HIV-1 Molecular Epidemiology, Transmission Clusters and Transmitted Drug Resistance Mutations in Central Brazil

Abstract

We aimed to characterize HIV-1 molecular epidemiology and transmission clusters among heterosexual (HET) and men who have sex with men (MSM) individuals, as well as transmitted drug resistance mutations (TDRM) in Central-Western Brazil. This cross-sectional survey was conducted among 190 antiretroviral naïve HIV-1 infected individuals. Proviral DNA was extracted, and nested PCR amplified partial polymerase gene (PR/RT). After sequencing, subtypes were assigned, and the sequences were analyzed for the occurrence of possible transmission networks. Calibrated Population Resistance (CPR) tool from Stanford HIV Database was used to investigate the presence of TDRM. Among 150 individuals whose samples were successfully sequenced, the most prevalent HIV-1 subtype was B, followed by recombinant forms. The occurrence of twenty transmission clusters composed by at least two sequences was verified, suggesting the existence of transmission clusters among individuals from the same or distinct sexual orientations. Intermediate level of TDRM (12%) was found in the study population, and almost half of the subjects with TDRM had more than one resistance mutation. No correlations between sexual orientation and the presence of TDRM, HIV-1 subtypes/recombinants forms were verified. Taken together, the necessity of the continuous monitoring of the TDRM to verify the importance of pre-genotyping and to delineate future strategies in primary antiretroviral therapy. Likewise, the knowledge of the HIV-1 transmission networks in Brazil would allow the implementation of effective HIV-1 prevention strategies in local settings.

Keywords: HIV; MSM; molecular epidemiology; transmission network; transmitted drug resistance.

FIGURE 1

Map of Brazil indicating Brazilian regions and MS State, from which HIV-1 sequences were obtained. The pie chart shows HIV-1 subtypes distribution based on pol sequences included in this study.

FIGURE 2

ML phylogenetic tree of 150 HIV-1 PR/RT sequences from Mato Grosso do Sul, Central-West Brazil. The analyzed PR/RT alignment covered a fragment of 1261 bp, corresponding to nucleotides 2254 to 3514 relative to HXB2 genome. Reference sequences retrieved from GenBank are not labeled. ALRT values are represented only if greater > 0.90. Possible HIV-1 transmission clusters were indicated by numbers. HET = sample obtained from heterosexual individual; HSH = sample obtained from men who have sex with men. (A) Pure HIV-1 subtypes and (B) Recombinant sequences.

FIGURE 3

ML phylogenetic tree highlighting HIV-1 subtype B transmission clusters. The confirmed HIV-1 transmission clusters were highlighted in green and numbered according to the previous grouping from Figure 1. All clusters present aLRT ≥ 0.90 and low mean pairwise genetic distances (≤4.5). The analysis involved 520 HIV-1 B PR/RT sequences (102 sequences from the present study, 331 Brazilian reference sequences, 82 non-Brazilian reference sequences, and 5 HIV-1 Subtype C sequences as outgroup). The analyzed fragment corresponds to 891 bp (2262 to 3251 nt relative to HXB2 genome) and drug-resistance mutations positions were stripped.

FIGURE 4

ML phylogenetic tree showing the transmission clusters among HIV-1 subtypes of D and F1 sequences. The confirmed HIV-1 transmission clusters were highlighted in green and numbered according to the previous grouping from Figure 1. All clusters present aLRT ≥ 0.90 and low mean pairwise genetic distances (≤4.5). The sub-subtype F1 analysis involved 493 PR/RT sequences (15 sequences from the present study, 467 Brazilian reference sequences, 6 non-Brazilian reference sequences, and 5 HIV-1 Subtype C sequences as outgroup). From subtype D analysis, 94 sequences were used as follows: 2 detected in the present study, 17 HIV-1 Brazilian reference sequences, 72 non-Brazilian reference sequences and HIV-1 Subtype C sequences as outgroup).