In contrast to mutants with site-directed mutations, a panel created from clinical isolates contains drug resistance mutations in their naturally occurring genetic context. This genetic context may include known accessory drug resistance mutations, as well as changes at positions that are not currently known to be associated with drug resistance.
The highest levels of raltegravir resistance (>200-fold decrease in susceptibility) were observed in clones containing both G140S and Q148H and in the clone containing Y143C. Lower levels of resistance (48- to 116-fold decreases in susceptibility) were found in clones containing N155H. These results are consistent with those reported by several other groups (3
). The clone with Y143C and T97A had an extraordinarily high level of raltegravir resistance, confirming the highly synergistic interaction previously demonstrated only in site-directed mutants (4
). Indeed, the level of raltegravir resistance associated with this pair of mutations is striking considering that Y143C alone reduces raltegravir susceptibility by only 3.5-fold (4
) and T97A is a polymorphism with a 1 to 2% prevalence in raltegravir-naïve patients (12
) that does not reduce raltegravir susceptibility (15
Our data set contains the first reported clinical sequences with the mutations H51Y and Y143H. H51Y has been selected in vitro
by elvitegravir and shown, using the PhenoSense assay, to reduce elvitegravir susceptibility 5-fold (7
). A comparison of clones containing N155H/E92Q with and without H51Y suggests that H51Y has little impact on raltegravir resistance but may lower virus fitness (Table ). Susceptibility data for Y143H have not been published previously.
E157Q, a polymorphism occurring in about 1 to 2% of INI-naïve patients (12
), has been associated with virological failure during raltegravir therapy in one patient (11
) and with a 3.3-fold reduction in elvitegravir susceptibility (7
). However, the one sample in our panel with this mutation was fully susceptible to raltegravir.
Other than H51Y and S230R, each of the minor mutations listed in Table is polymorphic, occurring at a frequency of >1.0% in the absence of therapy (12
). With the exception of D41H, K160T, Q216H, I220M, and D229E, each of the mutations listed under “Other” in Table is also polymorphic (12
). Their potential impact, if any, on raltegravir susceptibility is not known.
In conclusion, investigational INIs which are active against the viruses in this panel are likely to retain activity against the most clinically relevant or, possibly, all raltegravir-resistant variants. Moreover, the use of a standard publicly available set of virus clones makes it possible for the relative activity of different INIs to be compared with one another. Researchers planning to create their own recombinant viruses can also do so using the pNL4.3ΔIN vector as described above. We plan to expand this panel as new INIs become licensed and new patterns of INI resistance mutations emerge.