TABLE 2.
Evolutionary rates (10−3 codon substitutions/site/year) in the V1-C3 env regions determined using a strict clock hierarchical phylogenetic modela
| Genetic region |
All individualsc |
CD4% stratification |
|||||
|---|---|---|---|---|---|---|---|
| CD4% decline rate |
CD4% level and the combined coefficientb
|
||||||
| Fast progressorsc |
Slow progressorsc |
Bayes factord | Fast progressorsc |
Slow progressorsc |
Bayes factord | ||
| V1-C3 | 23.5 (20.3-26.6) | 24.7 (20.1-29.6) | 21.9 (19.1-24.9) | 0.3 | 28.6 (24.2-33.5) | 14.9 (12.2-17.6) | 20.3 |
| V1V2 | 29.5 (25.1-34.2)a | 30.1 (24.6-36.0) | 28.8 (23.7-34.0) | 0.3 | 35.4 (28.9-42.2) | 19.6 (14.8-24.7) | 11.8 |
| C2 | 18.0 (15.2-20.7)a | 18.6 (15.3-21.9) | 16.7 (13.9-19.5) | 0.3 | 21.5 (17.6-25.7) | 12.0 (9.2-15.2) | 28.4 |
| V3 | 21.2 (17.0-25.7)a | 21.6 (16.5-26.8) | 20.8 (15.7-25.9) | 0.3 | 24.1 (18.0-30.6) | 16.5 (11.0-22.2) | 2.4 |
| C3 | 26.6 (22.6-31.1)a | 27.0 (22.0-32.4) | 26.0 (21.6-30.6) | 0.2 | 30.4 (24.3-27.0) | 20.2 (15.2-25.8) | 6.1 |
P values for Wilcoxon signed rank tests for comparisons of rates between regions were as follows: for V1V2 versus C2, <0.001; for V1V2 versus V3, 0.002; for V1V2 versus C3, 1; for C2 versus V3, 0.005; for C2 versus C3, <0.001; for V3 versus C3, <0.001.
The combined coefficient values represent a combination of CD4% decline rate and CD4% level.
Data correspond to 10−3 codon substitutions per site per year (95% highest posterior density interval).
Bayes factor (BF) support for association between codon substitution rate and disease progression (faster versus slower progressors). BF >3 was considered evidence of a significant association.