Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations

Abstract

Objectives: We characterized pairwise and higher order patterns of non-nucleoside reverse transcriptase inhibitor (NNRTI)-selected mutations because multiple mutations are usually required for clinically significant resistance to second-generation NNRTIs.

Patients and methods: We analysed viruses from 13 039 individuals with sequences containing at least one of 52 published NNRTI-selected mutations, including 1133 viruses from individuals who received efavirenz but no other NNRTI and 1510 viruses from individuals who received nevirapine but no other NNRTI. Of the 17 reported etravirine resistance-associated mutations (RAMs), Y181C/I/V, L100I, K101P and M230L were considered major based on published in vitro susceptibility data.

Results: Efavirenz preferentially selected for 16 mutations, including L100I (14% versus 0.1%, P < 0.001), K101P (3.3% versus 0.4%, P < 0.001) and M230L (2.8% versus 1.3%, P = 0.004), whereas nevirapine preferentially selected for 12 mutations, including Y181C/I/V (48% versus 6.9%, P < 0.001). Twenty-nine pairs of NNRTI-selected mutations covaried significantly, including Y181C with seven other mutations (A98G, K101E/H, V108I, G190A/S and H221Y), L100I with K103N, and K101P with K103S. Two pairs (Y181C + V179F and Y181C + G190S) were predicted to confer >10-fold decreased etravirine susceptibility. Seventeen percent of sequences had three or more NNRTI-selected mutations, mostly in clusters of covarying mutations. Many clusters had Y181C plus a non-major etravirine RAM; few had more than one major etravirine RAM.

Conclusions: Although major etravirine RAMs rarely occur in combination, 2 of 29 pairs of covarying mutations were associated with >10-fold decreased etravirine susceptibility. Viruses with three or more NNRTI-selected mutations often contained Y181C in combination with one or more minor etravirine RAMs; however, phenotypic and clinical correlates for most of these higher order combinations have not been published.

Figure 1

Treatment associations of NNRTI-selected mutations. This figure shows the associations of 52 NNRTI-selected mutations on treatment with efavirenz (EFV) or nevirapine (NVP), based on a Pearson's χ² analysis of the frequency of the mutation among sequences from individuals treated with EFV or NVP but no other NNRTI. (a) The 16 mutations preferentially selected (P < 0.05) by efavirenz; (b) the 12 mutations preferentially selected by nevirapine; (c) the remaining 24 mutations, which were not significantly associated with either drug.

Figure 2

Multidimensional scaling of NNRTI-selected mutations. This figure is a 2-D projection of the distances among 21 of the 22 mutations occurring in significantly covarying pairs (corrected P < 0.05, Table 1) in sequences containing at least one NNRTI-selected mutation: (a) compares the first and second principal coordinates; (b) compares the first and third principal coordinates; (c) compares the second and third principal coordinates. The distance between any two mutations is measured by their Jaccard dissimilarity coefficient, J_D, where J_D is equal to 1 minus the Jaccard similarity coefficient. The R command cmdscale was used to compare the first three principal coordinates from a table of J_Ds for each pairwise comparison. V179F is not included in this graphic; despite a significant positive correlation with Y181C, the comparison produces a high Jaccard dissimilarity coefficient, causing a misleading placement in multidimensional scaling.