Molecular epidemiology of HIV-1 in Panama: origin of non-B subtypes in samples collected from 2007 to 2013

Abstract

Phylogenetic studies have suggested that the HIV-1 epidemic in the Americas is mainly dominated by HIV subtype B. However, countries of South America and the Caribbean have recently reported changes in their circulating HIV-1 genetic profiles. The aim of this study was to characterize the molecular profile of the HIV-1 epidemic in Panama by the analysis of 655 polymerase gene (pol) sequences that were obtained from HIV-infected Panamanians diagnosed between 1987 and 2013. Blood samples were collected from recently infected, antiretroviral drug-naïve and treatment-experienced subjects since mid-2007 to 2013. Viral RNA from plasma was extracted and sequences of HIV protease and reverse transcriptase genes were obtained. Bootscanning and phylogenetic methods were used for HIV subtyping and to trace the putative origin of non-B subtype strains. Our results showed that HIV-1 infections in Panama are dominated by subtype B (98.9%). The remaining 1.1% is represented by a diverse collection of recombinant variants including: three URFs_BC, one CRF20_BG, and one CRF28/29_BF, in addition to one subtype F1 and one subtype C, none of which were previously reported in Panama. The non-B subtype variants detected in Panama were probably introduced from Brazil (subtype F1 and CRF28/29_BF), Cuba (CRF20_BG), Dominican Republic (URFs_BC) and India (subtype C). Panama is the geographical vertex that connects the North with South America and the Caribbean through trade and cultural relations, which may explain the observed introductions of non-B subtype HIV-1 variants from both the Caribbean and South America into this Central American country.

Figure 1. Geographic distribution of Panamanian subjects living with HIV participating in the study.

Map of Panama indicating the number of infected subjects located in each of the nine provinces (Bocas del Toro, Chiriquí, Veraguas, Herrera, Los Santos, Coclé, Colón, Panamá and Darién) and native territories of Comarcas Ngöbe Buglé, Kuna Yala and Emberá Wouman. The pie chart that represents the proportion of subjects located at the different districts from eastern Panama which includes the provinces of Panama, Colón, Darién and Comarca Kuna Yala.

Figure 2. Phylogenetic Neighbor-Joining tree of HIV pol gene sequences from Panamanian infected subjects sampled from 2007 to 2013.

(A) Panamanian HIV (black circles) are clustered with highly support within the clade of subtype B (n = 648), subtype F1 (n = 1) and subtype C (n = 1) reference sequences. For clarification purposes, branches have been compressed by each subtype. Bootstrap values higher than 80 are shown at branches. (B) Clustering of subtype B sequences defined by colored range of diagnostic age.

Figure 3. Phylogenetic Neighbor-Joining tree of HIV pol gene sequences from Panamanian HIV recombinant variants BF1, BC and BG clustered with circulating recombinant forms (CRF) references.

Subtypes and CRF references are indicated at right of the brackets. Only bootstrap values of more than 80 are shown at the corresponding nodes. Panamanian isolates are shown with black circles. For clarity purposes, branches have been compressed by each subtype. Bootscanning plots of these recombinants are shown aside. Reference sequences used for bootscanning analyses shown by color (subtype B, blue; subtype F1, green; subtype C, purple; subtype G, dark-green and subtype A1, red).

Figure 4. pol gene ML phylogenetic tree of non-B HIV-1 Panamanian sequences and 50 highly similar (nucleotide similarity > 94%) sequences from other countries selected with Blastn analyses.

(A) BC recombinant. (B) BF1 recombinant. (C) BG recombinant. (D) subtype F1 (E) subtype C. Panamanian non-B sequences are shown in highlighted red color. The tree was rooted using reference subtype sequences. The numbers along branches correspond to aLRT values. Bar is in nucleotide substitutions per site. The pie chart shows the proportion of countries represented by the Blastn analysis. Countries correspond with defined colors which are specified in each pie chart.