|
Estimates of viral diversity close to the time of transmission |
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| Patient |
Best-fitting demographic model |
μa |
Nτ b |
Nτ close to transmissionc |
|
|
|
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| Meand |
HPDe upper |
||||
|
|
|||||
| Horizontal transmission |
|||||
|
|
|||||
| p1 |
Logistic |
0.0123 |
2293 |
36.00 |
153.19 |
| p2 |
Logistic |
0.0166 |
4441 |
27.98 |
148.32 |
| p3 |
Logistic |
0.0175 |
1612 |
29.02 |
80.12 |
| p5 |
Exponential |
0.0223 |
2439 |
287.78 |
670.67 |
| p6 |
Logistic |
0.0195 |
1511 |
7.86 |
20.39 |
| p7 |
Logistic |
0.0085 |
8632 |
253.78 |
1173.95 |
| p8 |
Exponential |
0.0162 |
6003 |
1722.98 |
2911.65 |
| p9 |
Logistic |
0.0071 |
7168 |
1283.11 |
3211.35 |
| p11 |
Logistic |
0.0128 |
6505 |
9.76 |
34.48 |
| Mean |
0.0148 |
4512 |
406.47 |
933.79 |
|
| Vertical transmission |
|||||
|
|
|||||
| p1 |
Logistic |
0.0201 |
4183 |
15.48 |
79.99 |
| p2 |
Constant |
0.0560 |
275 |
275.46 |
511.97 |
| p3 |
Constant |
0.0163 |
383 |
383.27 |
714.69 |
| p4 |
Exponential |
0.0098 |
67696 |
1214.76 |
5810.63 |
| p5 |
Exponential |
0.0133 |
7372 |
1360.46 |
3444.98 |
| p6 |
Constant |
0.0251 |
183 |
181.98 |
323.10 |
| p7 |
Exponential |
0.0226 |
1165 |
151.26 |
294.62 |
| p8 |
Constant |
0.0145 |
521 |
521.84 |
857.01 |
| p9 |
Exponential |
0.0120 |
2740 |
191.34 |
405.22 |
| p10 |
Logistic |
0.0188 |
1050 |
384.47 |
877.21 |
| p11 |
Logistic |
0.0163 |
740 |
410.67 |
926.82 |
| p12 |
Exponential |
0.0206 |
1730 |
121.83 |
254.40 |
| p13 |
Exponential |
0.0218 |
2603 |
81.27 |
173.89 |
| p14 |
Exponential |
0.0164 |
1865 |
208.00 |
411.70 |
| p15 |
Logistic |
0.0397 |
889 |
1.55 |
4.80 |
| p16 |
Logistic |
0.0173 |
269904 |
261.90 |
577.67 |
| p18 |
Logistic |
0.0097 |
146723 |
960.34 |
1978.63 |
| p19 |
Exponential |
0.0095 |
2842 |
342.42 |
655.38 |
| p21 |
Exponential |
0.0053 |
302840 |
1712.90 |
4936.78 |
| p22 |
Exponential |
0.0046 |
547670 |
3159.60 |
11050.00 |
| p23 |
Logistic |
0.0093 |
123360 |
371.85 |
706.09 |
| p24 |
Logistic |
0.0102 |
97018 |
524.69 |
814.59 |
| p25 |
Logistic |
0.0071 |
2508 |
2194.63 |
4321.04 |
| pa |
Constant |
0.0280 |
640 |
638.53 |
895.76 |
| pb |
Constant |
0.0076 |
2006 |
2000.48 |
3593.83 |
| pc |
Constant |
0.0094 |
879 |
879.45 |
1626.67 |
| pd |
Constant |
0.0146 |
254 |
254.26 |
526.95 |
| Mean |
0.0169 |
58890 |
696.47 |
1732.39 |
|
|
aSubstitution rate in number of changes per site per year bProduct of the effective population size and generation time in days at the most recent time point cSeroconversion or birth for horizontally and vertically infected patients respectively dMean of the marginal posterior probability distribution of parameter values eHighest Posterior Density | |||||
Edwards et al. BMC Evolutionary Biology 2006 6:28 doi:10.1186/1471-2148-6-28 |
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