TABLE 4.
Analysis of other intersubtype recombinantsa
| Isolate | Gene | Region HXB2 | Putative subtype | Constrained to subtype | − ln L | Difference −ln L | P value | Significant |
|---|---|---|---|---|---|---|---|---|
| ZAM184 | pol | 3173-3973 | C | C | 6690.35 | (best) | ||
| A | 6747.78 | 57.43 | 0.0032 | Yes | ||||
| env-nef | 6511-9463 | A | A | 32524.71 | (best) | |||
| C | 32619.66 | 94.94 | 0.0001 | Yes | ||||
| 92RW009 | pol-vpr | 2573-6071 | C | C | 28378.06 | (best) | ||
| A | 28806.18 | 428.12 | <0.0001 | Yes | ||||
| env | 6109-8195 | A | A | 22831.00 | (best) | |||
| C | 22967.94 | 136.94 | <0.0001 | Yes | ||||
| MAL | gag | 789-1883 | A | A | 9571.50 | (best) | ||
| D | 9713.38 | 141.87 | <0.0001 | Yes | ||||
| vpr-env | 5559-8751 | D | D | 33543.66 | (best) | |||
| A | 33725.95 | 182.29 | <0.0001 | Yes | ||||
| IBNG | gag | 789-2292 | A | A | 13962.19 | (best) | ||
| G | 14049.00 | 86.80 | <0.0001 | Yes | ||||
| pol | 2293-3173 | G | G | 6442.77 | (best) | |||
| A | 6468.69 | 25.92 | 0.0096 | Yes | ||||
| 93BR029 | pol | 2085-5096 | B | B | 23128.62 | (best) | ||
| F | 23276.56 | 147.94 | <0.0001 | Yes | ||||
| env | 6220-8795 | F | F | 27885.77 | (best) | |||
| B | 28273.97 | 388.19 | <0.0001 | Yes | ||||
| BFP90 | gag | 789-1583 | A | A | 7309.43 | (best) | ||
| J | 7346.98 | 37.54 | 0.0261 | Yes | ||||
| G | 7338.20 | 28.77 | 0.0133 | Yes | ||||
| env | 6261-7312 | G | G | 12646.18 | (best) | |||
| J | 12675.35 | 29.17 | 0.0225 | Yes | ||||
| A | 12749.43 | 103.24 | <0.0001 | Yes | ||||
| nef | 8424-9463 | J | J | 12280.21 | (best) | |||
| A | 12335.76 | 55.55 | 0.0003 | Yes | ||||
| G | 12327.69 | 47.47 | 0.005 | Yes | ||||
| 94CY032 | gag | 789-1883 | A | A | 9611.10 | (best) | ||
| G | 9682.93 | 71.82 | <0.0001 | Yes | ||||
| I | 9635.65 | 24.55 | 0.012 | Yes | ||||
| pol | 2189-4673 | I | I | 20009.92 | (best) | |||
| A | 20140.33 | 130.41 | <0.0001 | Yes | ||||
| G | 20036.07 | 26.14 | 0.0423 | Yes | ||||
| env | 6311-6773 | G | G | 4386.51 | (best) | |||
| A | 4404.26 | 17.75 | 0.0605 | No | ||||
| I | 4387.39 | 0.88 | 0.9251 | No |
The Kishino-Hasegawa test was used to test the hypothesis of recombination in seven isolates thought to be formed by intersubtype recombination events. Genomic regions corresponding to different subtypes were analyzed by the Kishino-Hasegawa test. The ML tree for each region was compared to the best constrained topology, grouping the recombinant isolate with the subtypes that formed the variant The region tested is indicated by its relative position in HXB2 (nucleotide positions are given). For each topology the negative log likelihood score (−ln L) is shown along with the difference in scores between the various topologies and P values for each Kishino-Hasegawa test. Significance is assessed at an α of 0.05.