Background:  Mutations at amino acids 143, 148, and 155 of HIV-1 integrase (IN) define primary pathways of resistance in subjects failing raltegravir (RAL). Although each pathway appears to be genetically distinct and non-overlapping, shifts in the predominant resistant virus subpopulation have been reported under continued drug pressure. To better understand this dynamic, we characterized the susceptibility and replication capacity of viruses containing Y143R or C and how they compare to viruses containing mutations at position 155 or 148.

Methods:  We included in this study 93 subjects failing RAL. Molecularly cloned IN sequences and a series of site-directed mutants containing mutations at positions 143, 148, 155 alone, or in combination with other IN resistance associated mutations were evaluated. Susceptibility to RAL and IN replication capacity was assessed using PhenoSense Integrase. The nucleotide sequences of all IN coding regions were determined.

Results:  A small number of subjects failing RAL with mutations at position 143 were compared with failures through the 155 or 148 pathway. Most subjects failing via the 143 pathway also contained the mutation T97A. Comparison of subjects failing with Y143R/C to N155H or Q148R/H showed that failures via the 143 and 148 pathways consistently displayed high-level resistance to RAL, while reductions in susceptibility (fold change in IC₅₀) varied for N155H containing viruses. Based on site-directed mutant data, susceptibility to RAL varied depending on the amino acid at position 143 (Y143R fold-change = 20; Y143C fold change = 3.5). The reduction in susceptibility conveyed by the Y143R mutation is consistent with site-directed mutants containing N155H, Q148R, and Q148H. In all cases, the addition of secondary mutations caused further reductions in RAL susceptibility. IN replication capacity of the Y143R site-directed mutant was greater than Y143C, N155H, Q148R, or H alone (95 vs 54, 69, 59, 43%, respectively). Additional mutations resulted in further reductions in IN replication capacity in all site-directed mutants except Q148H, which increased with the addition of G140S. Virus clones containing N155H exhibited lower IN replication capacity and were present in lower proportions than clones bearing 143 or 148 mutations within the same virus populations. 

Conclusions:  Mutations at position 143 or 148 appear to have less effect on replication capacity and cause higher levels of resistance to RAL than 155 mutations, which may explain reported shifts from the N155H pathway to either the 143 or 148 pathways under continued drug pressure.