Characterization of V3 sequence heterogeneity in subtype C human immunodeficiency virus type 1 isolates from Malawi: Underrepresentation of X4 variants

We have examined the nature of V3 sequence variability among subtype C huma n 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 tr acking assay (V3-HTA), and selected sequence analysis of molecular clones d erived from the PCR products. Sequence variability in V3 among the subtype C viruses was not associated with the presence of basic amino acid substitu tions. This observation is in contrast to that for subtype B HIV-1, where s equence variability is associated with such substitutions, and these substi tutions are determinants of altered coreceptor usage. Evolutionary variants in subtype C V3 sequences, as defined by the V3-HTA, were not correlated w ith the CD4 level in the infected person, while such a correlation was foun d with subtype B V3 sequences. Viruses were isolated from a subset of the s ubjects; 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 t he 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 V 3 sequences that do not carry the basic amino acid substitutions associated with altered coreceptor usage. Our results indicate that altered corecepto r 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 absenc e of altered coreceptor usage.