Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1.

摘要: Nucleotide sequences in three hypervariable regions of the human immunodeficiency virus type 1 (HIV-1) env gene were obtained by sequencing provirus present peripheral blood mononuclear cells HIV-infected individuals. Single molecules target isolated limiting dilution and amplified two stages polymerase chain reaction, using nested primers. The product was directly sequenced to avoid errors introduced Taq during amplification process. There extensive variation between from same individual as well different Interpatient variability markedly less individuals infected a common source. A high proportion amino acid substitutions altered number positions potential N-linked glycosylation sites. Sequences frequently contained short (3- 15-bp) duplications or deletions, amplifying cell DNA containing 10(2) 10(3) proviral analyzing high-resolution electrophoresis, total abundance distinct length variants within an could be estimated, providing more comprehensive analysis than would alone. many showed frequent at certain key for neutralizing-antibody cytotoxic T-cell recognition immunodominant loop. rates synonymous nonsynonymous nucleotide substitution region this flanking indicate that strong positive selection change is operating generation antigenic diversity.