Table 6. Resistance Mutations in the Protease of drug-naive and drug-treated individuals.
| Amino Acids | A/AEa | B patients diagnosed from 2001 on | p A/AE vs. B | ||||||||||
| Naive n = 234 | Treated n = 78 | p Naive A/AE vs. Treated A/AE | Naïve n = 254 | Treated n = 60 | p Naive B vs. Treated B | Naive A/AE vs. Naive B | Treated A/AE vs. Treated B | ||||||
| No | % | No | % | No | % | No | % | ||||||
| Major resistance mutations | D30N | 0 | 0 | 0 | 0 | NS | 0 | 0 | 1 | 0 | NS | NS | 1 |
| N88D/S | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | NS | 1 | |||
| L90M | 0 | 0 | 0 | 0 | 6 | 2.4 | 3 | 5 | 0.03 | 0.08 | |||
| Accessory resistance mutations | K20R | 44 | 19 | 14 | 18 | NS | 8 | 3 | 6 | 10 | 0.03 | <0.0001 | 0.2 |
| I62V | 19 | 8 | 7 | 9 | 130 | 51 | 36 | 60 | 0.3 | <0.0001 | <0.0001 | ||
| L63P | 61 | 26 | 27 | 36 | 148 | 58 | 58 | 97 | <0.0001 | <0.0001 | <0.0001 | ||
| A71V | 0 | 0 | 1 | 1 | 6 | 2 | 19 | 32 | <0.0001 | 0.03 | <0.0001 | ||
| T74S | 15 | 6 | 5 | 7 | 0 | 0 | 1 | 2 | 0.2 | <0.0001 | 0.2 | ||
| V77I | 29 | 12 | 5 | 7 | 129 | 51 | 24 | 40 | 0.2 | <0.0001 | <0.0001 | ||
| I93L | 143 | 61 | 39 | 51 | 85 | 34 | 19 | 32 | 0.9 | <0.0001 | 0.04 | ||
| A/AE signature mutations | E35D | 211 | 90 | 70 | 92 | NS | 90 | 35 | 26 | 43 | 0.3 | <0.0001 | <0.0001 |
| M36I | 234 | 100 | 76 | 100 | 29 | 11 | 13 | 22 | 0.05 | <0.0001 | <0.0001 | ||
| H69K | 233 | 100 | 76 | 100 | 0 | 0 | 3 | 5 | 0.007 | <0.0001 | <0.0001 | ||
| L89M | 231 | 99 | 71 | 93 | 2 | 0.8 | 13 | 6 | <0.0001 | <0.0001 | <0.0001 | ||
| No. of patient having resistanceconferring mutations | PI-m | 2 | 0.9 | 4 | 5 | 0.02 | 9 | 3.5 | 5 | 8 | 0.003 | <0.05 | NS |
| TAMs | 1 | 0.4 | 8 | 10 | 0.001 | 9 | 3.5 | 10 | 17 | 0.001 | 0.02 | ||
| Other N | 4 | 2 | 27 | 35 | <0.0001 | 1 | 0.4 | 15 | 25 | <0.0001 | 0.2 | ||
| Any N | 4 | 2 | 30 | 38 | <0.0001 | 9 | 3.5 | 19 | 32 | <0.0001 | 0.3 | ||
| NN only | 8 | 3 | 7 | 9 | <0.0001 | 9 | 3.5 | 3 | 5 | 0.7 | 1 | ||
| Any NN | 10 | 4 | 30 | 38 | <0.0001 | 10 | 4 | 16 | 27 | <0.0001 | 1 | ||
| N+NN | 2 | 1 | 18 | 23 | <0.0001 | 1 | 0.4 | 15 | 25 | <0.0001 | 0.6 | ||
| N+NN+PI | 0 | 0 | 3 | 4 | 0.003 | 0 | 0 | 0 | 0 | NA | NA | ||
| Any | 12 | 5 | 37 | 47 | <0.0001 | 18 | 7 | 22 | 37 | <0.0001 | 0.5 | ||
250 samples from 234 drug-naive patients and 115 samples from 78 treated A/AE patients were genotyped. 31 patients were sampled both prior to treatment and after treatment failure. PI mutations found in all A/AE naive patients were compared to those found in A/AE drug-treated ones and to samples from 254 drug naive and 60 drug treated B individuals diagnosed since 2001. The first available sample from each drug-naive individual was used for analysis. For mutation-frequency analysis of drug-treated patients each mutation was counted once. Only mutations showing statistically significant differences between drug-naive and drug-treated patients and/or between A/AE and B frequencies are included.
Mutations in the Protease: The PI mutations L23I, L24I, D30N, V32I, M46I/L, I47A, G48V, I50L/V, I54V, V82A/S, I84V/A/C, N88S/T and L90M were considered major mutations. Secondary PI mutations included L10V/I/F/M, K20R, L33F, M36I, F53L, A71V/I and G73S/T/C/A.
N – NRTIs; NN – NNRTIs; NNRTIs – Non-nucleosides reverse transcriptase inhibitors; NS – Not significant; NRTIs – Nucleosides reverse transcriptase inhibitors; PI – Protease inhibitors;
Subtyping was performed using the Stanford Database Rapid Subtyping Tool [23]–[24]. According to that classification 192 patients had virus containing protease of subtype A and RT most similar to CRF01_AE; for 70 both the protease and the RT were CRF01_AE; 52 were of subtype A; and four had protease classified as CRF01_AE and RT classified as A. Other subtyping tools such as Geno2Pheno (http://www.geno2pheno.org/) or the Rega Subtyping Tool (http://jose.med.kuleuven.be/subtypetool/html/) [57] vary to some extent in the classification of variants.