Phylodynamics of the HIV-1 Epidemic in Cuba

<div><p>Previous studies have shown that the HIV-1 epidemic in Cuba displayed a complex molecular epidemiologic profile with circulation of several subtypes and circulating recombinant forms (CRF); but the evolutionary and population history of those viral variants remains unknown. HIV-1 <i>pol</i> sequences of the most prevalent Cuban lineages (subtypes B, C and G, CRF18_cpx, CRF19_cpx, and CRFs20/23/24_BG) isolated between 1999 and 2011 were analyzed. Maximum-likelihood analyses revealed multiple introductions of subtype B (<i>n</i>≥66), subtype C (<i>n</i>≥10), subtype G (<i>n</i>≥8) and CRF18_cpx (<i>n</i>≥2) viruses in Cuba. The bulk of HIV-1 infections in this country, however, was caused by dissemination of a few founder strains probably introduced from North America/Europe (clades B_CU-I and B_CU-II), east Africa (clade C_CU-I) and central Africa (clades G_CU, CRF18_CU and CRF19_CU), or locally generated (clades CRFs20/23/24_BG). Bayesian-coalescent analyses show that the major HIV-1 founder strains were introduced into Cuba during 1985–1995; whereas the CRFs_BG strains emerged in the second half of the 1990s. Most HIV-1 Cuban clades appear to have experienced an initial period of fast exponential spread during the 1990s and early 2000s, followed by a more recent decline in growth rate. The median initial growth rate of HIV-1 Cuban clades ranged from 0.4 year⁻¹ to 1.6 year⁻¹. Thus, the HIV-1 epidemic in Cuba has been a result of the successful introduction of a few viral strains that began to circulate at a rather late time of the AIDS pandemic, but then were rapidly disseminated through local transmission networks.</p></div

Additional file 2: of Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa

Figure S2. Maximum likelihood phylogenetic tree based on the CRF09/11/13/45_cpx pol fragment sequences for HIV-1 subtype (re)classification. Branches were colored according to HIV-1 subtype classification provided by the Los Alamos HIV database and indicated at the legend. Black dots represent the reference genomes of each CRF. For visual clarity, other subtypes not directly related to the CRF09/11/13/45_cpx were collapsed into triangles. The branch support values are indicated as * (SH-aLRT > 0.80 and < 0.90) or ** (SH-aLRT > 0.90) at key nodes. Horizontal branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site. (TIF 287 kb

Additional file 7: of Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa

Figure S4. Geographic distribution of the HIV-1 CRFs09/11/13/45_cpx pol (a) and env (b) gene fragments. Tips colors indicate the country of isolation of each sequence, according to the map. Country names are indicated using a two-letter code in accordance with ISO 3166. The external circular segments highlight the position of each specific clade as indicated at the line. Asterisks point to key nodes with a high (>0.90) PP support. Branch lengths are drawn to scale with the concentric circles indicating years. The trees were automatically rooted under the assumption of a relaxed molecular clock. (TIF 2346 kb

ML phylogenetic tree of HIV-1 subtype C <i>pol</i> (∼1000 pb) sequences circulating in Cuba (<i>n</i> = 49), and in central (<i>n</i> = 53), eastern (<i>n</i> = 330) and southern (<i>n</i> = 545) African countries.

<p>Branches are colored according to the origin of each sequence, as indicated at the legend (bottom left). The circular bracket highlights the position of the subtype C east African clade (C_EA). Shaded boxes highlight the position of the two major HIV-1 subtype C Cuban clades (C_CU-I and C_CU-II). Key nodes with <i>a</i>LRT support values >0.80 (*) and ≥0.90 (**) are indicated. The tree was rooted using HIV-1 subtype A1 and D reference sequences (gray branches). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.</p

Coalescent estimates of epidemic growth rate of the major HIV-1 Cuban clades.

<p>The box plots and the numbers above represent the median growth rates (years⁻¹) and the 95% HPD intervals of the posterior distributions estimated under the logistic growth coalescent model for each of the eight HIV-1 Cuban clades analyzed.</p

ML phylogenetic trees of HIV-1 CRFs_cpx <i>pol</i> (∼1000 pb) sequences.

<p>A) HIV-1 CRF18_cpx from Cuba (<i>n</i> = 62), were combined with those isolated in African (<i>n</i> = 12), American (<i>n</i> = 1) and European (<i>n</i> = 2) countries. The tree was rooted using HIV-1 subtype G reference sequences (black branches). B) HIV-1 CRF19_cpx sequences from Cuba (<i>n</i> = 160) and European countries (<i>n</i> = 3) were combined with subtype D sequences of African origin (<i>n</i> = 1,112). Branches are colored according to the origin of each sequence, as indicated at the legend (bottom left). Shaded boxes highlight the position of the major HIV-1 CRF18_cpx (CRF18_CU) and CRF19_cpx (CRF19_CU) Key nodes with <i>a</i>LRT support values >0.80 (*) and ≥0.90 (**) are indicated. The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.</p

ML phylogenetic tree of HIV-1 subtype G <i>pol</i> (∼1000 pb) sequences circulating in Cuba (<i>n</i> = 35), and in central (<i>n</i> = 71), western (<i>n</i> = 366), eastern (<i>n</i> = 10) and southern (<i>n</i> = 3) African countries.

<p>Branches are colored according to the origin of each sequence, as indicated at the legend (bottom left). Shaded boxes highlight the position of the major HIV-1 subtype G Cuban clade (G_CU). Key nodes with <i>a</i>LRT support values >0.80 (*) and ≥0.90 (**) are indicated. The tree was rooted using HIV-1 subtype A1 and B reference sequences (gray branches). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.</p

Evolutionary rate and time-scale of major HIV-1 Cuban clades.

*<p>Estimates obtained from the combined CRF20/23/24_BG data set.</p

ML phylogenetic tree of HIV-1 subtype B <i>pol</i> (∼1000 pb) sequences circulating in Cuba (<i>n</i> = 322), US (<i>n</i> = 525), France (<i>n</i> = 348), and other Caribbean countries (<i>n</i> = 418).

<p>The branches are colored according to the origin of each sequence, as indicated at the legend (bottom left). The circular brackets highlight the position of the pandemic (B_PANDEMIC, green line) and non-pandemic (B_CARIBBEAN, blue line) HIV-1 subtype B clades. Shaded boxes highlight the position of the two major HIV-1 subtype B Cuban clades (B_CU-I and B_CU-II). The number of Cuban sequences distributed accordingly to the clade size is shown (top left). Key nodes with <i>a</i>LRT support values >0.80 (*) and ≥0.90 (**) are indicated. The tree was rooted using HIV-1 subtype D reference sequences (gray branches). The branch lengths are drawn to scale with the bar at the bottom indicating nucleotide substitutions per site.</p

Additional file 5: of Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa

Table S2. HIV-1 CRFs_cpx pol dataset. (PDF 69 kb