Data_Sheet_1_The HIV-1 Subtype B Epidemic in French Guiana and Suriname Is Driven by Ongoing Transmissions of Pandemic and Non-pandemic Lineages.PDF

<p>The HIV-1 subtype B epidemic in French Guiana and Suriname is characterized by the co-circulation of the globally disseminated “B_PANDEMIC” lineage and of non-pandemic subtype B lineages of Caribbean origin (B_CAR). To reconstruct the spatiotemporal pattern of spread of those viral lineages circulating in these two countries, a total of 361 HIV-1 subtype B pol sequences recovered from treatment-naive adult patients from French Guiana and Suriname between 2006 and 2012 were combined with B_PANDEMIC and B_CAR reference sequences. Major Guianese/Surinamese B_PANDEMIC and B_CAR lineages were identified by Maximum Likelihood phylogenetic analysis and the spatiotemporal and demographic parameters estimated using a Bayesian coalescent-based method. We detected four B_CAR and three B_PANDEMIC transmission chains of large size that together comprise most pandemic and non-pandemic subtype B sequences from French Guiana (≥52%) and Suriname (≥70%) here analyzed. These major lineages were probably introduced into French Guiana and Suriname from the Caribbean (B_CAR) and North/South America (B_PANDEMIC) between the middle 1970s and the late 1980s and spread among populations from both countries with roughly comparable demographic growth rates. We detected a significant trend for higher viral loads and higher proportion of homosexual/bisexual men among subjects infected with B_PANDEMIC relative to B_CAR strains in French Guiana. These results show that the HIV subtype B epidemic in French Guiana and Suriname has been driven by multiple active B_CAR and B_PANDEMIC transmission chains that arose since the middle 1970s onward and operate in both countries simultaneously. Although no significant differences in the epidemic potential of major B_CAR and B_PANDEMIC lineages were observed, relevant associations between the infecting subtype B lineage and epidemiological and clinical characteristics were detected in French Guiana.</p

Table_3_The HIV-1 Subtype B Epidemic in French Guiana and Suriname Is Driven by Ongoing Transmissions of Pandemic and Non-pandemic Lineages.DOCX

<p>The HIV-1 subtype B epidemic in French Guiana and Suriname is characterized by the co-circulation of the globally disseminated “B_PANDEMIC” lineage and of non-pandemic subtype B lineages of Caribbean origin (B_CAR). To reconstruct the spatiotemporal pattern of spread of those viral lineages circulating in these two countries, a total of 361 HIV-1 subtype B pol sequences recovered from treatment-naive adult patients from French Guiana and Suriname between 2006 and 2012 were combined with B_PANDEMIC and B_CAR reference sequences. Major Guianese/Surinamese B_PANDEMIC and B_CAR lineages were identified by Maximum Likelihood phylogenetic analysis and the spatiotemporal and demographic parameters estimated using a Bayesian coalescent-based method. We detected four B_CAR and three B_PANDEMIC transmission chains of large size that together comprise most pandemic and non-pandemic subtype B sequences from French Guiana (≥52%) and Suriname (≥70%) here analyzed. These major lineages were probably introduced into French Guiana and Suriname from the Caribbean (B_CAR) and North/South America (B_PANDEMIC) between the middle 1970s and the late 1980s and spread among populations from both countries with roughly comparable demographic growth rates. We detected a significant trend for higher viral loads and higher proportion of homosexual/bisexual men among subjects infected with B_PANDEMIC relative to B_CAR strains in French Guiana. These results show that the HIV subtype B epidemic in French Guiana and Suriname has been driven by multiple active B_CAR and B_PANDEMIC transmission chains that arose since the middle 1970s onward and operate in both countries simultaneously. Although no significant differences in the epidemic potential of major B_CAR and B_PANDEMIC lineages were observed, relevant associations between the infecting subtype B lineage and epidemiological and clinical characteristics were detected in French Guiana.</p

Table_2_The HIV-1 Subtype B Epidemic in French Guiana and Suriname Is Driven by Ongoing Transmissions of Pandemic and Non-pandemic Lineages.DOCX

<p>The HIV-1 subtype B epidemic in French Guiana and Suriname is characterized by the co-circulation of the globally disseminated “B_PANDEMIC” lineage and of non-pandemic subtype B lineages of Caribbean origin (B_CAR). To reconstruct the spatiotemporal pattern of spread of those viral lineages circulating in these two countries, a total of 361 HIV-1 subtype B pol sequences recovered from treatment-naive adult patients from French Guiana and Suriname between 2006 and 2012 were combined with B_PANDEMIC and B_CAR reference sequences. Major Guianese/Surinamese B_PANDEMIC and B_CAR lineages were identified by Maximum Likelihood phylogenetic analysis and the spatiotemporal and demographic parameters estimated using a Bayesian coalescent-based method. We detected four B_CAR and three B_PANDEMIC transmission chains of large size that together comprise most pandemic and non-pandemic subtype B sequences from French Guiana (≥52%) and Suriname (≥70%) here analyzed. These major lineages were probably introduced into French Guiana and Suriname from the Caribbean (B_CAR) and North/South America (B_PANDEMIC) between the middle 1970s and the late 1980s and spread among populations from both countries with roughly comparable demographic growth rates. We detected a significant trend for higher viral loads and higher proportion of homosexual/bisexual men among subjects infected with B_PANDEMIC relative to B_CAR strains in French Guiana. These results show that the HIV subtype B epidemic in French Guiana and Suriname has been driven by multiple active B_CAR and B_PANDEMIC transmission chains that arose since the middle 1970s onward and operate in both countries simultaneously. Although no significant differences in the epidemic potential of major B_CAR and B_PANDEMIC lineages were observed, relevant associations between the infecting subtype B lineage and epidemiological and clinical characteristics were detected in French Guiana.</p

High Prevalence and Onward Transmission of Non-Pandemic HIV-1 Subtype B Clades in Northern and Northeastern Brazilian Regions

<div><p>The Human immunodeficiency virus type-1 (HIV-1) epidemic in Brazil is mainly driven by the subtype B pandemic lineage (B_PANDEMIC), while Caribbean non-pandemic subtype B clades (B_CAR) seem to account for a very low fraction of HIV-infections in this country. The molecular characteristics of the HIV-1 subtype B strains disseminated in the Northern and Northeastern Brazilian regions, however, have not been explored so far. In this study, we estimate the prevalence of the HIV-1 B_PANDEMIC and B_CAR clades across different Brazilian regions and we reconstruct the spatiotemporal dynamics of dissemination of the major Brazilian B_CAR clades. A total of 2,682 HIV-1 subtype B <i>pol</i> sequences collected from 21 different Brazilian states from the five country regions between 1998 and 2013 were analyzed. Maximum Likelihood phylogenetic analyses revealed that the B_CAR strains reached 16 out 21 Brazilian states here analyzed. The B_CAR clades comprise a low fraction (<10%) of subtype B infections in most Brazilian states analyzed, with exception of Roraima (41%), Amazonas (14%) and Maranhão (14%). Bayesian phylogeographic analyses indicate that B_CAR strains originally from the Hispaniola and Trinidad and Tobago were introduced at multiple times into different states from all Brazilian regions and a few of those strains, probably introduced into Roraima, Maranhão and São Paulo between the late 1970s and the early 1980s, established secondary outbreaks in the Brazilian population. These results support that the HIV-1 subtype B epidemics in some Brazilian states from the Northern and Northeastern regions display a unique molecular pattern characterized by the high prevalence of B_CAR lineages, which probably reflects a strong epidemiological link with the HIV-1 epidemics in the Caribbean region.</p></div

Spatiotemporal dynamics of dissemination of HIV-1 B_CAR clades circulating in the Caribbean and Brazil.

<p>A) Time-scaled Bayesian MCMC tree of <i>pol</i> PR/RT sequences of HIV-1 B_CAR lineages from Brazil (n = 97) and the Caribbean (<i>n</i> = 258), and subtype D reference sequences (<i>n</i> = 10) from the Democratic Republic of Congo. Branches are colored according to the most probable location state of their descendent nodes as indicated in the legend at right. Colored boxes indicate the positions of major B_CAR clades detected in Brazil, Jamaica and Trinidad and Tobago. Branch lengths are depicted in units of time (years). The tree was automatically rooted under the assumption of a relaxed molecular clock. B) Lines between locations represent branches in the Bayesian MCC tree along which location transitions occurred and were colored according to the location of origin (see the legend at left). Maps were created from templates obtained from d-maps.com (Caribbean: <a href="http://d-maps.com/carte.php?numcar=1389&lang=en" target="_blank">http://d-maps.com/carte.php?numcar=1389&lang=en</a>; South America: <a href="http://d-maps.com/carte.php?numcar=2313&lang=en" target="_blank">http://d-maps.com/carte.php?numcar=2313&lang=en</a>; and Brazil: <a href="http://d-maps.com/carte.php?numcar=4843&lang=en" target="_blank">http://d-maps.com/carte.php?numcar=4843&lang=en</a>). AC: Acre; AM: Amazonas; AP: Amapá; CD: Democratic Republic of Congo; ES: Espírito Santo; GO: Goiás; HISP: Hispaniola; JM: Jamaica; MA: Maranhão; MG: Minas Gerais; MS: Mato Grosso do Sul; PA: Pará; PI: Piauí; RJ: Rio de Janeiro; RR: Roraima; RS: Rio Grande do Sul; SP: Sao Paulo; TO: Tocantins; TT: Trinidad and Tobago.</p

HIV-1 subtype B <i>pol</i> (PR/RT and RT) Brazilian sequences.

<p>HIV-1 subtype B <i>pol</i> (PR/RT and RT) Brazilian sequences.</p

Bayesian T_MRCA estimates for major B_CAR clades from Brazil and the Caribbean.

<p>Bayesian T_MRCA estimates for major B_CAR clades from Brazil and the Caribbean.</p

Estimated proportion of B_CAR and B_PANDEMIC clades among HIV-1 subtype B infected individuals from different Brazilian states.

<p>The total number of sequences analyzed in each locality is indicated. States were colored according to the Brazilian region of origin as indicated in the legend at bottom, with exception of those states with no HIV-1 sequences included in this study (white). Map was created from a template obtained from d-maps.com (<a href="http://d-maps.com/carte.php?numcar=4843&lang=en" target="_blank">http://d-maps.com/carte.php?numcar=4843&lang=en</a>).</p