Table 3.
Longitudinal Analyses of Compartmentalization of Human Immunodeficiency Virus env Sequences From Cerebrospinal Fluid (CSF) or Semen and Blood Plasma
| Subject | SM Test | Migration Events, Total No. |
Migration Events From Plasma to CSF, No. (%)c | Migration Events From CSF to Plasma, No. (%)c | Gene Flow, Migration Events per d | |
|---|---|---|---|---|---|---|
| SM Testa | Markov Jump Count (95% HPD)b | |||||
| P409 | 0 | 19 | 31 (16–57) | 16 (52) | 15 (48) | 0.69 |
| P487 | 0 | 22 | 25 (11–40) | 12 (48) | 13 (52) | 2.27 |
| P686 | 0 | 3 | 1 (1–4) | 0 | 1 (100) | 0.11 |
| P839 | 0 | 13 | 17 (9–26) | 4 (24) | 13 (76) | 0.33 |
| Migration Events From Plasma to Semen, No. (%)c | Migration Events From Semen to Plasma, No. (%)c | |||||
| G1 | 0 | 3 | 1 (1–3) | 0 | 1 (100) | 0.02 |
| G8 | 0 | 11 | 19 (8–24) | 11 (52) | 10 (48) | 0.30 |
| WA | 0 | 50 | 74 (50–102) | 34 (42) | 43 (58) | 0.37 |
| WB | 0.633 | 12 | 27 (17–52) | 15 (56) | 12 (44) | 0.08 |
| WE | 0.056 | 18 | 53 (34–65) | 29 (55) | 24 (45) | 0.03 |
| WF | 0 | 5 | 5 (4–11) | 3 (60) | 2 (40) | 0.01 |
| L3 | 0 | 20 | 24 (9–48) | 12 (50) | 12 (50) | 0.12 |
| L7 | 0 | 26 | 34 (16–46) | 22 (65) | 12 (35) | 0.35 |
| M8 | 0.016 | 9 | 37 (13–69) | 16 (43) | 21 (57) | 0.04 |
| P9 | 0 | 20 | 17 (11–29) | 9 (53) | 8 (47) | 0.01 |
| X3 | 0.307 | 35 | 29 (14–62) | 17 (59) | 12 (41) | 0.41 |
a Total number of migration events was calculated by the Slatkin-Maddison (SM) test as implemented in HyPhy (57).
b Location state transitions estimated by Markov jump counts, with 95% high posterior densities (HPDs).
c Migration direction according to Bayesian discrete phylogeographic analysis. Gene flow was defined as the number of location state transitions per day.