Background:  Integrase (IN) inhibitors represent a promising new class of therapeutic agents for treatment of HIV. Knowledge of naturally occurring IN gene polymorphisms is useful for delineation of pathways to resistance, to identify potential group/subtype effects and to assess prevalence of resistance-associated mutations.

Methods:  HIV-1 infected plasma samples collected from 1265 IN-inhibitor-näive subjects in Africa, Asia, Europe, Middle East, and North and South America and 39 viral isolates were analyzed. Reverse-transcriptase (RT) polymerase chain reaction was used to amplify gag p24, env gp41 IDR and full-length pol IN. Amplicons were sequenced directly. Subtype, determined using PHYLIP, was based on all 3 regions.

Results:  Phylogenetic analysis revealed that this panel is composed of 1200 group M (A-D, F-H, CRF01_AE, CRF02_AG, CRF03_AB, CRF06_cpx, CRF09_cpx, CRF11_cpx, CRF13_cpx, CRF22_01A1, CRF25_cpx, unique recombinant forms, unclassified), 100 group O and 4 group N strains. Of 288 amino acids, 121 (42%) were polymorphic at a level of 1% or greater. The catalytic triad (D64, D116, E152) and HHCC motif were highly conserved. One subtype C harbored a D64E substitution; 3 strains (2 CRF02; 1 CRF03) had an E152K interchange. Inspection of amino acids at positions previously associated with resistance to IN inhibitors revealed that T66, E92, F121, Q146, S147, and Q148 were completely non-polymorphic. Rare polymorphisms were seen at H51, E138, G140, and N155, none resistance-associated. Notably, certain natural polymorphisms associated with resistance occurred at substantial frequencies: V72I (55%), L74M (5% of grp M), T97A (5%), T112I (11% grp M, 35% grp O), V151I (2%), K156N (1%), E157Q (4%), V165 (5%), and I203M (3%). Less frequently observed were M154I (<1%), G163R (<1%) and A128T, Y143C, S230R and R263K (once each).

Conclusions:  Key functional residues involved in catalytic activity are highly conserved across group/subtype. Some resistance-associated mutations are naturally occurring polymorphisms. Notably, residues 148 and 155 associated with primary resistance are highly conserved. Sequence information from this large set of genetically and geographically diverse strains enhances our understanding of the range and nature of polymorphisms within IN. This provides an important foundation for assessing evolution of resistance within and across subtypes/groups of HIV-1.