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Table 3 Estimates of viral diversity close to the time of transmission

From: Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1

Patient

Best-fitting demographic model

μ a

NÏ„ b

NÏ„ close to transmissionc

    

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

  1. aSubstitution rate in number of changes per site per year
  2. bProduct of the effective population size and generation time in days at the most recent time point
  3. cSeroconversion or birth for horizontally and vertically infected patients respectively
  4. dMean of the marginal posterior probability distribution of parameter values
  5. eHighest Posterior Density