Background:  HIV-1 integrase inhibitors (INI) are in advance stage of clinical trials. We evaluate clinical HIV-1 variants of INI-naïve patients infected with subtypes B and non-B to analyze the polymorphism including the prevalence of mutations previously described as associated with INI resistance.

Methods:  The entire integrase (IN) gene (867 bases) was amplified and sequenced using ABI technology. Selection of patients was based on plasma availability and known non-B subtypes based on RT/Pr sequences. Subtyping was determined by phylogenetic analysis of RT, Pr, and IN sequences. Patients with identical RT and Pr sequences were excluded from the analysis.

Results:  We sequenced full-length HIV-1 IN genes from 36 patients infected by subtype B and 53 patients by subtypes non-B including A (n = 4), C (8), D (2), F (3), G (1), J (1), K (1), and CRF-01 (4), -02 (14), -03 (1), -09 (1), -10 (1), -11 (9), -13 (2), -14 (1),  and -18 (1). Phylogenetic analysis revealed similar subtyping for RT, Pr, and IN genes. Analysis of the 89 patients revealed that 48% of the amino acid positions were polymorphic (32% for subtype B and 40% for subtypes non-B). Overall, the heterogeneity as determined by pairwise comparison varied from 0.2 to 12% at both nucleotide and amino acid levels (mean, 8% and 7%, respectively). Similar heterogeneity was found within subtypes B and non-B with a mean of 6% (range 1 to 11%) and 6% (0.2 to 11%), respectively. The catalytic triad (DDE) and the HHCC motif were highly conserved in both subtypes B and non-B. Among the IN mutations previously reported as associated with INI resistance, 11 occurred as natural polymorphism:  V72I (17% in B, 19% in non-B), L74M (0% in B, 4% in non-B), T97A (0% in B, 4% non-B), K156N (3% in B, 0% in non-B), V165I (11% B, 9% non-B), V201I (11% B, 17% non-B), T206S (9% B, 47% non-B), and S230N (14% B, 2% non-B). Some substitutions can be classified as subtype specific amino acids (B-position-non-B):  T112V/A/I, G134D/N, K136Q/T, L234I/V, and S283G. Comparison of amino acid sequences identified similar variable regions in subtypes B and non-B (amino acids residues:  121-128, 205-223, and 249-256).

Conclusions:  Catalytic triad and HHCC motif were highly conserved in both subtypes B and non-B. Heterogeneity was comparable within subtypes B and non-B. Polymorphism at positions associated with INI resistance was present at the same level in both subtypes B and non-B.