Phylodynamic profile of HIV-1 subtype B and CRF01_AE among men who have sex with men (MSM) in Kuala Lumpur, Malaysia.

<p>The Malaysian MSM sequences (35 subtype B and 35 CRF01_AE) along with respective reference sequences were analyzed separately. For illustration purposes, all 70 MSM sequences were presented in the same maximum clade credibility (MCC) tree. (<b>A</b>) Bayesian’s MCC tree of 1022 bp <i>pro-rt</i> gene (HXB2∶2253–3275) of 70 Malaysian MSM sequence data collected between March 2006 and August 2012 and reference sequences (black branches) is shown. The Bayesian coalescent-based relaxed molecular clock model was performed in BEAST 1.7, with uncorrelated lognormal model nested in general time-reversible (GTR) nucleotide substitution model and a proportion of invariant sites. The Markov chain Monte Carlo (MCMC) analysis was computed for 50 million states sampled every 10,000 states and output was assessed for convergence by means of effective sampling size (ESS) after a 10% burn-in. Transmission clusters are defined based on strong statistical supports generated at the internal nodes of the maximum likelihood and MCC tree reconstructions (bootstrap values of more than 90% and posterior probability of 1, respectively). A total of 12 monophyletic transmission clusters of different sizes (2–7 sequences) were determined, of which 6 clusters (B.1– B.6) were found within the subtype B lineages (blue branches) and another 6 clusters (AE.1– AE.6) were identified within the CRF01_AE lineages (red branches). The mean tMRCA and 95% highest posterior distribution (HPD) for each cluster are indicated in parentheses. In addition, 25 single unique lineages (green branches) involving subtype B and CRF01_AE are indicated in the phylogenetic analysis. The scale bar indicates the time in years and the alphabet at the tip of each branch represents the ethnicity of the subject, namely Malay (M), Chinese (C), Indian (I) and others (O). (<b>B</b>) Bayesian skyline plots (BSPs) generated from 35 HIV-1 subtype B and 35 CRF01_AE heterochronously sampled <i>pro-rt</i> gene from the MSM population in Kuala Lumpur. The origin and changes in effective population size through time for subtype B and CRF01_AE in the country were estimated. The 95% HPD of the effective population size is indicated in dashed lines. (<b>C</b>) Relative posterior probability distribution of the tMRCAs for the respective subtype B and CRF01_AE transmission clusters.