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

Additional file 3: Figure S2. of Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species

Positions of PCR primers used to amplify the indicated fragments of the MHC class II loci in C. perspicillata, D. rotundus and M. molossus, based on cDNA. The structure of the cDNA of the MHC class II DRB gene is based on [50]. According to each species, boxes indicate the amplified region using each couple of primers. The shaded region represents the region of interest, namely exon 2. Sequences and references of all primers used are given in Table 1. (PDF 26 kb

Additional file 1: Table S1. of Spatial pattern of genetic diversity and selection in the MHC class II DRB of three Neotropical bat species

Supplementary methods, including the characteristics of all capture sites (Table S1)ďťż, the list of samples successfully amplified for the MHC class II DRB loci (Table S2), the distribution of DRB alleles per species (Table S3-5), the pairwise differentiation computations per species (Table S6-8), as well as the correlations of genetics and geographic distance (Table S9). (XLS 179 kb

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

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

Heatmap based on the viral-associated contigs of 51 families of insect, phage, plant/protozoan and vertebrate viruses in each pooled sample.

<p>Location information is provided above each column (Caves F and M for <i>D</i>. <i>rotundus</i>, Urban and Forest for <i>M</i>. <i>molossus</i>). The names of the viral families are presented in alphabetical order in the middle. The boxes colored from green to dark red represent the number of contigs observed. Contigs varied between 1 and 450 for the saliva samples and between 1 and 1465 for feces. The scales are given for each type of sample.</p

Phylogenetic analysis of partial RdRp protein sequences (alignment of 341 amino acids) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Nairoviridae</i> family.

<p>The tree was inferred using the Bayesian method with the WAG + G model. Sequence identifiers include the NCBI accession number and the isolate name. The blue arrows indicate the bat-sourced nairovirus sequence obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p

Characteristics of the sampling sites and number of collected feces and saliva samples for <i>Molossus molossus</i> and <i>Desmodus rotundus</i>.

<p>Characteristics of the sampling sites and number of collected feces and saliva samples for <i>Molossus molossus</i> and <i>Desmodus rotundus</i>.</p

Phylogenetic analysis of partial sequences of the <i>pol</i> s region (alignment of 107 amino acids) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Spumavirus</i> genus.

<p>The tree was inferred using the Bayesian method with the WAG + G model. Sequence identifiers include the NCBI accession number and the isolate name. The blue arrows indicate the sequence of bat-sourced spumavirus obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p

Phylogenetic analysis of partial <i>pol</i> gene sequences (alignment of 951 nucleotides) directly obtained from the metagenomic data of pooled fecal samples of <i>M</i>. <i>molossus</i> with other representative members of the <i>Herpesviridae</i> family.

<p>The tree was inferred using the Bayesian method with the GTR + G + I model. Sequence identifiers include the NCBI accession number and the isolate name. The blue arrows indicate the bat-sourced herpesvirus obtained in the present study. Posterior probabilities of the Bayesian analysis (>50%) are shown next to each node. The scale bar indicates amino acid substitutions per site.</p