TABLE 3.
Genetic distances to MRCAsa
| Patient | Method | MRCA-to-base plasma virus distance ± SE (%) | No. of clones analyzed | MRCA-to-year 2 viral isolate ± SE (%) | No. of clones analyzed | Wilcoxon rank sum (P) | Difference mean branch lengths to MRCA |
|---|---|---|---|---|---|---|---|
| A | BL | 4.194 ± 0.287 | 9 | 4.062 ± 0.273 | 10 | 0.667 | −0.132 |
| DD | 3.892 ± 0.226 | 4.210 ± 0.238 | 0.44 | 0.318 | |||
| B | BL | 0.233 ± 0.043 | 10 | 0.022 ± 0.037 | 13 | 0.0023 | −0.21 |
| DD | 0.232 ± 0.043 | 0.022 ± 0.037 | 0.0023 | −0.21 | |||
| C | BL | 3.345 ± 0.427 | 9 | 5.491 ± 0.427 | 10 | 0.001 | 2.146 |
| DD | 2.696 ± 0.164 | 2.731 ± 0.164 | 0.507 | 0.035 | |||
| K | BL | 1.67 ± 0.089 | 7 | 1.924 ± 0.074 | 10 | 0.0208 | 0.254 |
| DD | 1.677 ± 0.092 | 1.912 ± 0.077 | 0.07 | 0.235 | |||
| L | BL | 2.16 ± 0.142 | 10 | 0.114 ± 0.135 | 10 | 0.0002 | −2.046 |
| DD | 1.67 ± 0.141 | 1.276 ± 0.134 | 0.112 | −0.39 | |||
| M | BL | 2.72 ± 0.166 | 10 | 6.56 ± 0.198 | 7 | 0.0006 | 3.84 |
| DD | 2.584 ± 0.272 | 5.251 ± 0.326 | 0.0006 | 2.67 |
a
Genetic distances to MRCA from plasma-derived sequences and year 2 viral isolates by summation of branch lengths (BL) generated with fastDNAML (7, 30) or direct calculation from sequences (DD) generated with DNAML (PHYLIP 3.6) (7, 8). (The results shown are from analyses based on selection of an MRCA for all plasma and viral isolate sequences.) The standard error (SE) was computed with a pooled estimate of error variance. Wilcoxon rank sums compare values to MRCA from plasma virus with those from year two viral isolates. The difference of mean branch lengths to MRCA were computed by subtracting the mean plasma virus-to-MRCA branch lengths from the mean year 2 viral isolate-to-MRCA branch lengths.