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Table 1 Genetic distance, aLRT and posterior probability of 8 major clusters of Slovenian sequences and substitution rate (*10 -2 ) obtained by employing Bayesian analysis on two different sets of sequences; set comprised of all Slovenian subtype B sequences and separate sets of only clustered sequences

From: Bridging epidemiology with population genetics in a low incidence MSM-driven HIV-1 subtype B epidemic in Central Europe

 

Maximum pairwise genetic distance2

aLRT2

Posterior probability3

Substitution rate - full analysis3

Substitution rate - analysis based on cluster strains3

  

Mean

Median

95% HPD

Mean

Median

95% HPD

Cluster 1

2.38%

0.986

1

3.20

2.85

0.80–6.53

1.71

1.70

1.24–2.22

Cluster 2

2.56%

0.991

1

3.85

3.55

1.29–7.34

1.41

1.38

0.76–2.14

Cluster 3

1.85%

0.985

0.9998

2.19

2.02

0.76–4.00

   

Cluster 4

2.12%

0.999

0.9999

2.74

2.49

0.92–5.23

   

Cluster 5 1

3.14%

0.928

0.9996

2.46

2.16

0.50–5.27

   

Cluster 6

3.73%

0.981

1

2.46

2.19

0.63–4.97

   

Cluster 7

1.32%

0.972

1

2.06

1.87

0.60–3.86

   

Cluster 8

1.01%

0.999

1

2.41

2.25

1.04–4.29

   
  1. NOTE: The Bayesian analysis was performed in duplicate by using a relaxed clock model with uncorrelated lognormal distribution and Bayesian skyline coalescent model.
  2. 1numbers are shown for the newly defined Cluster 5 with only 10 patients.
  3. 2values obtained by maximum likelihood analysis.
  4. 3values obtained by Bayesian analysis.
  5. aLRT = approximate likelihood ratio test branch support values, HPD = highest posterior density.