Table 2. HIV-2 group A IN polymorphisms.
| Position ROD | Shannon entropy | RAL-naïve patients (63 sequences) | ||
| 30–50% | N-terminal Domain HHCC Zinc coordination finger | L2 | 0.824 | I (19%) |
| 51–70% | K4 | 0.803 | N (1%), S (1%), R (24%) | |
| 71–90% | Y15 | 0.571 | F (10%) | |
| V19 | 1.058 | I (29%), M (8%) | ||
| K20 | 0.665 | Q (10%), R (3%) | ||
| S23 | 1.037 | A (8%), C (10%), T (3%) | ||
| I28 | 0.991 | M (1%), L (50%) | ||
| N30 | 1.279 | K (60%), M (2%), L (2%), Q (13%), T (6%) | ||
| L31 | 0.554 | I (5%) | ||
| V32 | 0.373 | I (2%) | ||
| R34 | 0.780 | K (14%) | ||
| S39 | 0.533 | T (92%) | ||
| A41 | 1.075 | G (2%), N (2%), P (14%), T (17%) | ||
| A49 | 0.266 | P (2%) | ||
| Catalytic Core Domain (with DDE Catalytic Triad) | I50 | 0.682 | M (5%), T (8%), V (5%) | |
| (*) H51 | 0.079 | Q (2%) | ||
| N55 | 0.308 | D (10%) | ||
| E57 | 0.493 | A (2%), D (8%) | ||
| L58 | 0.923 | F (2%), I (8%), V (8%) | ||
| T60 | 0.651 | A (1%), I (9%), M (2%), V (3%) | ||
| E69 | 0.373 | D (2%) | ||
| (*) I72 | 0.980 | V (40%) | ||
| (*) I84 | 0.266 | V (6%) | ||
| E87 | 0.137 | K (2%) | ||
| S93 | 0.937 | T (57%) | ||
| R95 | 0.576 | K (2%) | ||
| Q96 | 0.349 | H (6%), Y (2%) | ||
| L101 | 0.308 | I (2%) | ||
| S106 | 0.349 | G (2%) | ||
| I110 | 0.079 | V (2%) | ||
| T111 | 0.137 | R (2%) | ||
| L113 | 0.531 | V (2%) | ||
| H114 | 0.231 | Q (2%) | ||
| A119 | 0.536 | D (2%), G (2%), P (8%), R (1%) | ||
| T122 | 0.231 | I (2%), M (1%), V (1%) | ||
| Q124 | 0.450 | H (2%) | ||
| (*) E125 | 0.386 | D (2%) | ||
| V129 | 0.216 | A (2%) | ||
| I133 | 1.104 | A (2%), T (3%), V (74%) | ||
| (*) S138 | 0.582 | T (19%) | ||
| V141 | 0.386 | I (2%) | ||
| (*) A153 | 0.274 | S (3%) | ||
| (*) H156 | 0.388 | L (2%), P (2%), R (2%) | ||
| (*) H157 | 0.310 | P (2%) | ||
| (*) S163 | 0.913 | D (21%), G (1%), N (7%) | ||
| R164 | 0.406 | K (10%) | ||
| E167 | 0.921 | D (41%) | ||
| N170 | 0.464 | E (2%), I (2%) | ||
| I172 | 1.056 | M (10%), V (65%) | ||
| E173 | 0.310 | K (2%) | ||
| (*) I175 | 0.531 | L (2%), V (17%) | ||
| L177 | 0.450 | V (2%) | ||
| M178 | 0.159 | I (2%), R (2%) | ||
| I180 | 0.773 | A (6%), T (5%), V (78%) | ||
| H181 | 0.079 | Y (2%) | ||
| C182 | 0.079 | Y (2%) | ||
| R188 | 0.079 | W (2%) | ||
| G189 | 0.079 | E (2%) | ||
| G190 | 0.079 | E (2%) | ||
| S197 | 0.781 | A (65%) | ||
| L200 | 0.464 | F (2%), V (2%) | ||
| (*) I201 | 0.386 | T (2%), V (2%) | ||
| (*)T206 | 0.895 | A (41%), S (2%) | ||
| E207 | 0.137 | D (3%) | ||
| I210 | 0.266 | V (6%) | ||
| F212 | 0.271 | L (2%) | ||
| C-terminal Domain | F213 | 0.187 | F (5%) | |
| Q214 | 0.454 | H (10%) | ||
| A215 | 0.788 | N (2%), S (10%), T (11%) | ||
| K216 | 0.079 | R (2%) | ||
| D217 | 0.216 | D (2%), K (2%) | ||
| S218 | 0.476 | L (13%) | ||
| K219 | 0.374 | E (2%), N (2%), R (5%) | ||
| L220 | 0.629 | F (33%) | ||
| K221 | 0.608 | Q (19%), R (2%) | ||
| N222 | 0.419 | K (11%) | ||
| R224 | 0.231 | Q (6%) | ||
| F227 | 0.079 | Y (2%) | ||
| R228 | 0.079 | K (2%) | ||
| E229 | 0.137 | K (2%) | ||
| Q233 | 0.079 | H (2%) | ||
| L234 | 0.080 | Q (2%) | ||
| W235 | 0.079 | S (2%) | ||
| E240 | 0.688 | D (2%), K (3%), Q (2%) | ||
| L241 | 0.159 | H (2%) | ||
| E246 | 0.713 | D (33%) | ||
| (*) V249 | 0.295 | I (5%) | ||
| L250 | 0.556 | I (87%), V (1%) | ||
| V251 | 0.349 | A (8%) | ||
| T255 | 0.744 | A (27%) | ||
| D256 | 0.680 | E (11%) | ||
| I259 | 0.870 | V (59%) | ||
| I260 | 0.949 | M (1%), V (52%) | ||
| I267 | 0.310 | V (2%) | ||
| I268 | 0.216 | V (3%) | ||
| R269 | 0.940 | K (33%) | ||
| R274 | 0.388 | K (2%) | ||
| Q275 | 0.159 | K (2%) | ||
| E276 | 0.344 | G (2%) | ||
| M277 | 1.090 | L (43%), V (6%) | ||
| D278 | 0.159 | G (2%) | ||
| S279 | 0.431 | C (2%), N (5%) | ||
| (*) G280 | 0.680 | S (19%) | ||
| S281 | 0.906 | P (41%) | ||
| H282 | 0.597 | N (12%), R (2%) | ||
| L283 | 0.630 | V (8%) | ||
| G285 | 0.431 | D (2%), S (5%) | ||
| A286 | 0.879 | T (30%) | ||
| D289 | 0.466 | N (8%), T (2%) | ||
| E291 | 0.349 | G (2%) | ||
| M292 | 0.791 | V (73%) |
Polymorphisms of the HIV-2 group A IN sequences from 63 treatment-naïve patients are reported with respect to the ROD reference sequence. The three different domains of IN are indicated: the N-terminal domain (AA 1–49); the catalytic core domain (AA 50–212) containing the conserved catalytic triad (DDE motif); and the C-terminal domain (AA 213–288). Positions known to confer resistance to INSTIs in HIV-1 or HIV-2 are marked with a star (*). The frequency (percentage) of each of each of the polymorphisms is indicated in brackets. Only positions where variations were detected are reported. Shannon's entropy at each variable position is indicated; an entropy value of 0 corresponds to an amino acid strictly conserved, and higher entropy values indicate more variability.