum likelihood tree with bootstrap values for 1000 replicates drawn at the branches. Figure b – time scaled Bayesian MCMC tree. On the tree branches estimated time to the most recent common ancestor (tMRCA) and posterior probabilities expressed as percentage are shown. For both figures clustered sequences are marked in red and four identified clusters indicated as blue boxes and numbered are drawn on the right. Drug resistance mutations are marked at the tip nodes after the sequence identifier. *source patient for the transmission of the drug resistance within the cluster.</p

Frequency of secondary drug resistance mutations in patients failing antiretroviral therapy.

<p>Frequency of secondary drug resistance mutations in patients failing antiretroviral therapy.</p

Bayesian skyline plot for estimation of the number of subtype D HIV-1 cases in the local population.

<p>95% CI are marked in blue. Y-axis: predicted number of cases (log scale), X-axis: timescale (years).</p

Multivariate model of factors associated with probability of survival in the cohort.

<p>Selection of factors was based on Akaike Information Criterion (AIC) and statistical significance.</p

Hazard ratio changes during observation period.

<p>For calculation multivariate Cox regression adjusted for the six selected factors was used. Upper and lower confidence intervals are indicated as the external limits in the plot. For the values of borderline significance (p = 0.1–0.50) the field is marked in green while values of statistical significance (P<0.05) are marked in blue. a-<i>CCR5</i> genotype, b- gender, c-antiretroviral treatment history, d- CD4 count >500 cells/µl maintained for at least half a year, e-the most recent CD4 count of 100 cells/µl, f- AIDS diagnosis.</p

Kaplan-Meyer plots presenting the <i>CCR5 Δ32/wt</i> genotype based survival prior to cART introduction (a) and on antiretroviral therapy (b).

<p>Kaplan-Meyer plots presenting the <i>CCR5 Δ32/wt</i> genotype based survival prior to cART introduction (a) and on antiretroviral therapy (b).</p

Multivariate Cox regression model of factors modifying 15 year mortality among HIV infected patients (favorable versus unfavorable parameter).

<p>Dots represent adjusted hazard ratio (HR) for the unfavorable parameters, lines represent confidence intervals for the HR.</p