Substitutions at Amino Acid Positions 143, 148, and 155 of HIV-1 Integrase Define Distinct Genetic Barriers to Raltegravir Resistance In Vivo

Abstract

Mutations at amino acids 143, 148, and 155 in HIV-1 integrase (IN) define primary resistance pathways in subjects failing raltegravir (RAL)-containing treatments. Although each pathway appears to be genetically distinct, shifts in the predominant resistant virus population have been reported under continued drug pressure. To better understand this dynamic, we characterized the RAL susceptibility of 200 resistant viruses, and we performed sequential clonal analysis for selected cases. Patient viruses containing Y143R, Q148R, or Q148H mutations consistently exhibited larger reductions in RAL susceptibility than patient viruses containing N155H mutations. Sequential analyses of virus populations from three subjects revealed temporal shifts in subpopulations representing N155H, Y143R, or Q148H escape pathways. Evaluation of molecular clones isolated from different time points demonstrated that Y143R and Q148H variants exhibited larger reductions in RAL susceptibility and higher IN-mediated replication capacity (RC) than N155H variants within the same subject. Furthermore, shifts from the N155H pathway to either the Q148R or H pathway or the Y143R pathway were dependent on the amino acid substitution at position 148 and the secondary mutations in Y143R-or Q148R-or H-containing variants and correlated with reductions in RAL susceptibility and restorations in RC. Our observations in patient viruses were confirmed by analyzing site-directed mutations. In summary, viruses that acquire mutations defining the 143 or 148 escape pathways are less susceptible to RAL and exhibit greater RC than viruses containing 155 pathway mutations. These selective pressures result in the displacement of N155H variants by 143 or 148 variants under continued drug exposure.

Impact of HIV-1 Integrase L74F and V75I Mutations in a Clinical Isolate on Resistance to Second-Generation Integrase Strand Transfer Inhibitors

“…To date, clinical studies demonstrated that three major resistance pathways, Y143C/ H/R, Q148H/K/R, and N155H were frequently observed in patients with virological failure under a RAL-based regimen (19)(20)(21)(22). The N155H mutation was usually accompanied by the secondary mutation L74M, E92Q, T97A, G136R, or V151I (23)(24)(25).…”

Multiple Genetic Pathways Involving Amino Acid Position 143 of HIV-1 Integrase Are Preferentially Associated with Specific Secondary Amino Acid Substitutions and Confer Resistance to Raltegravir and Cross-Resistance to Elvitegravir

“…However, longitudinal evaluations have demonstrated that RAL-resistant viruses with substitutions at position 148 or 155 may be replaced by variants with Y143 substitutions upon continued RAL treatment (25)(26)(27). In a majority of cases, Y143 substitutions comprise C and R, both of which can confer significant reductions in RAL susceptibility (17,18,25,27).…”

“…In a majority of cases, Y143 substitutions comprise C and R, both of which can confer significant reductions in RAL susceptibility (17,18,25,27). RAL-resistant viruses with Y143H substitutions have also been reported, albeit much less frequently (27,28).…”

“…For example, E92Q and G140A, S are associated with N155H and Q148H,K,R, respectively (16,29), whereas T97A is associated with Y143C,R (27,30). In addition, L74I,M, E92Q, E138K, V151I, G163R, I203M, and S230R have been associated with RAL treatment failure (31).…”

Drug Susceptibility and Viral Fitness of HIV-1 with Integrase Strand Transfer Inhibitor Resistance Substitution Q148R or N155H in Combination with Nucleoside/Nucleotide Reverse Transcriptase Inhibitor Resistance Substitutions

“…Instead, INSTI primary resistance mutants may coexist as distinct subpopulations that evolve over time with or without development of secondary INSTI resistance substitutions (9,31,34). Temporal shifts in resistance pathways from IN-N155H to IN-Q148H/K/R have been observed in patients failing RAL-containing regimens, likely due to the selective advantage of more resistant IN-Q148H/ K/R mutants under continued drug pressure (35)(36)(37)(38). Our data support these findings in the context of EVG, with the less resistant IN-N155H mutant appearing to have a fitness advantage over the IN-Q148R mutant at low EVG concentrations and the reverse occurring at high EVG concentrations.…”