Natural selection results in conservation of HIV-1 integrase activity despite sequence variability

BACKGROUND: Integration of the HIV genome by integrase is absolutely required for productive infection. OBJECTIVE: To determine the role of natural selection on HIV integrase biology. DESIGN: To study the activities of HIV integrases from a limited panel of North American clinical isolates from HIV-infected patients and to compare these proteins with integrases from two laboratory adapted reference strains (HI(VIIIRF) and HIV(NL4--3)). METHODS: HIV was isolated and the particle-associated RNA was reverse transcribed and sequenced. Replication kinetics of molecularly cloned viruses containing each variant integrase were studied in tissue culture. The mutant integrase proteins were expressed, purified and specific activities of the enzymes were derived for both 3' end-processing and disintegration reactions. RESULTS: Despite 3--5% variability in integrase at the amino acid level, viruses showed no statistically significant differences in growth kinetics compared with the reference HIV(NL4--3) virus and only minor differences were observed in 3' end-processing and disintegration activities. All integrase proteins demonstrated similar sensitivity to an integrase inhibitor l-chicoric acid. CONCLUSIONS: These results demonstrate that integrase genes derived from HIV-infected individuals can differ from reference sequences but these mutations do not result in loss of function, including susceptibility to an integrase inhibitor; therefore, integrase remains an attractive target for antiviral drug design, as mutability appears to be restricted by function.