Phylogenetic analysis of full-length<i>env</i> sequences.

<p>The 40 <i>env</i> sequences of the early/transmitted viruses included in our study were aligned with 160 <i>env</i> sequences isolated at time of primo-infection from clade B -infected patients, with documented year (1990–2009) and country (25 were from Europe, 113 from USA, 6 from Australia, 15 from Trinidad and 1 from Zambia) of infection. A neighbor-joining tree was constructed using the MEGA software <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003477#ppat.1003477-Tamura2" target="_blank">[89]</a>. Open, grey filled and black filled circles identify the sequences derived from the historical, intermediate and contemporary patients of our study, respectively. Bootstrap values above 70% are indicated.