Table 1.
Frequencies of HIV-1 subtypes (≥10 isolates) and most frequent (≥10%) predefined polymorphisms at amino acid positions of interest in gp160a in the LANL HIV Sequence Databaseb
| Subtype | N | Percentage in database | No predefined polymorphismsa, n (% of subtype) | Predefined polymorphismsa |
|
|---|---|---|---|---|---|
| amino acid | n (% of subtype) | ||||
| Allc | 7560 | 4679 (61.9) | S375H | 921 (12.2) | |
| Group M | |||||
| B | 2651 | 35.1 | 1709 (64.5) | S375Td,e | 473 (17.8) |
| C | 1626 | 21.5 | 1255 (77.2) | M434I | 216 (13.3) |
| CRF01_AE | 674 | 8.9 | 2 (0.3) | S375H | 669 (99.3) |
| M475I | 514 (76.3) | ||||
| A1 | 273 | 3.6 | 156 (57.1) | M434I | 95 (34.8) |
| CRF02_AG | 199 | 2.6 | 145 (72.9) | M434I | 36 (18.1) |
| BF1 | 136 | 1.8 | 87 (64.0) | S375Te,f | 15 (11.0) |
| M426L | 18 (13.2) | ||||
| D | 133 | 1.8 | 105 (78.9) | none | |
| G | 128 | 1.7 | 114 (89.1) | none | |
| A6 | 108 | 1.4 | 99 (91.7) | none | |
| BC | 106 | 1.4 | 92 (86.8) | none | |
| 01B | 99 | 1.3 | 16 (16.2) | S375H | 71 (71.7) |
| M475I | 49 (49.5) | ||||
| A1D | 98 | 1.3 | 64 (65.3) | M434I | 30 (30.6) |
| A1C | 79 | 1.0 | 57 (72.2) | M434I | 20 (25.3) |
| F1 | 63 | 0.8 | 48 (76.2) | none | |
| CRF07_BC | 61 | 0.8 | 57 (93.4) | none | |
| CRF08_BC | 41 | 0.5 | 38 (92.7) | none | |
| 01BC | 39 | 0.5 | 16 (41.0) | S375H | 19 (48.7) |
| M434I | 7 (17.9) | ||||
| M475I | 9 (23.1) | ||||
| 02A1 | 30 | 0.4 | 13 (43.3) | S375Te,g | 4 (13.3) |
| M434I | 11 (36.7) | ||||
| A1CD | 30 | 0.4 | 18 (60.0) | M434I | 8 (26.7) |
| 0107 | 26 | 0.3 | 11 (42.3) | S375H | 14 (53.8) |
| M475I | 11 (42.3) | ||||
| CD | 26 | 0.3 | 17 (65.4) | S375Te | 4 (15.4) |
| M434I | 5 (19.2) | ||||
| CRF11_cpx | 25 | 0.3 | 19 (76.0) | M426L | 3 (12.0) |
| CRF12_BF | 18 | 0.2 | 6 (33.3) | S375I | 2 (11.1) |
| M426L | 8 (44.4) | ||||
| CRF35_AD | 17 | 0.2 | 13 (76.5) | M426L | 2 (11.8) |
| M434I | 2 (11.8) | ||||
| 02A | 16 | 0.2 | 15 (93.8) | none | |
| A1G | 14 | 0.2 | 11 (78.6) | M434I | 2 (14.3) |
| CRF06_cpx | 13 | 0.2 | 10 (76.9) | none | |
| F2 | 13 | 0.2 | 12 (92.3) | none | |
| CRF71_BF1 | 12 | 0.2 | 8 (66.7) | S375Te | 3 (25.0) |
| 02G | 11 | 0.1 | 10 (90.9) | none | |
| 01C | 10 | 0.1 | 8 (80.0) | S375H | 2 (20.0) |
| M475I | 2 (20.0) | ||||
| 02B | 10 | 0.1 | 8 (80.0) | none | |
| CRF13_cpx | 10 | 0.1 | 4 (40.0) | M426Lh | 2 (20.0) |
| M434I | 5 (50.0) | ||||
| Group O | 48 | 0.63 | 1 (2.1) | S375Hi | 47 (97.9) |
| M434I | 7 (14.6) | ||||
| Group N | 11 | 0.15 | 0 (0) | S375M | 11 (100) |
| M426L | 11 (100) | ||||
| M434I | 11 (100) | ||||
S375H/I/M/N/T/Y, M426L/P, M434I/K and M475I are the predefined polymorphisms. Predefined polymorphisms listed in column are only shown if they represented ≥10% of total isolates.
LANL database entries to 31 December 2019.
Including 239 subtypes, recombinants and CRFs and 135 sequences with subtype reported as unclassified or no subtype reported.
Other polymorphisms at positions of interest: M426R in 596 (22.5%) isolates (this polymorphism had no effect on temsavir susceptibility in an LAI background; fold change in IC50=0.86).
S375T had no measurable effect on in vitro temsavir susceptibility in an LAI background (fold change in IC50=1.0) and has less of an impact on temsavir susceptibility than other amino acids at this position.10
Other polymorphisms at positions of interest: M426R in 29 (21.3%) isolates (this polymorphism had no effect on temsavir susceptibility in an LAI background; fold change in IC50=0.86).
Other polymorphisms at positions of interest: M426V in 5 (16.7%) isolates (this polymorphism had a minor effect on temsavir susceptibility in an LAI background; fold change in IC50=3.3).1
Other polymorphisms at positions of interest: M426I in 2 (20.0%) isolates (this polymorphism had no effect on temsavir susceptibility in an LAI background; fold change in IC50=1.8).
Other polymorphisms at positions of interest: M426S in 44 (91.7%) isolates and M434L in 37 (77.1%) isolates.