Extreme genetic divergence is required for coreceptor switching in HIV-1 subtype C

Abstract

Background: Coreceptor switching from CCR5 to CXCR4 is less common in subtype C HIV-1 infection than in subtype B for reasons that are unclear. We have examined sequential virus samples from a subtype C-infected child who had evidence of coreceptor switching.

Methods: To examine HIV-1 envelope evolution towards CXCR4 usage, env sequences were correlated with phenotypic characteristics determined by entry assays, as well as the ability to use alternative coreceptors such as FPRL1, CCR3, CCR8 and others. The value of a phenotype predictor based on V3 sequences was also assessed.

Results: Ninety-three sequences revealed 3 distinct coexistent virus lineages and only some members of one lineage evolved to use CXCR4. These lineages also had diverse alternative coreceptor patterns including the ability to use FPRL1, CCR3, CCR8, APJ, CMKLR1, RDC-1, CXCR6, CCR1, GPCR1, GPR15 and CCR6. Coreceptor switching was associated with extensive and rapid sequence divergence in the V1/V2 region in addition to V3 changes. Furthermore, interlineage recombination within the C2 region resulted in low predictability of a V3 sequence-based phenotype algorithm, and highlighted the importance of V1/V2 and V3 sequences in coreceptor usage.

Conclusion: These results suggest that the evolution to coreceptor switching in subtype C infection requires more mutations than other subtypes, and this contributes to the reduced incidence of R5X4 viruses.

Figure 1

Phylogenetic tree of the V1-V4 region clones depicting an atemporal topology with three lineages. The neighbor joining tree was drawn using Kimura-2-parameter and bootstraps values >85% indicated (*) on branches with only non-recombinant clones represented. Circle indicated time point A, triangles time point B and squares time point C samples. Open symbols indicate full-length env clones with biologically determined coreceptor usage indicated next to symbol. C-PSSM predicted coreceptor usage is indicated in small letters on major branches.

Figure 2

Characterization of the V3 region for lineage 1, 2 and 3. (A) Consensus V3 sequence for each time point within a lineage, highlighting the amino acid changes that occurred over time compared to the time point A within that lineage. (B) Distribution of C-PSSM scores for the three lineages representing clones with known and predicted coreceptor usage. Open triangles represent clones with confirmed coreceptor usage determined biologically and black circles clones with predicted coreceptor usage.

Figure 3

Entry mediated by full-length env clones representing the three different lineages described in Figure 1 using CCR5, CXCR4 and alternative coreceptors. Open circles indicate lineage 1 clones; black squares represent lineage 2 and gray squares represent lineage 3. The mean log RLU value for viral entry via a specific coreceptor is also shown for each lineage. Pseudoviruses were characterized as being able to use a coreceptor if RLU were >5000.