Neighbour-joining phylogeny of HIV-1 quasispecies based on <i>env</i> V1–V4.

<p>(A) Phylogeny of quasispecies isolated from Argentinean MSM and (B) Phylogeny of quasispecies isolated from Trinidadian heterosexuals. The sequences were isolated from samples collected soon after seroconversion. Percentage intrapatient diversity is presented for each patient and * highlights the patient who is infected by distantly related strains.</p

Comparison of the median length and number of N-Linked Glycosylation Sites in the <i>Env</i> V2 and V3 of Subtype B HIV-1 from Trinidad and the Rest of the World (p-values represent comparison between recently transmitted HIV-1 from Trinidadian heterosexuals and others).

<p>ns =  not significant, </p><p>*bulk database sequences for two Argentinians within 3 months of seroconversion were included in the analyses,</p><p>**bulk database sequences <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019995#pone.0019995-Nadai1" target="_blank">[2]</a>.</p

Features of subtype B HIV-1 quasispecies isolated from Argentinian men who have sex with men and Trinidadian heterosexuals recently following seroconversion.

<p>DPS = days post seroconversion.</p

Multiple alignment of <i>env</i> V2. All available (n = 46) V2 loop sequences from subtype B HIV-1 from Trinidad are present in the alignment.

<p>Multiple alignment of <i>env</i> V2. All available (n = 46) V2 loop sequences from subtype B HIV-1 from Trinidad are present in the alignment.</p

Phylogeny of subtype B HIV-1 from Trinidad.

<p>Phylogeny was inferred using the neighbour-joining algorithm and is based on <i>env</i> V1-V4.</p

Phylogenetic analysis of 14 nearly full genome sequences of HIV-1 Subtype B from Caribbean countries: Trinidad and Tobago (TT), Dominican Republic (DO), Haiti (HT) and Jamaica (JM).

<p>Reference subtype B sequences are indicated by the country of origin; they are: US: MN, JRCSF, SF2, WR27, P896, NY5, BCSG3C, YU2, RF, U23487; DE: D31, HAN; GB: CAM1, study sequences (bold) are identified by name. A neighbor-joining phylogenetic tree was built using the Kimura 2-parameter model and significant parsimony bootstrap values (>70%) were placed next to the nodes. The genetic distance corresponding to the lengths of the branches is shown by the scale below the tree.</p

Amino acid sites that differ between the Caribbean B strains and the subtype B reference strains.

<p>Amino acid sites that differ between the Caribbean B strains and the subtype B reference strains.</p

Allocation, follow-up, and analysis cohorts for HVTN 060 and HVTN 063.

<p>Allocation, follow-up, and analysis cohorts for HVTN 060 and HVTN 063.</p

Number of vaccinations received.

<p>Abbreviations: NA – not applicable.</p><p>For vaccinations 1, 2 and 3, the denominator is the number of persons randomized to receive either 3 or 5 study injections.</p><p>For vaccinations 4 and 5, the denominator is the number randomized to 5 study injections.</p><p>The numerator is the number of people who actually received the specified vaccination.</p

Study schema for HVTN 060/063.

<p>N3-5 – Number of participants randomized to either 3 dose or 5 dose regimen; N5 – Number of participants randomized to a 5 dose regimen.</p