Maximum likelihood phylogenetic analysis of study subjects infected with HIV-1 of subtype B.

<p>The upper panel shows the complete tree, which includes sequences from 605 study subjects, 194 MSM diagnosed as HIV-1 infected in Stockholm 1992–2002 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033484#pone.0033484-Lindstrm1" target="_blank">[17]</a>, and four subtype B and four subtype D reference sequences (<a href="http://www.hiv.lanl.gov" target="_blank">www.hiv.lanl.gov</a>). The tree was generated using partial HIV-1 pol gene sequences using PhyML and the best fitted nucleotide substitution model (i.e. GTR+I+G). Twenty-three codons with resistance mutations were removed from the alignment so that the final alignment contained 987 unambiguously aligned nucleotides. The tree is rooted using the four subtype D reference sequences. Red branches represent sequences with mutations indicative of TDR according to the WHO 2009 list of mutations for surveillance of transmitted drug resistance <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033484#pone.0033484-Bennett3" target="_blank">[20]</a>. Numbers indicate significantly supported (aLRT>0.95) clusters of TDR sequences. The two bottom panels show detailed sub-trees for TDR clusters 1 and 4. The asterisks in the sequence identifiers in cluster 4 indicate that these sequences were obtained from the 1992–2002 dataset <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033484#pone.0033484-Lindstrm1" target="_blank">[17]</a>. The scale indicates nucleotide substitutions per site.