The HIV-1 epidemic is characterized by the dominance of distinct viral subtypes in different regions of the world, and intersubtype recombinants are common. Traditional subtyping methods analyze only a small fragment of the HIV-1 genome, so the true extent of diversity and recombination has been difficult to examine. We developed a heteroduplex tracking assay (HTA) to identify viral subtypes and rapidly detect recombinant HIV-1 genomes. By using probes that target seven regions across the HIV-1 genome, HTAs can identify intersubtype recombinants on the basis of the heteroduplex mobility pattern. We used this method to analyze HIV-1 strains from 12 patients from the United States and Kenya, comparing the results with those obtained by sequencing. HTA analysis correctly identified the subtype of each region of the genome, revealing that several isolates were recombinants. This method is suitable for studies of HIV-1 diversity and recombination in areas of the world where multiple subtypes are found.
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