Genetic distances and phylogenetic tree constructed using a maximum-likelihood method from concatenated regions of HIV RNA (indicated by black circles) and proviral DNA (indicated by black squares) marked with Arabic numbers 1 and 2 from patient 010BR_IMT_020 along with HIV-1 reference sequences from the Los Alamos HIV-1 database representing 11 genetic subtypes.

<p>For purposes of clarity, the tree was midpoint rooted. The approximate likelihood ratio test (aLRT) values of ≥70% are indicated at nodes. The scale bar represents 0.05 nucleotide substitutions per site.</p

Genetic distances and phylogenetic tree constructed using a maximum-likelihood method of HIV isolates recovered from patient 01BR_IMT_041.

<p>A: Phylogenetic tree from concatenated regions assigned as subtype B from the BF1 recombinant isolate. B: Phylogenetic tree showing the clustering pattern of F1 sequences (marked by dotted box). F1 region from genuine F1 sequence recovered from plasma and PBMCs are marked by a black circle and square, respectively while the F1 region from the BF1 recombinant sequence is marked by an empty square. The approximate likelihood ratio test (aLRT) values of ≥70% are indicated at nodes. The scale bar represents 0.05 nucleotide substitutions per site.</p

Drug-resistance mutations detected in plasma.

*<p>copies/Ml.</p><p>Regions not sequenced are indicated by empty boxes.</p><p>High resistance mutation are indicated by bold lettering.</p

Drug-resistance mutations detected in PBMC.

1<p>Displayed insertion at position 69.</p><p>Regions not sequenced are indicated by empty boxes.</p><p>High resistance mutations are indicated by bold lettering.</p

Schematic representation of the NFLG, partial structure and breakpoint profiles of the BF1 sequences identified in this study both from HIV RNA and proviral DNA.

<p>Samples that were identified in this study to host distinct viruses are indicated with the star symbol. The region of subclade F1 and subtypes B are indicated at the bottom.</p

Patient characteristics for the study population.

<p>Patient characteristics for the study population.</p

Maximum-likelihood phylogenetic trees form each non-recombinant fragment were constructed using all available sequences from proviral DNA (indicated by black circles) and plasma isolate (indicated by an empty circles) along with HIV-1 reference sequences from the Los Alamos HIV-1 database representing 11 genetic subtypes.

<p>The numbering for the HIV-1 fragment A, B1, B2 and C sequences corresponds to the HXB2 reference sequence. For purposes of clarity, the tree was midpoint rooted. The approximate likelihood ratio test (aLRT) values of ≥70% are indicated at nodes. The scale bar represents 0.05 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

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

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

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