HIV-1 CRF 02 AG polymerase genes in Southern Ghana are mosaics of different 02 AG strains and the protease gene cannot infer subtypes.

ABSTRACT:

Background

Little is known about the detailed phylogeny relationships of CRF 02_AG HIV-1 polymerase genes in Ghana. The use of the protease gene of HIV-1 for subtyping has shown conflicting results.

Methods

The partial polymerase gene sequences of 25 HIV-1 strains obtained with Viroseq reagents were aligned with reference subtypes and alignments trimmed to a 300 bp protease, 661 bp and 1005 reverse transcriptase sequence alignments. Phylogenetic relationships of these alignments were determined with the Neighbour-Joining method using 1000 replicates and recombination patterns determined for the sequences with RIP 3.0 in the HIV sequence database.

Results

Unlike the other alignments, the protease gene had nodes with bootstrap values < 100% for repeat control sequences.

SUBMITTER: Sagoe KW 

PROVIDER: S-EPMC2655287 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature