Comparison of rate and ratio estimates between H and T subgroups.

<p>* the mean value for evolutionary and growth rates were estimated using BEAST, under the best fitting model (GTR+Γ+I and exponential growth); the mean values for the Non Synonymous (dN) versus synonymous (dS) mutation ratios were estimated using HyPhy under the GTR model.</p><p>^$ the 95% Higher Posterior Densities (HPD) upper and lower bound for evolutionary and growth rates were estimated using BEAST, under the best fitting model (GTR+Γ+I and exponential growth).</p><p>^£ the 95% confidence intervals (CI) for the Non Synonymous (dN) versus synonymous (dS) mutation ratios were estimated using HyPhy under the GTR model.</p><p>^# the p-value for the difference between two means was calculated using student T test; the Likelihood Ratio Test p-value against the hypothesis of a single rate was estimated using HyPhy under the GTR model.</p><p>Comparison of rate and ratio estimates between H and T subgroups.</p

Phylogenetic analysis of HIV-1 sequences.

<p><b>a)</b> Maximum likelihood tree inferred from the 190 concatenated group O sequences, with white diamonds at nodes with bootstrap values >70 and colours highlighting the nature of the residue at position 181 in the Reverse Transcriptase: Pink = C (N = 116); Green = Y (N = 71); Blue = mixed Y and C (N = 3); Grey = sequences from patients non NNRTI-naïve or with no data about NNRTI treatment. <b>b)</b> Maximum likelihood tree inferred from the 190 concatenated group M sequences.</p

Dynamics of group O populations over time and contemporaneous contextual elements in Cameroon.

<p><b>a)</b> Bayesian Skyline Plot (BSP) inferred from the 154 concatenated group O sequences for which the three genome regions were obtained from a single time-point sample. <b>b)</b> BSP inferred from a subset of these sequences (N = 137), including the H strains (N = 124) and clusters T1 (N = 6) and T2 (N = 7) from the T strains. <b>c)</b> Periods of high viral growth rates for HIV-1 group M CRF02_AG [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref022" target="_blank">22</a>] (dark gray box), HIV-1 group O (grey boxes), HCV-1 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref023" target="_blank">23</a>] (dark pink box), HCV-2 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref023" target="_blank">23</a>] (pink box) and HCV-4 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref023" target="_blank">23</a>] (brown box) in Cameroon; cohort with high HCV seroprevalence in Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref024" target="_blank">24</a>] (orange box); population-scaled risk factors for iatrogenic transmission during trypanosomiaisis control campaigns in rural Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref025" target="_blank">25</a>] (peak period: dark blue box), pentamidine prophylaxis campaigns in rural Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref025" target="_blank">25</a>,<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref026" target="_blank">26</a>] (blue box) and intra-venous treatment for yaws and syphilis in Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref025" target="_blank">25</a>] (peak period: light blue box).</p

Estimates of group O tMRCA.

<p>The marginal posterior density curves obtained using four different population growth models are shown. Different colours identify the distribution of tMRCA estimates for global group O (black), subgroup H (green), and subclusters H1, H2 and H3 (blue, red and yellow, respectively).</p