Table 1.
Wild type and mutant codon frequency by subtype.
| DRM Position | Codon | AA | A n = 2968 | B n = 1725 | C n = 9405 | D n = 1355 | G n = 597 | CRF_01 n = 5590 | CRF_02 n = 2342 |
|---|---|---|---|---|---|---|---|---|---|
| 65 | WT (23,365; 98.1) | ||||||||
| AAA | K | 96.7 | 97.8 | 0.9 | 97.6 | 98.8 | 98.9 | 97.7 | |
| AAG | K | 3.3 | 2.2 | 99.1 | 2.4 | 1.2 | 1.1 | 2.4 | |
| Mutant (446; 1.9) | |||||||||
| AGA | R | 84.6 | 100 | 3.7 | 100 | 100 | 85.9 | 93.1 | |
| AGG | R | 7.7 | 0 | 95.6 | 0 | 0 | 1.9 | 3.5 | |
| AAT | N | 7.7 | 0 | 0.7 | 0 | 0 | 2.8 | 0 | |
| AAC | N | 0 | 0 | 0 | 0 | 0 | 9.4 | 3.5 | |
| Total coverage | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | ||
| 103 | WT (20,748; 89.8) | ||||||||
| AAA | K | 95.6 | 95.7 | 91.6 | 96.5 | 92.2 | 95.7 | 98.0 | |
| AAG | K | 4.2 | 2.1 | 6.4 | 3.2 | 6.8 | 3.8 | 1.7 | |
| AGA | R | 0.3 | 2.3 | 2.0 | 0.2 | 1.0 | 0.6 | 0.2 | |
| Mutant (2369; 10.3) | |||||||||
| AAC | N | 84.1 | 77.8 | 77.3 | 75.5 | 80.8 | 77.6 | 82.6 | |
| AAT | N | 11.2 | 17.8 | 18.5 | 20.4 | 19.2 | 19.2 | 16.9 | |
| AGC | S | 4.7 | 4.3 | 4.3 | 2.0 | 0 | 2.5 | 0.5 | |
| ACA | T | 0 | 0 | 0 | 2.0 | 0 | 0.7 | 0 | |
| Total coverage | 99.83 | 99.58 | 99.65 | 99.92 | 99.28 | 99.64 | 99.96 | ||
| 106 | WT (22,427; 96.0) | ||||||||
| GTA | V | 97.51 | 90.1 | 13.3 | 95.4 | 96.2 | 86.4 | 97.4 | |
| GTG | V | 1.7 | 2.6 | 86.6 | 4.0 | 1.2 | 8.5 | 1.9 | |
| ATA | I | 0.8 | 7.4 | 0.2 | 0.6 | 2.6 | 5.2 | 0.7 | |
| Mutant (926; 3.4) | |||||||||
| GCA | A | 85.7 | 70.8 | 0.4 | 80.0 | 90.9 | 37.5 | 75.0 | |
| GCG | A | 0 | 0 | 2.4 | 0 | 0 | 0 | 0 | |
| ATG | M | 14.3 | 29.2 | 97.2 | 20.0 | 9.1 | 62.5 | 25.0 | |
| Total coverage | 99.49 | 99.64 | 99.34 | 99.55 | 100 | 99.48 | 99.66 | ||
| 181 | WT (21,972; 93.5) | ||||||||
| TAT | Y | 95.7 | 97.5 | 96.3 | 95.5 | 10.0 | 98.4 | 8.6 | |
| TAC | Y | 4.3 | 2.5 | 3.8 | 4.5 | 90.0 | 1.6 | 91.4 | |
| Mutant (1541; 6.6) | |||||||||
| TGT | C | 81.8 | 96.4 | 88.3 | 88.4 | 9.4 | 86.5 | 8.5 | |
| TGC | C | 7.3 | 0.9 | 4.3 | 4.7 | 87.1 | 3.0 | 87.3 | |
| ATT | I | 5.5 | 0.9 | 3.9 | 0 | 0 | 4.8 | 0 | |
| ATC | I | 0 | 0.9 | 0.2 | 0 | 2.4 | 0.2 | 2.1 | |
| GTT | V | 5.5 | 0.9 | 3.2 | 7.0 | 0 | 5.5 | 0.7 | |
| GTC | V | 0 | 0 | 0 | 0 | 1.2 | 0.2 | 1.4 | |
| Total coverage | 100.0 | 99.9 | 100.0 | 100.0 | 99.8 | 100.0 | 100.0 | ||
| 184 | WT (19,231; 81.0) | ||||||||
| ATG | M | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | |
| Mutant (4498; 19.0) | |||||||||
| GTG | V | 90.3 | 78.1 | 90.2 | 89.4 | 83.3 | 81.5 | 87.6 | |
| GTA | V | 9.7 | 7.3 | 6.9 | 9.6 | 15.4 | 14.7 | 10.4 | |
| ATA | I | 0 | 14.6 | 3.0 | 1.0 | 1.3 | 3.8 | 2.0 | |
| Total coverage | 100.0 | 99.5 | 99.9 | 99.9 | 99.8 | 99.8 | 99.9 | ||
| 190 | WT (22,097; 94.7) | ||||||||
| GGA | G | 95.2 | 95.3 | 95.4 | 96.4 | 90.1 | 94.6 | 92.8 | |
| GGC | G | 1.5 | 3.2 | 1.3 | 0.5 | 1.3 | 3.4 | 1.6 | |
| GGG | G | 3.3 | 1.5 | 3.3 | 3.1 | 8.6 | 2.0 | 5.7 | |
| Mutant (1243; 5.3) | |||||||||
| GCA | A | 92.9 | 70.7 | 83.4 | 89.7 | 92.3 | 87.9 | 89.0 | |
| GCG | A | 0 | 1.2 | 1.7 | 3.5 | 2.6 | 2.2 | 1.4 | |
| GCC | A | 0 | 2.4 | 0.8 | 0 | 0 | 1.2 | 0 | |
| AGC | S | 2.9 | 24.4 | 3.9 | 3.5 | 2.6 | 2.7 | 2.7 | |
| AGT | S | 0 | 1.2 | 1.9 | 0 | 2.6 | 1.9 | 2.7 | |
| TCA | S | 1.4 | 0 | 0.9 | 0 | 0 | 1.5 | 1.4 | |
| GAA | E | 2.9 | 0 | 4.5 | 0 | 0 | 1.7 | 2.7 | |
| CAA | Q | 0 | 0 | 3.0 | 3.5 | 0 | 1.0 | 0 | |
| Total coverage | 99.7 | 99.9 | 99.5 | 99.6 | 99.1 | 99.8 | 99.8 |
The frequency of all codons of at least 1% frequency in any of the seven most common subtypes or circulating recombinant forms (CRFs) are shown by subtype for both wild type and mutant codons. The 23,982 sequences from the most seven most common subtypes or CRFs were included in this analysis. Within the analysis of each drug resistance mutation (DRM position, sequences bearing mixtures in the codon of interest were excluded. The number and proportion of wild type and mutant sequences used in the analysis of each DRM are listed in the Codon columns (N; %). Total coverage represents the number of codons from all sequences in the database of that subtype that would match one of the codons listed here for that DRM position. Notable inter-subtype differences in codon frequencies appear in bold font. Abbreviations: AA, amino acid; WT, wild type.