Analysis of a Large Collection of Natural HIV-1 Integrase Sequences, Including Those From Long-Term Nonprogressors

Abstract

A large collection of natural HIV-1 integrase (IN) sequences has not previously been described. We reasoned that analysis of such sequences would address whether natural variation of HIV-1 IN contributes to the pathogenesis of AIDS and might also identify amino acid residues important for IN function. Sequences encoding HIV-1 IN were amplified from cryopreserved lymphocytes or plasma obtained at different times from 10 hemophilia patients who had been observed for up to 17 years. The region of the HIV-1 genome that encodes the 288-amino acid IN protein was sequenced from a total of 102 clones; information was obtained for 99.97% of 29,478 amino acid positions. Phylogenetic analysis indicated that patient samples were unique. Interpatient nucleic acid distances ranged from 0.8% to 4.9%, highlighting the tight conservation of this genomic region. No major differences were found between DNA and RNA or between early and late time points from the same patient. Significantly, no amino acid changes that might account for the variable rate of disease progression between patients were evident. Only one amino acid substitution involved a highly conserved residue known to be important for enzymatic activity. However, several interesting amino acid substitutions were noted, including residues within the C-terminal region of the protein for which sequence comparisons between animal retroviruses have not been very informative. These results should encourage the pursuit of anti-integrase therapies, especially inasmuch as the apparent biologic constraints on the IN sequence may deter the development of drug resistance.

Role of the Nonspecific DNA-binding Region and α Helices within the Core Domain of Retroviral Integrase in Selecting Target DNA Sites for Integration

“…Amino acid 119 is a Ser in HIV-1 integrase, and the corresponding residue in FIV integrase is a Pro. Substituting the Ser at position 119 with Thr or Gly is one of the most frequently observed integrase variants in viral isolates from HIV-1-infected patients (65).…”

An Amino Acid in the Central Catalytic Domain of Three Retroviral Integrases That Affects Target Site Selection in Nonviral DNA

“…Future studies should correlate these in vitro findings with the target site preferences of preintegration complexes that mediate integration in vivo. However, it is worth noting that natural HIV-1 isolates contain several amino acids at integrase position 119 (18,27,37,40), and our preliminary data indicate that RSV virions with the S124A substitution replicate at levels similar to that of wild-type virus (Harper and Katzman, unpublished). Indeed, viral fitness is unlikely to be adversely affected by nonviral target site preferences that do not cause frequent integration into sites critical for cell survival.…”

Use of Patient-Derived Human Immunodeficiency Virus Type 1 Integrases To Identify a Protein Residue That Affects Target Site Selection

“…We also predicted that many of the proteins would be active for processing and joining because of in vivo selection but hypothesized that biological pressures on noncritical aspects of integrase function, such as the choice of nonviral target sites, would be minimal. Although we realized that some viral sequences recovered from clinical samples might not come from infectious genomes, we had already established that 85% of integrase sequences that we had amplified from HIV-infected patients encoded full-length proteins (33). Moreover, substitutions at any of the seven highly conserved amino acids known to be important for integrase activity were rare.…”

“…We previously described 102 HIV-1 integrase sequences that were amplified from viral DNA in blood cells or viral RNA in plasma that had been obtained many years ago from 10 HIVinfected hemophiliacs (33). These sequences encode 87 fulllength proteins, of which 75 are unique.…”