TABLE 1.
Patient and sequence characteristics of patients harboring putative APOBEC3G-hypermutated, APOBEC3F-hypermutated, and nonhypermutated HIV-1 proviral DNA
| Characteristic or score | Value for indicated type of DNAa
|
||
|---|---|---|---|
| NH | HM-3G | HM-3F | |
| Patient characteristics | |||
| No. | 112 | 12 | 3 |
| CD4+ count (cells/ml) | 367.2 ± 306.1 | 491.3 ± 236.7 | 421.3 ± 152.1 |
| CD4+ percentage | 18.5 ± 10.7 | 24.7 ± 11.4 | 28.3 ± 8.3 |
| Viral load (log10 copies/ml) | 4.981 ± 0.747 | 4.476 ± 0.50* | 3.721 ± 0.680* |
| HIV-1 sequence characteristics | |||
| No. of nucleotides sequenced per patient | 6,906 ± 1,016 | 6,571 ± 1,549 | 4,591 ± 3,182 |
| No. of non-G→A mutations | 290 ± 66 | 295 ± 97 | 246 ± 129 |
| No. of G→A substitutions | 75 ± 18 | 210 ± 107 | 110 ± 40 |
| G→A rate (per 100 nucleotides) | 1.08 ± 0.21 | 3.4 ± 1.8 | 3.3 ± 2.4 |
| G→A substitutions: all substitutions | 0.206 ± 0.029 | 0.40 ± 0.123 | 0.321 ± 0.049 |
| G→A burden (% of consensus G's) | 4.6 ± 0.9 | 14.2 ± 7.5 | 14.9 ± 11.4 |
| GG (% of G→A substitutions)b | 17.7 ± 5.0 | 42.7 ± 8.7 | 10.8 ± 5.2 |
| GA (% of G→A substitutions)b | 32.1 ± 6.0 | 26.1 ± 7.0 | 59.9 ± 11.3 |
| Hypermutation scoresc | |||
| General G→A hypermutation | −0.06 ± 0.06 | 0.22 ± 0.11 | 0.14 ± 0.08 |
| 3G-specific G→A substitutions | −0.21 ± 0.13 | 0.19 ± 0.11 | −0.45 ± 0.25 |
| 3F-specific G→A substitutions | −0.05 ± 0.08 | −0.15 ± 0.11 | 0.22 ± 0.06 |
| Consolidated 3G | −0.28 ± 0.15 | 0.41 ± 0.16 | −0.30 ± 0.16 |
| Consolidated 3F | −0.12 ± 0.11 | 0.07 ± 0.15 | 0.36 ± 0.15 |
a
Numbers are expressed as means ± standard deviations where appropriate. *, <5% significance level compared to NH sequences.
b
GG and GA represent percentages of G→A substitutions that occurred in the GG and GA dinucleotide contexts, respectively.
c
See Materials and Methods for log10 transformed values; significance not determined for HIV-1 sequence characteristics or hypermutation scores, as these were the basis of the classifications.