TABLE 3.
Analysis of population structure between free plasma virus and provirus derived from monocytes, PBMC, and activated CD4+ T cells
| Patient 154a analysis | Gene amplified | No. of independent sequences
|
SM analysisb
|
AMOVA analysis
|
Molecular diversity (π)
|
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Free plasma virus | Integrated provirus |
P
|
Adjusted Pc
|
Migration events (ML/BI) | % Variation among or within populations | P | Adjusted P | Free plasma virus | Provirus | |||||
| ML | BI | ML | BI | |||||||||||
| Plasma virus vs provirus derived from activated CD4+ T cells | RT | 238 | 25 | 0.000 | 0.002 | 0.000 | 0.002 | 19/21 | 46.76 | 53.24 | 0.000 | 0.000 | 0.011 | 0.019 |
| Plasma virus vs provirus derived from monocytes | RT | 238 | 17 | 0.000 | 0.000 | 0.000 | 0.000 | 12/13 | 46.64 | 53.36 | 0.000 | 0.000 | 0.011 | 0.020 |
| Plasma virus vs provirus derived from unfractionated PBMC | RT | 238 | 83 | 0.000 | 0.000 | 0.000 | 0.000 | 35/36 | 42.27 | 57.73 | 0.000 | 0.000 | 0.011 | 0.021 |
a
Patient sequences were derived from Bailey et al. (1).
b
ML, phylogenetic trees were generated via a classical ML approach; BI, phylogenetic trees were generated via a Bayesian inference approach.
c
“Adjusted P” refers to P values obtained for both the SM tests and the AMOVA tests were subjected to Benjamini-Hochberg FDR corrections, treating P values obtained using the ML approach separately from those obtained using BI and both separately from the AMOVA tests (2).