HIV Subtypes in Caribbean Figure 1. Phylogenetic analysis of 67 partial pol sequences of HIV-1 from Caribbean countries: Trinidad and Tobago (TT), Dominican Republic (DO), Haiti (HT) and Jamaica (JM). A neighbor-joining phylogenetic tree was built using the Kimura 2- parameter model and significant parsimony bootstrap values (.70%) were placed next to the nodes. The genetic distance corresponding to the lengths of the branches is shown by the scale below the tree. Reference samples are those named, preceded by the subtype; one of the study samples (the B/C recombinant) is also named. doi:10.1371/journal.pone.0004814.g001 The nine genes of HIV-1 were translated from the nucleotide sequence and visually examined to identify sites that might distinguish the Caribbean strains. The prevalence of particular amino acids were compared between the Caribbean sequences and reference B sequences using Fisher’s Exact Test without correcting for multiple comparisons. Results A total of 67 partial pol sequences of HIV-1 from the four Caribbean countries were analyzed: Trinidad and Tobago (n = 30), Dominican Republic (n = 18), Haiti (n = 16) and Jamaica (n = 3). Phylogenetic analysis classified 66 partial pol sequences as HIV-1 subtype B and one, from the Dominican Republic, as a recombinant between subtypes B and C (Figure 1). Based on the genetic analysis, some of the Trinidad samples were probably epidemiologically linked but aside from those clusters there was no clustering within Caribbean subtype B by country, island or language. Of the 67 samples with partial pol sequences, 15 specimens were also successfully amplified for the nearly full-length genome from serum RNA. The 15 that underwent full-length analysis consisted of the one non-B and those that produced full length ampicons readily. Previous experience with the primers suggests that failure to amplify was not due to primer mismatch, but rather to sample quality. Fourteen strains were non-recombinant subtype B; all strains were analyzed for evidence of intersubtype recombination and none was observed. The nearly full-length sequence of the B/ C recombinant strain revealed that it was a unique recombinant form which was subtype B in protease and the amino terminus of RT, while the rest of the genome was subtype C. The sequence did not cluster with CRF31_BC or any other B/C recombinant in genbank. When analyzed with other subtype B strains from the pandemic, the 14 nearly full-length sequences of the subtype B strains from the Caribbean clustered together significantly with a bootstrap value of 82% (Figure 2). The only ‘non-Caribbean’ subtype B was RF, a virus collected from an Haitian woman in the United States [5]. Aside from one cluster between two of the Trinidad samples there was no significant clustering within the Caribbean strains, either by country, island or language. Analysis of the nine genes of HIV-1 for mutations more common in the Caribbean strains than in subtype B reference strains revealed a handful of sites that significantly distinguished the two populations (Table 1). Analysis of the protease/RT sequences revealed a lack of major drug resistance-conferring mutations among the Caribbean HIV- 1-infected samples except for one sample from the Dominican Republic. Tropism for co-receptor usage of HIV-1 was deter- mined in silico for 22 partial env sequences from the study population. The PSSM procedure was used to predict the phenotype [13]. Only 2 out of the 22 sequences had a preference for CXCR4 rather than CCR5, both of them from the Dominican Republic. PLoS ONE | www.plosone.org 3 March 2009 | Volume 4 | Issue 3 | e4814