Characterization of V3 Sequence Heterogeneity in Subtype C Human Immunodeficiency Virus Type 1 Isolates from Malawi: Underrepresentation of X4 Variants

Abstract

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.

The epidemiology and clinical correlates of HIV‐1 co‐receptor tropism in non‐subtype B infections from India, Uganda and South Africa

“…For example, some similarities can be observed between the findings of the present study and a previous study that assessed co-receptor tropism of HIV-1 strains in China: mainly that R5 tropism was seen exclusively in subtype C infections, and remained stable over time [24]. These data highlight the persistence of CCR5 tropism even in long-term infections, possibly related to differences within the env variable loops [37], and contrasts with other subtypes, especially subtype B, where X4 HIV-1 is more frequent during later stages of infection [6,[8][9][10]16,18,21,[37][38][39][40].…”

Impact of HIV‐1 viral subtype on disease progression and response to antiretroviral therapy

“…Viral genetic variation can influence phenotypic properties, such as cell tropism, co-receptor usage and the ability to form syncytia, although these properties have only recently been correlated with viral subtype. There is some evidence that subtype C uses only the CCR5 co-receptor, and has a preponderance of R5 or NSI viruses and a relative lack of X4 or SI viruses [37,38], while subtype D isolates tend to have a higher frequency of syncytium formation, CXCR4 (X4) coreceptor usage and rapidly replicating virus compared with other subtypes [39]. In a recent study of 31 Ugandan patients infected with subtype A and 35 with subtype D, there was a higher probability of X4 or dual tropic viruses in AIDS-free subtype D patients, which were also more replication competent.…”

HIV: Cell Binding and Entry

“…Interestingly, despite identification at earlier time points and despite high levels of CXCR4 expression on circulating HIV target cells, X4 or even R5X4 HIV rarely predominate until late in infection (Tersmette et al 1989;Schuitemaker et al 1992;Connor et al 1997). In addition, X4 viruses are less common in clade C HIVand SIV infection (Chen et al 1998;Ping et al 1999;Cecilia et al 2000;Huang et al 2007 Overview of HIV entry. To deliver the viral payload into cells, HIV Env, comprised of gp120 and gp41 subunits (1), first attaches to the host cell, binding CD4 (2).…”