Estimated proportion of B_CAR and B_PANDEMIC clades among HIV-1 subtype B infected individuals from different Caribbean countries according to the ML analyses.

<p>The total number of sequences analyzed in each locality is indicated.</p

Demographic history of the HIV-1 B_CAR (A, B), B_CAR-JM (C, D), and B_CAR-TT (E, F) clades circulating in Hispaniola, Jamaica and Trinidad and Tobago, respectively.

<p>Effective number of infections (y-axis; log10 scale) through time (x-axis; calendar years) estimated using Bayesian skyline (A, C, E) and logistic (B, D, F) growth coalescent model. Median estimates of the effective number of infections (solid line) and 95% HPD intervals of the estimates (dashed lines) are shown in each graphic. The median growth rate (with the corresponding 95% credibility interval in parenthesis) of each clade estimated under logistic growth model is indicated in the upper left corner.</p

Bayesian time-scale estimates for the origin of HIV-1 subtypes B and D.

<p>*Estimated by Gilbert <i>et al</i> (2007).</p

Best fit demographic model for different HIV-1 subtype B_CAR clades.

<p>Log marginal likelihood (ML) estimates for the logistic (Log), exponential (Expo) and expansion (Expa) growth demographic models obtained using the path sampling (PS) and stepping-stone sampling (SS) methods. The Log Bayes factor (BF) is the difference of the Log ML between of alternative (H1) and null (H0) models (H1/H0). Log BF >3 indicate that model H1 is more strongly supported by the data than model H0.</p

Spatiotemporal dynamics of dissemination of non-pandemic HIV-1 B_CAR clades in the Caribbean region.

<p>A–D) Viral migration events occurred between 1964 and 2005 are indicated. Lines between locations represent branches in the Bayesian MCC tree along which location transitions occurred. The line’s color informs the source location and only the earliest transitions between each location pair were represented. E) Most significant epidemiological links of the dissemination process of B_CAR clades. Only epidemiological links supported by Bayes factor rates >3 are displayed. The values of Bayes factor rates are indicated by a color gradient that ranges from light to dark grey as indicated at the legend (up left). F) Viral migrations among locations as measured using ‘Markov jump’ counts. The width of the arrows is proportional to the corresponding mean estimated number of viral transitions between locations. No arrows were displayed when the mean estimated number of transitions was below one.</p

HIV-1 subtype <i>pol</i> sequences.

<p>*Antigua and Barbuda (<i>n</i> = 7), Barbados (<i>n</i> = 14), Dominica (<i>n</i> = 3), Grenada (<i>n</i> = 4), Montserrat (<i>n</i> = 1), Saint Lucia (<i>n</i> = 4) and Saint Vincent and the Grenadines (<i>n</i> = 6).</p

ML phylogenetic tree.

<p>A) HIV-1 subtype B <i>pol</i> PR/RT sequences (∼1,000 nt) circulating in the Caribbean (<i>n</i> = 743), US (<i>n</i> = 525), and France (<i>n</i> = 340); B) HIV-1 subtype B <i>pol</i> RT (∼600 nt) sequences from Barbados (<i>n</i> = 14), Guadeloupe (<i>n</i> = 243), Haiti (<i>n</i> = 15), Martinique (<i>n</i> = 452), Puerto Rico (<i>n</i> = 285), US Virgin Islands (<i>n</i> = 54) and representative sequences of the B_PANDEMIC (US = 165, France = 135) and the B_CAR (Caribbean = 200) clades. Branches are colored according to the geographic origin of each sequence as indicated at the legend (bottom right). Arcs indicate the B_PANDEMIC and B_CAR clades. Purple and green shaded boxes highlight the position of the Caribbean clades B_CAR-TT and B_CAR-JM. The <i>a</i>LRT support values are indicated at key nodes: *(0.81–0.90), **(0.91–1). Trees were rooted using HIV-1 subtype D reference sequences. The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.</p

Root location of the HIV-1 subtype B.

<p>Graphics depict the location state posterior probability distributions at the root of the subtype B_CAR clades at the Bayesian MCC trees obtained from complete dataset (A) and country “balanced” sub-sets (B to G) from the Caribbean region. Color code is indicated at the legend at bottom left.</p

Distribution of viruses of the subtype F cluster sequenced by us according to city of sample collection.

<p>Distribution of viruses of the subtype F cluster sequenced by us according to city of sample collection.</p

Bayesian skyline plot of the population growth of the subtype F cluster.

<p>The black line represents the median estimate of the effective number of infections through time (logarithmic scale) and the shaded area represents the 95% HPD credibility interval. The horizontal axis represents calendar years.</p