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To assess in vivo sequence heterogeneity of the human immunodeficiency virus type 1 (HIV-1) env gene, we used the polymerase chain reaction to amplify proviral sequences present in peripheral blood mononuclear cell DNA of a patient with acquired immunodeficiency syndrome (AIDS). The amplified env gene fragment (575 bp) contains the first hypervariable region and part of the first conserved region. Eleven and twelve clones were sequenced, respectively, from specimens collected two months apart. Notable heterogeneity was observed among sequences recovered from both specimens. Also, the proviral population recovered from the first specimen varied significantly from that found in the second specimen. Both specimens contained forms with and without an 18 bp duplication. The presence or absence of this duplication, in addition to several point mutations, appear to define two molecular groups evolving in parallel within this patient. Several genotypes which had sequences characteristic of both groups occurred primarily in the second specimen; these can best be explained by multiple recombinational events between representatives of the two groups during reverse transcription. This study demonstrates that recombination may contribute significantly to the generation of diversity among HIV variants within a single individual.

In order to examine the in vivo prevalence of AZT resistance mutations in AID patients after long-term therapy we amplified, by polymerase chain reaction (PCR), a 654 bp pol gene fragment from peripheral blood mononuclear cell DNA samples from a patient before, and 19 months after, the start of AZT therapy. PCR products from each sample were cloned and 9 clones from each sample were sequenced. Seven of 9 clones from the post-AZT sample, but none from the pre-AZT sample, contained an amino acid substitution (Thr215 to Tyr) requiring two nucleotide changes within the same codon (ACC to TAC). This change had previously been shown by Larder and Kemp (Science, 246:1155-1158, 1989) to correlate with partial AZT resistance of virus isolates. In colony hybridizations using synthetic oligonucleotides corresponding to the mutant and wild-type sequences, 22 of 22 clones from the pre-AZT sample hybridized only to the wild-type probe while 21 of 26 clones from the post-AZT sample hybridized only to the mutant. Clinically, this patient remains well, indicating that while Tyr215 may be the first amino acid substitution leading to resistance, it alone does not appear to have significantly influenced the clinical status of this patient.