PMC4674743_01
Molecular phylogenetic analysis by maximum likelihood method. Branches derived from Case 1 are shown in red while those from Case 2 are shown in blue. Branches in black were derived from reference sequences obtained from the NCBI database. The evolutionary history was inferred by using the maximum likelihood method based on the General Time Reversible model. The tree with the highest log likelihood (-7594. 0650) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pair-wise distances estimated using the maximum composite likelihood approach and then selecting the topology with superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences among sites (five categories [+G, parameter = 0.2316]). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 51.4057% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 104 nucleotide sequences. Codon positions included were 1st+2nd+3rd+Non-coding. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data and ambiguous bases were allowed at any position. There were a total of 1006 positions in the final dataset. Evolutionary analyses were conducted in MEGA6. Bootstrap values >70% are illustrated on the tree (1000 bootstrap replicates). Final editing was carried out using Figtree v1.4.2.
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PMC4674743_01_10.1177_0956462415571671-fig1.jpg
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T200A, I202V, Q207K, R211K. This virus, showed high-level resistance to lamivudine and nevirapine and low-level resistance to abacavir. The sequences were highly divergent exhibiting 45 nucleotide differences of which 20 were non-synonymous including the four resistance-associated mutations (Figure 1).
PMC4674743_02