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Geographic variation in the HIV-1 virus is extensive but incompletely documented. We herein report the first genetic characterization of HIV-1 isolates from Zambia. The genomic region encoding the GAG polyprotein has been compared among 22 Zambian isolates and 14 North American isolates using a combination of polymerase chain reaction (PCR) and DNA sequencing methods. The Zambian isolates were similar to one another but distinct from other HIV-1 isolates. They exhibited a characteristic PCR "fingerprint" wherein certain primer combinations were unable to amplify because of mispairing. The sequence of the complete gag gene of three isolates from Zambia has been determined, and phylogenetic tree analysis placed them in a branch distinct from other African isolates and North American isolates. The PCR procedure used here may be widely applicable for genetic characterization of HIV-1.

Amplification of DNA by polymerase chain reaction (PCR) is influenced by the homology of oligonucleotide primers with the DNA template. We have developed a procedure, termed anchored PCR, whereby nucleotide sequence alterations in the template can be directly related to the quantity of amplified product. Genetic variation in the human immunodeficiency virus HIV-1 has been studied using anchored PCR. In four field isolates of the virus, the 3'LTR was compared both by PCR analysis of DNA from virus cultures and DNA sequencing. DNA templates that matched the primers varied less than threefold in PCR product yield, whereas significant 3' end primer-template mispairing decreased PCR product 10- to 100-fold. Using these guidelines for genetic variability manifested through PCR, 40 PCR primers encompassing the GAG, ENV, and 3' LTR segments of the genome were used to compare sequential HIV-1 isolates form six patients. Some primers were apparently located in genomic regions without significant interisolate variability, as they yielded equivalent amounts of amplified DNA from all the isolates. The quantity of amplified DNA obtained with other primers varied 10- to 100-fold among patients, but was consistent for sequential isolates from an individual patient. Two African HIV-1 isolates were readily distinguished from a panel of North American isolates by the same method. Systematic classification of HIV-1 genetic variants may be possible by anchored PCR.