Phylogenetic trees were constructed using a maximum-likelihood method from partial <i>pol</i> plasma RNA virus (1182 bp), concatenated regions of subtype B sequences (provirus nt 1724–1980, 3284–3498) and proviral DNA (4978 bp fragment) from patient 010BR_RJ033 along with 53 non-redundant Brazilian subtype B and HIV-1 reference sequences from the Los Alamos HIV-1 database representing 11 genetic subtypes.

<p>The recombinant proviral fragment (2173 bp) is evidenced by a Bootscan plot. Average coverage reads of both proviral fragments are indicated.