Table 3.
Compartmentalization analysis for HIV RNA between blood plasma and CSF supernatant.
| PID | TP | Timea (days) | RT |
GAG |
ENV |
Compartmentalized? |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| FST [CI] | P | FST [CI] | P | FST [CI] | P | RT | GAG | ENV | |||
| 24409 | 1 | 2 | 0.02 [−0.12:0.17] | 0.129 | −0.24 [−0.40:0.03] | 1.00 | 0.11 [0.05:0.18] | <0.01 | No | No | Yes |
| 24409 | 2 | 11 | 0.07 [−0.05:0.20] | <0.01 | −0.03 [−0.18:0.14] | 1.00 | 0.20 [0.14:0.29] | <0.01 | No | No | Yes |
| 24409 | 3 | 17 | −0.44 [−1.17: −0.00] | 1.00 | −0.15 [−0.95:0.14] | 1.00# | 0.07 [−0.58:0.24] | <0.01 | No | No | No |
| 24409 | 4 | 47 | 0.28 [0.10:0.40] | <0.01 | 0.22 [0.07:0.43] | <0.01 | 0.67 [0.58:0.78] | <0.01 | Yes | Yes | Yes |
| 24409 | 5 | 83 | NA | NA | NA | NA | 0.38 [0.19:0.57] | <0.01 | Yes | ||
| 25839 | Pre-ART | −2181 | 0.32 [0.07:0.57] | <0.01 | 0.18 [−0.10:0.71] | <0.01 | 0.18 [0.04:0.46] | <0.01§ | Yes | No | No |
| 25839 | 1 | 3.5 | −0.09 [−0.61:0.26] | 1.00# | 0.47 [−0.96:0.77] | <0.01 | −0.13 [−0.60:0.15] | 1.00 | No | No | No |
| 25839 | 2 | 10.5 | 0.08 [−0.05:0.24] | <0.01§ | −0.10 [−0.30:0.69] | 0.498 | 0.07 [−0.04:0.34] | <0.01 | No | No | No |
| 58704 | 1 | 3.5 | NA | NA | 0.87 [0.63:0.95] | <0.01 | 0.18 [0.00:0.44] | <0.01 | Yes | Yes | |
| 58704 | 2 | 10.5 | 0.17 [0.10:0.30] | <0.01 | 0.50 [0.13:0.67] | <0.01 | 0.02 [−0.02:0.09] | <0.01# | Yes | Yes | No |
| 58704 | 3 | 25.5 | −0.50 [−1.67: −0.07] | 1.00 | 0.23 [−0.12:0.45] | <0.01# | 0.23 [0.10:0.42] | <0.01 | No | No | Yes |
| 58704 | 4 | 31.5 | NA | NA | 0.32 [−0.02:0.67] | <0.01 | 0.10 [−0.51:0.46] | <0.01# | No | No | No |
| NM487 | 1 | 3.5 | 0.21 [0.15:0.30] | <0.01 | 0.24 [0.03:0.41] | <0.01 | 0.62 [0.24:0.86] | <0.01 | Yes | Yes | Yes |
| NM487 | 2 | 14.5 | 0.43 [0.28:0.61] | <0.01 | 0.60 [0.42:0.81] | <0.01 | 0.42 [0.30:0.61] | <0.01 | Yes | Yes | Yes |
| 58786 | 1 | 9 | 0.05 [−0.56:0.72] | 0.050 | 0.01 [−0.57:0.60] | <0.01§# | 0.36 [0.14:0.75] | <0.01 | No | No | Yes |
| 58786 | 2 | 23 | 0.03 [−0.27:0.45] | <0.01# | −0.01 [−0.37:0.43] | 1.00# | 0.08 [0.04:0.20] | <0.01§ | No | No | No |
| 24232 | 1 | 18 | 0.45 [0.23:0.65] | <0.01 | 0.36 [0.01:0.73] | <0.01§ | 0.41 [0.26:0.62] | <0.01 | Yes | No | Yes |
| 24232 | 2 | 375 | 0.65 [0.41:0.75] | <0.01 | 0.07 [−0.16:0.23] | <0.01# | −0.20 [−0.76:0.12] | 1.00 | Yes | No | No |
| 24273 | 1 | 11 | 0.21 [0.06:0.36] | <0.01 | 0.22 [0.06:0.37] | <0.01 | 0.30 [0.16:0.51] | <0.01 | Yes | Yes | Yes |
| 24273 | 2 | 383 | 0.21 [0.01:0.35] | <0.01 | 0.14 [−0.02:0.32] | <0.01 | 0.61 [0.46:0.71] | <0.01 | Yes | No | Yes |
| 23350 | 1 | 19 | 0.04 [−0.06:0.33] | <0.01 | −0.24 [−0.47:0.36] | 1.00 | −0.01 [−0.22:0.45] | 0.703 | No | No | No |
| 23350 | 2 | 557 | 0.01 [−0.01:0.06] | <0.01§# | 0.06 [−0.02:0.19] | <0.01§ | −0.01 [−0.60:0.06] | 1.00 | No | No | No |
| 26618 | 1 | 150 | 0.13 [−0.04:0.29] | <0.01 | 0.15 [−0.06:0.54] | <0.01 | 0.15 [0.03:0.29] | <0.01 | No | No | Yes |
| 26618 | 2 | 514 | −0.04 [−0.29:0.16] | 1.00 | 0.26 [−0.09:0.48] | <0.01 | 0.04 [−0.04:0.12] | <0.01 | No | No | No |
| 34535 | Pre-ART | −732 | 0.12 [−0.12:0.47] | <0.01 | 0.82 [0.18:0.94] | <0.01 | 0.19 [0.03:0.43] | <0.01 | No | Yes | Yes |
| 34535 | 1 | 37.5 | 0.09 [−0.22:0.42] | <0.01 | 0.07 [−0.13:0.23] | <0.01§ | 0.33 [0.08:0.46] | <0.01 | No | No | Yes |
| 58213 | 1 | 175 | 0.14 [−0.02:0.30] | <0.01 | 0.11 [−0.09:0.37] | <0.01 | 0.40 [0.24:0.60] | <0.01 | No | No | Yes |
| 58213 | 2 | 319 | 0.03 [−0.92:0.35] | <0.01# | 0.32 [−0.28:0.65] | <0.01 | 0.59 [0.46:0.69] | <0.01 | No | No | Yes |
| 26742 | 1 | 104 | −0.60 [−0.83: −0.30] | 1.00 | 0.01 [−0.10:0.18] | 0.079 | 0.00 [−0.04:0.07] | 0.337 | No | No | No |
| 26742 | 2 | 159 | 0.39 [0.12:0.62] | <0.01 | 0.01 [−0.09:0.15] | 0.050 | 0.01 [−0.00:0.07] | <0.01§# | Yes | No | No |
| 26919 | Pre-ART | −21 | 0.25 [0.10:0.42] | <0.01 | 0.13 [0.02:0.32] | <0.01 | 0.20 [0.11:0.34] | <0.01 | Yes | Yes | Yes |
| 26919 | 1 | 7 | NA | NA | 0.18 [−0.02:0.34] | <0.01 | 0.08 [−0.02:0.18] | <0.01 | No | No | |
| 26919 | 2 | 16 | 0.06 [0.02:0.14] | <0.01 | 0.30 [−0.07:0.64] | <0.01 | 0.08 [0.01:0.14] | <0.01 | Yes | No | Yes |
| 26919 | 3 | 99 | −0.01 [−0.06:0.08] | 0.743 | 0.13 [0.01:0.26] | <0.01 | 0.19 [0.11:0.29] | <0.01 | No | Yes | Yes |
| CA149 | 1 | 137 | 0.08 [−0.28:0.28] | <0.01# | −0.06 [−0.83:0.37] | 1.00 | −0.45 [−0.65: −0.24] | 1.00 | No | No | No |
| CA149 | 2 | 503 | 0.60 [0.48:0.72] | <0.01 | 0.68 [0.50:0.83] | <0.01 | 0.71 [0.62:0.79] | <0.01 | Yes | Yes | Yes |
TP, time point collected sequentially after ART interruption, pre-ART time points were collected before starting antiretroviral therapy; ENV, envelope; RT, reverse transcriptase; BP, blood plasma; CSF, cerebrospinal fluid; confidence intervals are estimated by computing FST values for 100 replicates drawn by sampling alignment sites with replacement and adding noise to haplotype frequencies [see text]; P values <0.01 are derived from 100 bootstrap replicates, when 0/100 replicates had FST values equal to or greater than the estimate obtained from the data. Compartmentalization is called when four tests indicate compartmentalization [see text]
#Indicates tests which become significant (or not significant) if copy numbers are ignored during FST calculations.
§Indicates tests which become insignificant under the phylogeny-based SlatkinMaddison test [see text].
*time in days elapsed from viral rebound to sampling in CSF.