Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D

Abstract

Most HIV-1 infections in Uganda are caused by subtypes A and D. The prevalence of recombination and the sites of specific breakpoints between these subtypes have not been reported. HIV-1 pol sequences encoding protease (amino acids 1-99) and reverse transcriptase (amino acids 1-324) from 102 pregnant Ugandan women were analyzed by the Recombinant Identification Program, SimPlot, and examination of phylogenetically informative sites to identify sites of recombination between sequence segments belonging to different subtypes. Thirteen percent (13 of 102) of the pol sequences contained strong evidence of recombination between subtypes A and D. At least nine different patterns of recombination were observed. Five women infected with a recombinant virus transmitted the recombinant virus perinatally. In this population-based study, intersubtype recombinants were common. The large number of different types of pol recombinants identified suggests that recombination occurs readily in the pol region. Perinatal transmission of the recombinant viruses demonstrates their evolutionary stability.

FIG. 1

Bootscanning results for 13 HIV-1 viruses with strong evidence of recombination. The percentage of permuted trees (y axis) clustering with each subtype is shown along the length of the sequence (x axis). Bootscan results were originally obtained by using reference sequences of each of the nine pure subtypes and CRFs 1 and 2. The bootscan analysis was redone, using the two subtypes involved in recombination, subtypes A (blue) and D (pink), as well as one control subtype, subtype C (green). Isolates sharing similar patterns of recombination (151/479, 414/843, and 549/760/800) are grouped. The informative positions for each sequence and their assignments to either subtype A or subtype D are shown beneath the x axis.