TABLE 3.
Results of online subtyping methodsa
| Isolate | REGA (v3.0) |
jpHMM |
||
|---|---|---|---|---|
| Classification | Bootstrap support (%) | Classification | Posterior probability | |
| NGSID 1 | Recombinant of subtypes C and D | NA | Subtype C | 1 |
| NGSID 2 | HIV-1 subtype C | 100 | Subtype C | 1 |
| NGSID 3 | HIV-1 subtype D | 100 | Subtype D | 1 |
| NGSID 5 | HIV-1 subtype F1 | 100 | Subtype F1 | 1 |
| NGSID 6 | Recombinant of subtypes G, A1, and H | NAb | Recombinant of subtypes A1, G, and H | 0.8–1.0 |
| NGSID 7 | Recombinant of subtypes 25_cpx, A1, and G | NA | Recombinant of subtypes A1 and G | 0.7–1.0 |
| NGSID 8 | Recombinant of subtypes H, A1, 04_cpx, G, and K | NA | Recombinant of subtypes A1, H, and K | 0.9–1.0 |
| NGSID 10 | Recombinant of subtypes H, A1, 04_cpx, G, and K | NA | Recombinant of subtypes A1, H, and K | 0.9–1.0 |
| NGSID 12 | Recombinant of subtypes K, J, and F1 | NA | Recombinant of subtypes C, F1, and K | 0.6–1.0 |
| NGSID 13 | HIV-1 subtype J | 100 | Subtype J | 1 |
| NGSID 14 | HIV-1 subtype H | 100 | Subtype H | 1 |
| NGSID 15 | HIV-1 subtype H | 100 | Subtype H | 1 |
| NGSID 16 | HIV-1 subtype H | 100 | Subtype H | 1 |
| NGSID 18 | Recombinant of subtypes A1, J, K, and G | NA | Recombinant of subtypes A1, J, and K | 0.6–1.0 |
a
Fourteen whole-genome sequences were subtyped by the REGA (v3.0) and jpHMM online subtyping methods.
b
NA, not applicable.