We have examined the nature of V3 sequence variability among subtype C human immunodeficiency virus type 1 (HIV-1) sequences from plasma-derived viral RNA present in infected men from Malawi. Sequence variability was assessed by direct sequence analysis of the V3 reverse transcription-PCR products, examination of virus populations by a subtype C V3-specific heteroduplex tracking assay (V3-HTA), and selected sequence analysis of molecular clones derived from the PCR products. Sequence variability in V3 among the subtype C viruses was not associated with the presence of basic amino acid substitutions. This observation is in contrast to that for subtype B HIV-1, where sequence variability is associated with such substitutions, and these substitutions are determinants of altered coreceptor usage. Evolutionary variants in subtype C V3 sequences, as defined by the V3-HTA, were not correlated with the CD4 level in the infected person, while such a correlation was found with subtype B V3 sequences. Viruses were isolated from a subset of the subjects; all isolates used CCR5 and not CXCR4 as a coreceptor, and none was able to grow in MT-2 cells, a hallmark of the syncytium-inducing phenotype that is correlated with CXCR4 usage. The overall sequence variability of the subtype C V3 region was no greater than that of the conserved regions of gp120. This limited sequence variability was also a feature of subtype B V3 sequences that do not carry the basic amino acid substitutions associated with altered coreceptor usage. Our results indicate that altered coreceptor usage is rare in subtype C HIV-1 isolates in sub-Saharan Africa and that sequence variability is not a feature of the V3 region of env in the absence of altered coreceptor usage.

Multiple targets for immune recognition and cellular tropism are localized to the Vi and V2 hypervariable regions in the amino portion of human immunodeficiency virus type 1 (HIV-1) gpl20e`v. We have assessed genetic diversity in env Vl and V2 hypervariable domains in vivo within epidemiologically related strains of HIV-1. Our strategy was to analyze longitudinal samples from two seropositive mothers and multiple children infected by perinatal transmission. Although the Vi and V2 domains are closely linked in the HIV-1 genome, nucleotide sequences in Vl and in V2 evolved independently in maternal-infant viruses in vivo. A high proportion of the nucleotide substitutions would introduce amino acid diversity in Vl and in V2. A significant excess of nonsynonymous over synonymous substitutions was identified in HIV-1 env Vl and V2 peptides in the mothers and in two older children but was not generally apparent in HIV-1 sequences in infants. An excess of nonsynonymous over synonymous substitutions indicated that there is positive selection for independent genetic variation in the Vl and V2 domains in vivo. It is likely that there are host responses to complex determinants in the Vi or V2 hypervariable domain of HIV-1 gpl20. Genetic variability within the human immunodeficiency virus type 1 (HIV-1) genome is most pronounced in env, in which nucleotide substitutions, duplications, and deletions produce extensive amino acid diversity within five hypervariable domains in the envelope glycoprotein (7). The hypervariable domains, designated Vi through V5, are interspersed with conserved regions along the gp120 molecule (42, 44, 70). Sequence variation in env can affect an array of functional parameters of the virus in vivo and in culture (8, 9, 14, 16, 28, 52, 57, 59, 61, 62, 74). Major determinants critical for HIV-1 tropism, for cytopathology in culture, and for host immunological responses to HIV-1 infection have been mapped to the carboxyl half of gp120, where V3, V4, and V5 are localized (14, 15, 24, 35). The V3 hypervariable region in particular encodes the principal neutralizing domain in gp120 (25). Nucleotide variability in the V3 loop is characterized by a high proportion of nonsynonymous substitutions indicative of positive genetic selection (1, 60, 71). A principal mechanism contributing to evolution of genetic variability in the V3 domain of gp120 is the host immune response (6, 21, 30, 39). Complex functional determinants are not restricted to the V3 region of gpl20. Sequences associated with HIV-1 tropism for macrophages (49, 69) or encoding targets for immune recognition (13, 17, 26, 32, 67) are also localized in

No abstract