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. 2014 Aug 14;1(2):ofu056. doi: 10.1093/ofid/ofu056

Fig. 1.

Fig. 1.

ML tree of HIV-1 gp41 env sequences from the 50 VAX003 subjects. Each subject's sequence set is shown in a different color and labeled with the subject identifier. Reference sequences are shown in gray. Forty-six subjects were infected by CRF01_AE viruses; CRF15_01B and subtype B clades are specifically indicated. Individual subject sequence sets with bootstrap values >95% are annotated with an asterisk. There are 8 individual subject sequence lineages with bootstrap values >75%: the 2 acute-to-acute transmissions (subjects 3212 and 3017 and subjects 3184 and 3090), 3 subjects with related but distinct lineages (subjects 3189, 3111 and 3112), and subject 3156. Subject 3156 (shown in mustard orange and annotated with a hashtag at the top and bottom of tree) has sequences clustering with CRF01_AE and subtype B. The single long branch in subject 3156's viral sequences at the top of the figure is a unique interlineage recombinant shown in greater detail in Supplementary material, Figure S1. Genetic distance is indicated by the scale bar. Abbreviations: HIV-1, human immunodeficiency virus type 1; ML, maximum-likelihood.