Characteristics and main findings of the Brazilian HIV-1 recently infected individuals.

<p>Characteristics and main findings of the Brazilian HIV-1 recently infected individuals.</p

Schematic representation of the NFLG structure and breakpoint profiles of the BF1 sequences identified in this study and other BF1 URF and CRF published sequences.

<p>Sequences marked with the symbol (*) were originally classified as pure subtype but were characterized in the current analysis as pure B subtype, thus suggesting that a revised classification of these isolates in the GenBank and the HIV databases is appropriate. The region of subclade F1 and subtypes B are indicated at the bottom.</p

Phylogenetic relationships among subtype B HIV-1 NFLG sequences sampled from different countries.

<p>(a) Midpoint-rooted maximum-likelihood tree of 435 HIV-1 non recombinant subtype B NFLG sequences sampled from various global locations (colored branch). In addtion to previously published Brazilian subtype B NFLGs and other South American sequences from neighboring countries. The tree also contains 62 isolates sampled in São Paulo from HIV-1 recently infected patients over a 4- year period between 2002–2006 (the present datasets). (b) For clarity, the Brazilian isolates branched as a monophyletic cluster was displayed. Annotation of samples is as follows: symbol-brown square-F indicates heterosexual female, and symbol-black square indicates homosexual male. The approximate likelihood ratio test (aLRT) values of≥70% are indicated. The scale bar represents 0.01 nucleotide substitutions per site.</p

Maximum likelihood tree of sequences identified in this study (indicated by black circles) and reference strains inferred from full-length <i>gagpol</i> (A) and <i>env</i> (B) nucleotide sequences.

<p>For clarity purposes, the tree was midpoint rooted. The approximate likelihood ratio test (aLRT) values of≥90% are indicated at nodes. The scale bar represents 0.05 nucleotide substitutions per site.</p

Phylogenetic tree constructed using a maximum-likelihood method from the NFLG sequences of 64 patient samples and 37 HIV-1 reference sequences from the Los Alamos HIV-1 database representing 11 genetic subtypes.

<p>Annotation of samples is as follows: symbol-green circle (subtype B), symbol-blue square (subtype C), symbol-red triangle (subclade F1), symbol-brown square-M indicates heterosexual male, symbol-brown square-F indicates heterosexual female, and symbol-black square indicates homosexual male. The approximate likelihood ratio test (aLRT) values of≥90% are indicated. The scale bar represents 0.05 nucleotide substitutions per site.</p

HIV-1 strain subtyping by partial sequences.

<p>HIV-1 strain subtyping by partial sequences.</p

Drug-resistance mutations detected in antiretroviral (ARV) naïve patients.

<p>*HET ^M; heterosexual man, MSM; men who have sex with men.</p

Exploratory tree analysis based on fragments between breakpoints as indicated by bootscan plot of isolate 06BR 1114.

<p>Annotation of samples is as follows: symbol-green circle (subtype B), symbol-blue square (subtype C). The approximate likelihood ratio test (aLRT) values of≥90% are indicated at nodes. The scale bar represents 0.01 nucleotide substitutions per site. The region of subtype C, subtypes B, and subclade F1 are indicated at the bottom.</p